<?xml version="1.0"?>
<feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en">
	<id>https://wiki.biocomputeobject.org/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Twang9</id>
	<title>BCOeditor Wiki - User contributions [en]</title>
	<link rel="self" type="application/atom+xml" href="https://wiki.biocomputeobject.org/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Twang9"/>
	<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/Special:Contributions/Twang9"/>
	<updated>2026-05-20T05:42:19Z</updated>
	<subtitle>User contributions</subtitle>
	<generator>MediaWiki 1.38.2</generator>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1137</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1137"/>
		<updated>2025-10-06T20:26:54Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Communication and Support */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?''' Module 1 and Module 5 (Module 5.3.5.4 especially where the BCO is located) are required. A cover letter (states the purpose of the submission and the intentional submission center) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''Which center should the eCTD (containing BCO file(s)) be submitted to?''' Both CDER and CBER centers accept eCTD submissions and they both have the ability to review the submission files if requested.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Gateway.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing and identification. In addition, provide the shipping company name, transit number and expected delivery date when available to DCC (DCCEDR@fda.hhs.gov).&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is no minimum requirement; it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is the software used required for submission?''' Software used is not required to be submitted. However, some divisions would want software details; this depends very much on where the submission goes.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. &lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to the FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance-compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fd]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ a.go][https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the '''''&amp;lt;nowiki/&amp;gt;'''''prompts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machines).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. The FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
# '''For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.'''&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs).&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1136</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1136"/>
		<updated>2025-10-06T20:19:31Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Regulatory Applications and Use Cases */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?''' Module 1 and Module 5 (Module 5.3.5.4 especially where the BCO is located) are required. A cover letter (states the purpose of the submission and the intentional submission center) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''Which center should the eCTD (containing BCO file(s)) be submitted to?''' Both CDER and CBER centers accept eCTD submissions and they both have the ability to review the submission files if requested.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Gateway.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing and identification. In addition, provide the shipping company name, transit number and expected delivery date when available to DCC (DCCEDR@fda.hhs.gov).&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is no minimum requirement; it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is the software used required for submission?''' Software used is not required to be submitted. However, some divisions would want software details; this depends very much on where the submission goes.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. &lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to the FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance-compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fd]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ a.go][https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the '''''&amp;lt;nowiki/&amp;gt;'''''prompts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machines).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. The FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs).&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1135</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1135"/>
		<updated>2025-10-06T20:19:15Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Submission Process and Requirements */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?''' Module 1 and Module 5 (Module 5.3.5.4 especially where the BCO is located) are required. A cover letter (states the purpose of the submission and the intentional submission center) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''Which center should the eCTD (containing BCO file(s)) be submitted to?''' Both CDER and CBER centers accept eCTD submissions and they both have the ability to review the submission files if requested.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Gateway.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing and identification. In addition, provide the shipping company name, transit number and expected delivery date when available to DCC (DCCEDR@fda.hhs.gov).&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is no minimum requirement; it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is the software used required for submission?''' Software used is not required to be submitted. However, some divisions would want software details; this depends very much on where the submission goes.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. &lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to the FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance-compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fd]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ a.go][https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the '''''&amp;lt;nowiki/&amp;gt;'''''prompts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machines).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. The FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1134</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1134"/>
		<updated>2025-10-06T20:18:47Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Submitting BCOs to FDA */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?''' Module 1 and Module 5 (Module 5.3.5.4 especially where the BCO is located) are required. A cover letter (states the purpose of the submission and the intentional submission center) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''Which center should the eCTD (containing BCO file(s)) be submitted to?''' Both CDER and CBER centers accept eCTD submissions and they both have the ability to review the submission files if requested.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Gateway.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing and identification. In addition, provide the shipping company name, transit number and expected delivery date when available to DCC (DCCEDR@fda.hhs.gov).&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is no minimum requirement; it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is the software used required for submission?''' Software used is not required to be submitted. However, some divisions would want software details; this depends very much on where the submission goes.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. &lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to the FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance-compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fd]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ a.go][https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the '''''&amp;lt;nowiki/&amp;gt;'''''prompts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machines).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. The FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1133</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1133"/>
		<updated>2025-10-06T20:17:58Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Submission Process and Requirements */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?''' Module 1 and Module 5 (Module 5.3.5.4 especially where the BCO is located) are required. A cover letter (states the purpose of the submission and the intentional submission center) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Gateway.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing and identification. In addition, provide the shipping company name, transit number and expected delivery date when available to DCC (DCCEDR@fda.hhs.gov).&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is no minimum requirement; it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is the software used required for submission?''' Software used is not required to be submitted. However, some divisions would want software details; this depends very much on where the submission goes.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. &lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to the FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance-compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fd]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ a.go][https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the '''''&amp;lt;nowiki/&amp;gt;'''''prompts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machines).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. The FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1132</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1132"/>
		<updated>2025-10-06T20:17:05Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Submission Process and Requirements */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Gateway.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing and identification. In addition, provide the shipping company name, transit number and expected delivery date when available to DCC (DCCEDR@fda.hhs.gov).&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is no minimum requirement; it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is the software used required for submission?''' Software used is not required to be submitted. However, some divisions would want software details; this depends very much on where the submission goes.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. &lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to the FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance-compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fd]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ a.go][https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the '''''&amp;lt;nowiki/&amp;gt;'''''prompts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machines).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. The FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1131</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1131"/>
		<updated>2025-10-06T20:16:37Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Submission Process and Requirements */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing and identification. In addition, provide the shipping company name, transit number and expected delivery date when available to DCC (DCCEDR@fda.hhs.gov).&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is no minimum requirement; it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is the software used required for submission?''' Software used is not required to be submitted. However, some divisions would want software details; this depends very much on where the submission goes.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. &lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to the FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance-compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fd]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ a.go][https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the '''''&amp;lt;nowiki/&amp;gt;'''''prompts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machines).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. The FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1130</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1130"/>
		<updated>2025-10-06T20:16:19Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available for this pilot phase.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing and identification. In addition, provide the shipping company name, transit number and expected delivery date when available to DCC (DCCEDR@fda.hhs.gov).&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is no minimum requirement; it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is the software used required for submission?''' Software used is not required to be submitted. However, some divisions would want software details; this depends very much on where the submission goes.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. &lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to the FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance-compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fd]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ a.go][https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the '''''&amp;lt;nowiki/&amp;gt;'''''prompts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machines).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. The FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1129</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1129"/>
		<updated>2025-10-06T20:13:36Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Archived Pilot Project Related FAQs */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available for this pilot phase.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data for the pilot project. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing  and identification. In addition, provide the shipping company name, transit number and  expected delivery date when available to DCC (DCCEDR@fda.hhs.gov). &lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is not a minimum requirement, it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?'''  Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
# '''Is software used required to submit for the purpose of the pilot project?'''  Software used is not required to be submitted for the pilot. However, some divisions would want software details, this is very much depended on where the submission goes but for the pilot project, we would simplify the process by not requiring software detail submission.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fda.go]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the prom'''''&amp;lt;nowiki/&amp;gt;'''''pts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machine).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. Based on pilot testing with Industry volunteers, the FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1128</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1128"/>
		<updated>2025-10-06T20:13:09Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Submitting BCOs to FDA */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available for this pilot phase.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data for the pilot project. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing  and identification. In addition, provide the shipping company name, transit number and  expected delivery date when available to DCC (DCCEDR@fda.hhs.gov). &lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is not a minimum requirement, it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?'''  Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
# '''Is software used required to submit for the purpose of the pilot project?'''  Software used is not required to be submitted for the pilot. However, some divisions would want software details, this is very much depended on where the submission goes but for the pilot project, we would simplify the process by not requiring software detail submission.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fda.go]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the prom'''''&amp;lt;nowiki/&amp;gt;'''''pts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machine).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. Based on pilot testing with Industry volunteers, the FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
== Archived Pilot Project Related FAQs ==&lt;br /&gt;
&lt;br /&gt;
=== BCO Test Submission ===&lt;br /&gt;
&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## CDER: Participants should contact [[2]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## CBER: Participants should contact [[3]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''What is Electronic Submission Gateway (ESG)?''' The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?''' Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=Whirl:_BCO_R_package_converter&amp;diff=1126</id>
		<title>Whirl: BCO R package converter</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=Whirl:_BCO_R_package_converter&amp;diff=1126"/>
		<updated>2025-08-12T20:30:38Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Whirl, developed by Novo Nordisk, is an open-source R package designed to streamline the creation of BioCompute Objects (BCOs) from ready or near-ready YAML files that define computational pipeline structures. By automating the generation of BCOs compliant with the BioCompute standard, Whirl reduces the manual effort required to document complex bioinformatics workflows.&lt;br /&gt;
&lt;br /&gt;
This package is especially useful for researchers, bioinformaticians, and regulatory scientists who need to create reproducible, transparent, and standardized records of their data analysis pipelines. Whirl extracts relevant metadata, execution details, and file information from the YAML configuration and pipeline runs, packaging them into a structured JSON BCO suitable for FDA submissions or collaborative sharing.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Follow the steps below to try out the tool:&lt;br /&gt;
&lt;br /&gt;
# Install the whirl package:  &amp;lt;code&amp;gt;&amp;gt; install.packages(&amp;quot;devtools&amp;quot;)&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;&amp;gt; devtools::install_github(&amp;quot;NovoNordisk-OpenSource/whirl&amp;quot;)&amp;lt;/code&amp;gt;&lt;br /&gt;
# Load the package:   &amp;lt;code&amp;gt;&amp;gt; library(whirl)&amp;lt;/code&amp;gt;&lt;br /&gt;
# Prepare your YAML configuration (either already have a YAML or needs to define the pipeline manually):  &amp;lt;code&amp;gt;#example of a basic pipeline that meets the BCO requirements&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;&amp;gt; whirl_config &amp;lt;- list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+    steps = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        export_mtcars = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+            run = &amp;quot;step1.R&amp;quot;&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        )&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+    ),&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+    biocompute = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        object_id = &amp;quot;bco-mtcars-001&amp;quot;,&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        spec_version = &amp;quot;1.3.0&amp;quot;,&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        etag = &amp;quot;etag-mtcars-001&amp;quot;,&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        usability = list(&amp;quot;Example use case: exporting mtcars dataset&amp;quot;),&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        extension = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+            whirl_test_extension = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+                info = &amp;quot;Exporting mtcars dataset as test run&amp;quot;&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+            )&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        )&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+    )&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+ )&amp;lt;/code&amp;gt;&lt;br /&gt;
# Write to _whirl.yml:   &amp;lt;code&amp;gt;&amp;gt; writeLines(as.yaml(whirl_config), &amp;quot;_whirl.yml&amp;quot;)&amp;lt;/code&amp;gt;&lt;br /&gt;
# Run YAML config:   &amp;lt;code&amp;gt;&amp;gt; queue &amp;lt;- run(&amp;quot;_whirl.yml&amp;quot;)&amp;lt;/code&amp;gt;&lt;br /&gt;
# Write into a BCO:   &amp;lt;code&amp;gt;&amp;gt; write_biocompute(queue, file = &amp;quot;bco.json&amp;quot;)&amp;lt;/code&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=Whirl:_BCO_R_package_converter&amp;diff=1125</id>
		<title>Whirl: BCO R package converter</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=Whirl:_BCO_R_package_converter&amp;diff=1125"/>
		<updated>2025-08-12T20:29:25Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Whirl package BCO generation toturial&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Whirl, developed by Novo Nordisk, is an open-source R package designed to streamline the creation of BioCompute Objects (BCOs) from ready or near-ready YAML files that define computational pipeline structures. By automating the generation of BCOs compliant with the BioCompute standard, Whirl reduces the manual effort required to document complex bioinformatics workflows.&lt;br /&gt;
&lt;br /&gt;
This package is especially useful for researchers, bioinformaticians, and regulatory scientists who need to create reproducible, transparent, and standardized records of their data analysis pipelines. Whirl extracts relevant metadata, execution details, and file information from the YAML configuration and pipeline runs, packaging them into a structured JSON BCO suitable for FDA submissions or collaborative sharing.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Follow the steps below to try out the tool:&lt;br /&gt;
&lt;br /&gt;
# Install the whirl package: &amp;lt;code&amp;gt;&amp;gt; install.packages(&amp;quot;devtools&amp;quot;)&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;&amp;gt; devtools::install_github(&amp;quot;NovoNordisk-OpenSource/whirl&amp;quot;)&amp;lt;/code&amp;gt;&lt;br /&gt;
# Load the package:  &amp;lt;code&amp;gt;&amp;gt; library(whirl)&amp;lt;/code&amp;gt;&lt;br /&gt;
# Prepare your YAML configuration (either already have a YAML or needs to define the pipeline manually):  &amp;lt;code&amp;gt;#example of a basic pipeline that meets the BCO requirements&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;&amp;gt; whirl_config &amp;lt;- list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+    steps = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        export_mtcars = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+            run = &amp;quot;step1.R&amp;quot;&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        )&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+    ),&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+    biocompute = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        object_id = &amp;quot;bco-mtcars-001&amp;quot;,&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        spec_version = &amp;quot;1.3.0&amp;quot;,&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        etag = &amp;quot;etag-mtcars-001&amp;quot;,&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        usability = list(&amp;quot;Example use case: exporting mtcars dataset&amp;quot;),&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        extension = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+            whirl_test_extension = list(&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+                info = &amp;quot;Exporting mtcars dataset as test run&amp;quot;&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+            )&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+        )&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+    )&amp;lt;/code&amp;gt;  &amp;lt;code&amp;gt;+ )&amp;lt;/code&amp;gt; &lt;br /&gt;
# Write to _whirl.yml:  &amp;lt;code&amp;gt;&amp;gt; writeLines(as.yaml(whirl_config), &amp;quot;_whirl.yml&amp;quot;)&amp;lt;/code&amp;gt;&lt;br /&gt;
# Run YAML config:  &amp;lt;code&amp;gt;&amp;gt; queue &amp;lt;- run(&amp;quot;_whirl.yml&amp;quot;)&amp;lt;/code&amp;gt;&lt;br /&gt;
# Write into a BCO:  &amp;lt;code&amp;gt;&amp;gt; write_biocompute(queue, file = &amp;quot;bco.json&amp;quot;)&amp;lt;/code&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1121</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1121"/>
		<updated>2025-05-08T13:54:46Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== Galaxy Platform ===&lt;br /&gt;
[[File:Galaxy.png|frameless|162x162px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===&lt;br /&gt;
[[File:CGC v2.0.png|frameless|159x159px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. &lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[File:Biocomputing.gif|frameless|42x42px]]BioCompute Citations&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
# Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R.. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Mar;103884(3) [https://pubmed.ncbi.nlm.nih.gov/38219969/ PMID:38219969.]&lt;br /&gt;
# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; [https://pubmed.ncbi.nlm.nih.gov/35077912/ PMID: 35077912].&lt;br /&gt;
# Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. [https://doi.org/10.3233/DS-210053 Packaging research artefacts with RO-Crate]. Data Science, 2022&lt;br /&gt;
# Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; [https://pubmed.ncbi.nlm.nih.gov/33784373/ PMID:33784373].&lt;br /&gt;
# Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. [https://doi.org/10.1371/journal.pbio.3000099 Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results.] PLOS Biology; 16(12): e3000099.2018.&lt;br /&gt;
# Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 [https://pubmed.ncbi.nlm.nih.gov/27974626/ PMID:27974626].&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1120</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1120"/>
		<updated>2025-04-21T14:45:48Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== Galaxy Platform ===&lt;br /&gt;
[[File:Galaxy.png|frameless|162x162px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===&lt;br /&gt;
[[File:CGC v2.0.png|frameless|159x159px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. &lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[File:Biocomputing.gif|frameless|42x42px]]BioCompute Citations&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
# Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R.. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Mar;103884(3) [https://pubmed.ncbi.nlm.nih.gov/38219969/ PMID:38219969.]&lt;br /&gt;
# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; [https://pubmed.ncbi.nlm.nih.gov/35077912/ PMID: 35077912].&lt;br /&gt;
# Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. [https://doi.org/10.3233/DS-210053 Packaging research artefacts with RO-Crate]. Data Science, 2022&lt;br /&gt;
# Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; [https://pubmed.ncbi.nlm.nih.gov/33784373/ PMID:33784373].&lt;br /&gt;
# Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. [https://doi.org/10.1371/journal.pbio.3000099 Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results.] PLOS Biology; 16(12): e3000099.2018.&lt;br /&gt;
# Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 [https://pubmed.ncbi.nlm.nih.gov/27974626/ PMID:27974626].&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1119</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1119"/>
		<updated>2025-04-21T14:45:15Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== Galaxy Platform ===&lt;br /&gt;
[[File:Galaxy.png|frameless|162x162px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===&lt;br /&gt;
[[File:CGC v2.0.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. &lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[File:Biocomputing.gif|frameless|42x42px]]BioCompute Citations&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
# Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R.. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Mar;103884(3) [https://pubmed.ncbi.nlm.nih.gov/38219969/ PMID:38219969.]&lt;br /&gt;
# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; [https://pubmed.ncbi.nlm.nih.gov/35077912/ PMID: 35077912].&lt;br /&gt;
# Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. [https://doi.org/10.3233/DS-210053 Packaging research artefacts with RO-Crate]. Data Science, 2022&lt;br /&gt;
# Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; [https://pubmed.ncbi.nlm.nih.gov/33784373/ PMID:33784373].&lt;br /&gt;
# Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. [https://doi.org/10.1371/journal.pbio.3000099 Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results.] PLOS Biology; 16(12): e3000099.2018.&lt;br /&gt;
# Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 [https://pubmed.ncbi.nlm.nih.gov/27974626/ PMID:27974626].&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1118</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1118"/>
		<updated>2025-04-21T14:44:33Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== Galaxy Platform ===&lt;br /&gt;
[[File:Galaxy.png|frameless|162x162px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===&lt;br /&gt;
[[File:CGC v2.0.png|left|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. &lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[File:Biocomputing.gif|frameless|42x42px]]BioCompute Citations&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
# Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R.. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Mar;103884(3) [https://pubmed.ncbi.nlm.nih.gov/38219969/ PMID:38219969.]&lt;br /&gt;
# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; [https://pubmed.ncbi.nlm.nih.gov/35077912/ PMID: 35077912].&lt;br /&gt;
# Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. [https://doi.org/10.3233/DS-210053 Packaging research artefacts with RO-Crate]. Data Science, 2022&lt;br /&gt;
# Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; [https://pubmed.ncbi.nlm.nih.gov/33784373/ PMID:33784373].&lt;br /&gt;
# Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. [https://doi.org/10.1371/journal.pbio.3000099 Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results.] PLOS Biology; 16(12): e3000099.2018.&lt;br /&gt;
# Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 [https://pubmed.ncbi.nlm.nih.gov/27974626/ PMID:27974626].&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:CGC_v2.0.png&amp;diff=1117</id>
		<title>File:CGC v2.0.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:CGC_v2.0.png&amp;diff=1117"/>
		<updated>2025-04-21T14:43:33Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;CGC updated logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=Main_Page&amp;diff=1116</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=Main_Page&amp;diff=1116"/>
		<updated>2025-04-08T15:57:38Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Added pilot project link&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{DISPLAYTITLE:&amp;lt;span style=&amp;quot;position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);&amp;quot;&amp;gt;{{FULLPAGENAME}}&amp;lt;/span&amp;gt;}}&lt;br /&gt;
__NOTOC__&lt;br /&gt;
&amp;lt;!-- BANNER ACROSS TOP OF PAGE --&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw-topbanner&amp;quot; style=&amp;quot;clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;margin:0.4em; text-align:center;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;font-size:160%; padding:.1em;&amp;quot;&amp;gt;Welcome to BioCompute Objects Wiki,&amp;lt;/div&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;font-size:100%;&amp;quot;&amp;gt;The [https://www.mediawiki.org/wiki/MediaWiki MediaWiki] for the BioCompute Objects project. This wiki system provides complementary information to the [https://www.biocomputeobject.org/ BioCompute portal] and is divided into the following main sections: General information for the [https://www.biocomputeobject.org/ BioCompute portal], [[User_guide|Quick Start and User Guide]], [[Faq|FAQ]], [[Sop|Curation SOP]], and [[About|About]] for the [https://www.biocomputeobject.org/ BioCompute portal].&amp;lt;/div&amp;gt;You can also find the BioCompute White paper [[White paper|here]].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div style=&amp;quot;clear: both;&amp;quot;&amp;gt;&amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;clear: both;&amp;quot;&amp;gt;&amp;lt;br /&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[User guide|BioCompute Object (BCO) User Guide]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
This document specifies the structure of BioCompute Objects. The specification is split into multiple parts linked to this top-level document and is maintained in a [https://github.com/biocompute-objects/BCO_Specification GitHub repository] where contributions are welcome. This document was created by the [[Main_Page#BioCompute_Object_Consortium_members_(BCOC)|BioCompute Object Consortium members (BCOC)]].&lt;br /&gt;
&lt;br /&gt;
It is offered as support for IEEE-2791-2020: [https://standards.ieee.org/ieee/2791/7337/ IEEE Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication].&lt;br /&gt;
&lt;br /&gt;
Read more: [[Introduction|Introduction to BioCompute Objects]]&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Faq|Frequently Asked Questions]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The FAQ section contains a list of questions asked by users regarding using the portal, pipeline steps, and extensions as well as questions related to the prerequisite, knowledgebase recommendation, and saving and publishing BCOs.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Faq|Frequently Asked Questions]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Sop|BCO Curation SOP]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Intended audience: authors and developers&lt;br /&gt;
&lt;br /&gt;
This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Sop|BCO Curation SOP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BCO Pilot Project|Pilot Project]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We are currently running a pilot project of mock submission to the FDA. The purpose of the pilot is to bring both the sponsors and the FDA to an agreement around BCO usage to streamline and standardize computational workflow submissions and reviews. We expect to obtain first-hand knowledge of submitting computational analyses to the FDA and how to efficiently and effectively ease communication barriers between sponsors and the government agency.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[About]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
A BioCompute Object (BCO) is an instance of the BioCompute standard and is a computational record of a bioinformatics pipeline. A BCO is not an analysis but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result and includes additional metadata to identify provenance and usage.&lt;br /&gt;
&lt;br /&gt;
Read more: &lt;br /&gt;
*[[About|What is BioCompute?]]&lt;br /&gt;
*[[About|Wifi Analogy]]&lt;br /&gt;
*[[About|BioCompute Description]]&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Publications|Publication]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
'''For Citation Purpose:''' Simonyan, V., Goecks, J., &amp;amp; Mazumder, R. (2017). Biocompute Objects — A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA Journal of Pharmaceutical Science and Technology, 71(2), 136–146. doi: 10.5731/pdajpst.2016.006734&lt;br /&gt;
&lt;br /&gt;
See also full list of [[publications]] about BioCompute Object.&lt;br /&gt;
&lt;br /&gt;
=== Other links ===&lt;br /&gt;
# [[CDISC]]&lt;br /&gt;
# [[Galaxy]]&lt;br /&gt;
# [[RO-Crate]]&lt;br /&gt;
# [[CWL|Common Workflow Language (CWL)]]&lt;br /&gt;
# [https://fairsharing.org/4293 FAIRsharing]&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=Main_Page&amp;diff=1115</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=Main_Page&amp;diff=1115"/>
		<updated>2025-04-08T15:56:54Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{DISPLAYTITLE:&amp;lt;span style=&amp;quot;position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);&amp;quot;&amp;gt;{{FULLPAGENAME}}&amp;lt;/span&amp;gt;}}&lt;br /&gt;
__NOTOC__&lt;br /&gt;
&amp;lt;!-- BANNER ACROSS TOP OF PAGE --&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw-topbanner&amp;quot; style=&amp;quot;clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;margin:0.4em; text-align:center;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;font-size:160%; padding:.1em;&amp;quot;&amp;gt;Welcome to BioCompute Objects Wiki,&amp;lt;/div&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;font-size:100%;&amp;quot;&amp;gt;The [https://www.mediawiki.org/wiki/MediaWiki MediaWiki] for the BioCompute Objects project. This wiki system provides complementary information to the [https://www.biocomputeobject.org/ BioCompute portal] and is divided into the following main sections: General information for the [https://www.biocomputeobject.org/ BioCompute portal], [[User_guide|Quick Start and User Guide]], [[Faq|FAQ]], [[Sop|Curation SOP]], and [[About|About]] for the [https://www.biocomputeobject.org/ BioCompute portal].&amp;lt;/div&amp;gt;You can also find the BioCompute White paper [[White paper|here]].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div style=&amp;quot;clear: both;&amp;quot;&amp;gt;&amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;clear: both;&amp;quot;&amp;gt;&amp;lt;br /&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[User guide|BioCompute Object (BCO) User Guide]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
This document specifies the structure of BioCompute Objects. The specification is split into multiple parts linked to this top-level document and is maintained in a [https://github.com/biocompute-objects/BCO_Specification GitHub repository] where contributions are welcome. This document was created by the [[Main_Page#BioCompute_Object_Consortium_members_(BCOC)|BioCompute Object Consortium members (BCOC)]].&lt;br /&gt;
&lt;br /&gt;
It is offered as support for IEEE-2791-2020: [https://standards.ieee.org/ieee/2791/7337/ IEEE Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication].&lt;br /&gt;
&lt;br /&gt;
Read more: [[Introduction|Introduction to BioCompute Objects]]&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Faq|Frequently Asked Questions]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The FAQ section contains a list of questions asked by users regarding using the portal, pipeline steps, and extensions as well as questions related to the prerequisite, knowledgebase recommendation, and saving and publishing BCOs.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Faq|Frequently Asked Questions]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Sop|BCO Curation SOP]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Intended audience: authors and developers&lt;br /&gt;
&lt;br /&gt;
This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Sop|BCO Curation SOP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[Pilot Project]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We are currently running a pilot project of mock submission to the FDA. The purpose of the pilot is to bring both the sponsors and the FDA to an agreement around BCO usage to streamline and standardize computational workflow submissions and reviews. We expect to obtain first-hand knowledge of submitting computational analyses to the FDA and how to efficiently and effectively ease communication barriers between sponsors and the government agency.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[About]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
A BioCompute Object (BCO) is an instance of the BioCompute standard and is a computational record of a bioinformatics pipeline. A BCO is not an analysis but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result and includes additional metadata to identify provenance and usage.&lt;br /&gt;
&lt;br /&gt;
Read more: &lt;br /&gt;
*[[About|What is BioCompute?]]&lt;br /&gt;
*[[About|Wifi Analogy]]&lt;br /&gt;
*[[About|BioCompute Description]]&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Publications|Publication]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
'''For Citation Purpose:''' Simonyan, V., Goecks, J., &amp;amp; Mazumder, R. (2017). Biocompute Objects — A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA Journal of Pharmaceutical Science and Technology, 71(2), 136–146. doi: 10.5731/pdajpst.2016.006734&lt;br /&gt;
&lt;br /&gt;
See also full list of [[publications]] about BioCompute Object.&lt;br /&gt;
&lt;br /&gt;
=== Other links ===&lt;br /&gt;
# [[CDISC]]&lt;br /&gt;
# [[Galaxy]]&lt;br /&gt;
# [[RO-Crate]]&lt;br /&gt;
# [[CWL|Common Workflow Language (CWL)]]&lt;br /&gt;
# [https://fairsharing.org/4293 FAIRsharing]&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1114</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1114"/>
		<updated>2025-03-11T17:52:00Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;__NOTOC__&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== Galaxy Platform ===&lt;br /&gt;
[[File:Galaxy.png|frameless|162x162px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===&lt;br /&gt;
[[File:Cgc2.png|frameless|114x114px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. &lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[File:Biocomputing.gif|frameless|42x42px]]BioCompute Citations&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
# Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R.. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Mar;103884(3) [https://pubmed.ncbi.nlm.nih.gov/38219969/ PMID:38219969.]&lt;br /&gt;
# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; [https://pubmed.ncbi.nlm.nih.gov/35077912/ PMID: 35077912].&lt;br /&gt;
# Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. [https://doi.org/10.3233/DS-210053 Packaging research artefacts with RO-Crate]. Data Science, 2022&lt;br /&gt;
# Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; [https://pubmed.ncbi.nlm.nih.gov/33784373/ PMID:33784373].&lt;br /&gt;
# Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. [https://doi.org/10.1371/journal.pbio.3000099 Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results.] PLOS Biology; 16(12): e3000099.2018.&lt;br /&gt;
# Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 [https://pubmed.ncbi.nlm.nih.gov/27974626/ PMID:27974626].&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1113</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1113"/>
		<updated>2025-03-11T17:46:43Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Added Citations&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== Galaxy Platform ===&lt;br /&gt;
[[File:Galaxy.png|frameless|162x162px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===&lt;br /&gt;
[[File:Cgc2.png|frameless|114x114px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. &lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[File:Biocomputing.gif|frameless|42x42px]]BioCompute Citations&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
# Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R.. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Mar;103884(3) [https://pubmed.ncbi.nlm.nih.gov/38219969/ PMID:38219969.]&lt;br /&gt;
# King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; [https://pubmed.ncbi.nlm.nih.gov/35077912/ PMID: 35077912].&lt;br /&gt;
# Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble. [https://doi.org/10.3233/DS-210053 Packaging research artefacts with RO-Crate]. Data Science, 2022&lt;br /&gt;
# Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford).2021 March 31; [https://pubmed.ncbi.nlm.nih.gov/33784373/ PMID:33784373].&lt;br /&gt;
# Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. [https://doi.org/10.1371/journal.pbio.3000099 Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results.] PLOS Biology; 16(12): e3000099.2018.&lt;br /&gt;
# Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017;71(2):136-146 [https://pubmed.ncbi.nlm.nih.gov/27974626/ PMID:27974626].&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Biocomputing.gif&amp;diff=1112</id>
		<title>File:Biocomputing.gif</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Biocomputing.gif&amp;diff=1112"/>
		<updated>2025-03-11T17:41:55Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Biocomputing&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1111</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1111"/>
		<updated>2025-03-11T15:54:38Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== Galaxy Platform ===&lt;br /&gt;
[[File:Galaxy.png|frameless|162x162px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The Galaxy BCO API Extension enables Galaxy users to the export of Galaxy “workflow invocations” (i.e. realizations of a computational pipeline) in BCO format.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://www.cancergenomicscloud.org/ Cancer Genomics Cloud Seven Bridges] ===&lt;br /&gt;
[[File:Cgc2.png|frameless|114x114px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. &lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Cgc2.png&amp;diff=1110</id>
		<title>File:Cgc2.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Cgc2.png&amp;diff=1110"/>
		<updated>2025-03-11T15:46:37Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Seven Bridges&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Galaxy.png&amp;diff=1109</id>
		<title>File:Galaxy.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Galaxy.png&amp;diff=1109"/>
		<updated>2025-03-11T15:42:05Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Galaxy Logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1108</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1108"/>
		<updated>2025-03-11T15:41:05Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1107</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1107"/>
		<updated>2025-03-11T15:39:54Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;  &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt; &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt; &lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1106</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1106"/>
		<updated>2025-03-11T15:33:51Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform] ===&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;  &lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1105</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1105"/>
		<updated>2025-03-11T15:30:41Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Added more resources&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
[https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform]&lt;br /&gt;
&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/biocompute-objects/bcotool/tree/1.1.0 BCO-TOOL]&amp;lt;/h3&amp;gt;[[File:Octocat.png|frameless|96x96px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Command line tool for to create, validate, and export BioCompute Objects.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://cran.r-project.org/web/packages/biocompute/index.html CRAN BioCompute Tool]&amp;lt;/h3&amp;gt;[[File:Cran.png|frameless|71x71px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Tools to create, validate, and export BioCompute Objects in R. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
=== [https://hub.docker.com/r/dnanexus/bconexus BCO Nexus] ===&lt;br /&gt;
[[File:Dnanexus.png|frameless|60x60px]][[File:Velsera.jpg|frameless|127x127px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
BCOnexus developed by DNAnexus, now known as Velsera, as a platform-free Docker tool for quick BCO evaluation.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;  &lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Velsera.jpg&amp;diff=1104</id>
		<title>File:Velsera.jpg</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Velsera.jpg&amp;diff=1104"/>
		<updated>2025-03-11T15:29:52Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Velsera Logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Dnanexus.png&amp;diff=1103</id>
		<title>File:Dnanexus.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Dnanexus.png&amp;diff=1103"/>
		<updated>2025-03-11T15:28:20Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;DNAnexus logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Cran.png&amp;diff=1102</id>
		<title>File:Cran.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Cran.png&amp;diff=1102"/>
		<updated>2025-03-11T15:25:30Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Cran Logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Octocat.png&amp;diff=1101</id>
		<title>File:Octocat.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Octocat.png&amp;diff=1101"/>
		<updated>2025-03-11T15:23:32Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Git Logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1100</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1100"/>
		<updated>2025-03-11T15:21:32Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
[https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform]&lt;br /&gt;
&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
[https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform]&lt;br /&gt;
&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;  &lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1099</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1099"/>
		<updated>2025-03-11T15:19:29Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://biocomputeobject.org/api/docs/ BCODB API]&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
[https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform]&lt;br /&gt;
&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1098</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1098"/>
		<updated>2025-03-11T15:19:06Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;BCODB API&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[https://github.com/nextflow-io/nf-prov Nextflow]&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Automatically generate BCO from Nextflow pipelines with provenance information&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
[https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE Platform]&lt;br /&gt;
&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1097</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1097"/>
		<updated>2025-03-11T15:18:16Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Added BCO resources&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;BCODB API&amp;lt;/h3&amp;gt;[[File:Swagger.png|frameless|211x211px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;Nextflow&amp;lt;/h3&amp;gt;[[File:Nextflow.png|frameless|121x121px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The FAQ section contains a list of questions asked by users regarding using the portal, pipeline steps, and extensions as well as questions related to the prerequisite, knowledgebase recommendation, and saving and publishing BCOs.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Faq|Frequently Asked Questions]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
HIVE Platform&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
HIVE Platform&lt;br /&gt;
&lt;br /&gt;
[[File:Hive.png|frameless|155x155px]]&amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The High-throughput Integrated Virtual Environment (HIVE) for genome analysis has platform specific tools for generating BioCompute Objects from workflows.&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Hive.png&amp;diff=1096</id>
		<title>File:Hive.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Hive.png&amp;diff=1096"/>
		<updated>2025-03-11T15:13:38Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;HIVE logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Nextflow.png&amp;diff=1095</id>
		<title>File:Nextflow.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Nextflow.png&amp;diff=1095"/>
		<updated>2025-03-11T15:10:04Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Nextflow logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1094</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1094"/>
		<updated>2025-03-11T15:07:54Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;BCODB API&amp;lt;/h3&amp;gt;&lt;br /&gt;
[[File:Swagger.png|thumb]]&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Explore the BioCompute database RESTful APIs, generated by Swagger.&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Faq|Frequently Asked Questions]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The FAQ section contains a list of questions asked by users regarding using the portal, pipeline steps, and extensions as well as questions related to the prerequisite, knowledgebase recommendation, and saving and publishing BCOs.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Faq|Frequently Asked Questions]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Sop|BCO Curation SOP]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Intended audience: authors and developers&lt;br /&gt;
&lt;br /&gt;
This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Sop|BCO Curation SOP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=File:Swagger.png&amp;diff=1093</id>
		<title>File:Swagger.png</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=File:Swagger.png&amp;diff=1093"/>
		<updated>2025-03-11T15:07:30Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;Swagger Logo&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1092</id>
		<title>BCO Resources</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=BCO_Resources&amp;diff=1092"/>
		<updated>2025-03-11T15:02:01Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Created page with &amp;quot;hi&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;hi&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=About&amp;diff=1091</id>
		<title>About</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=About&amp;diff=1091"/>
		<updated>2025-03-11T14:33:07Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Added About Page content from the portal to this page&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main_Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== What is BioCompute? ==&lt;br /&gt;
&lt;br /&gt;
Tremendous insights can be found in genome data, and many of these insights are being used to drive personalized medicine. But the hundreds of millions of reads that come from a gene sequencer represent small, nearly random fragments of the genome that’s being sequenced, and there are countless ways in which that data can be transformed to yield insights into cancer, ancestry, microbiome dynamics, metagenomics, and many other areas of interest.&lt;br /&gt;
&lt;br /&gt;
Because there are so many different platforms and so many different scripts and tools to analyze genome data, there is a great need to standardize the way in which these steps are communicated. The more analysis steps and the more complicated a pipeline, the greater the need for a standardized mechanism of communication. The BioCompute standard brings clarity to an analysis, making it clear and reproducible.&lt;br /&gt;
&lt;br /&gt;
A [[Main Page|BioCompute Object]] (BCO) is an instance of the BioCompute standard, and is a computational record of a bioinformatics pipeline. A BCO is not an analysis, but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result, and includes additional metadata to identify provenance and usage.&lt;br /&gt;
[[File:About.3.png|800px|thumb|center]]&lt;br /&gt;
&lt;br /&gt;
A BioCompute Object (BCO) is an instance of the BioCompute standard, and is a computational record of a bioinformatics pipeline. A BCO is not an analysis, but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result, and includes additional metadata to identify provenance and usage.&lt;br /&gt;
&lt;br /&gt;
== Our Mission ==&lt;br /&gt;
BioCompute is a standard for workflow communication. It comes with very strong data provenance, researcher attribution, and descriptive metadata features.&lt;br /&gt;
&lt;br /&gt;
It is common to hear “x software was used” when reading about a computational pipeline. This is not enough to make informed scientific assessments of work, whether in academic publication reviews, regulatory decisions (e.g. at the FDA), internal process review (particularly for trade secrets), or in educational contexts. Poor workflow communication results in significant delays in reviews, or worse, outright rejection.&lt;br /&gt;
&lt;br /&gt;
The BioCompute mission is to overhaul the way that computational analyses in biology are shared, understood, and reproduced between the research community, the clinical community, and regulatory organizations.&lt;br /&gt;
&lt;br /&gt;
== Our Story ==&lt;br /&gt;
BioCompute is built through collaboration between the George Washington University and the Food and Drug Administration (FDA) and approved as an official standard of IEEE 2791-2020. BioCompute brings transparency of the workflow and clear expectations for data sharing between communities. The project has worked with individuals from NIH, Harvard, several biotech and pharma companies, EMBL-EBI, Galaxy Project, and many more, and can be integrated with any existing standard for HTS data. Associate tools have been developed by popular bioinformatics platforms such as DNAnexus, Seven Bridges, and Galaxy for BCO submission with minimal effort. More information about The current BioCompute standard can be found on the Open Science Foundation website (where the standard is developed and maintained), the HIVE website, and the Research Objects discussion of BioCompute.&lt;br /&gt;
&lt;br /&gt;
== Our Audience ==&lt;br /&gt;
BioCompute serves a broad range of stakeholders within the scientific and biomedical research communities, including but not limited to:&lt;br /&gt;
&lt;br /&gt;
* Researchers and Scientists&lt;br /&gt;
* Educators and Students&lt;br /&gt;
* Regulatory Bodies&lt;br /&gt;
* Bioinformatics and Data Analysts&lt;br /&gt;
* Software Developers and Engineers&lt;br /&gt;
&lt;br /&gt;
== Benefits of BioCompute Objects(BCOs) ==&lt;br /&gt;
&lt;br /&gt;
* '''Enhanced Transparency''': BCOs provide a clear and detailed account of documented computational analyses, ensuring all steps are visible and understandable.&lt;br /&gt;
* '''Improved Reproducibility:''' BCOs allow for documented analyses to be easily replicated to validate research findings.&lt;br /&gt;
* '''Streamlined Collaboration''': BCOs facilitate better collaboration among researchers by providing a common framework for sharing workflows.&lt;br /&gt;
* '''Regulatory Compliance''': BCOs support regulatory bodies in evaluating the validity and reliability of computational workflows, thereby enhancing the credibility of research.&lt;br /&gt;
* '''Educational Value:''' BCOs can make it easier for students and educators to grasp complected concepts and analyses much more easily through intuitive documentation.&lt;br /&gt;
&lt;br /&gt;
== Frequently Asked Questions ==&lt;br /&gt;
&lt;br /&gt;
# '''What role does standardization play in scientific collaboration?'''  Standardization, as provided by BCOs, is crucial for seamless collaboration across different institutions and disciplines, enabling researchers to build on each other’s work effectively.&lt;br /&gt;
# '''How can we improve reproducibility in Biomedical Research?''' Ensuring that research findings can be replicated by others is a cornerstone of scientific integrity. BCOs address this by providing a clear and detailed framework for documenting analyses.&lt;br /&gt;
# '''How can we ensure regulatory compliance in computational workflows?''' BCOs facilitate compliance by offering a transparent and consistent documentation method, helping regulatory bodies like the FDA evaluate computational analyses more efficiently.&lt;br /&gt;
&lt;br /&gt;
== WiFi Analogy ==&lt;br /&gt;
&lt;br /&gt;
The [https://en.wikipedia.org/wiki/IEEE%20802.11 802.11 standard] (more commonly called “WiFi”) is a way of standardizing communication between vastly different products on a wireless network. If a product manufacturer wants a product to be able to communicate on a wireless internet network, they can configure the device to use the WiFi standard and it will be able to communicate with most commercial routers, regardless of whether the product is a Mac, a PC, a cell phone, or a smart toaster.&lt;br /&gt;
[[File:Wifi analogy.png|800px|thumb|center]]&lt;br /&gt;
&lt;br /&gt;
BioCompute fills a similar need. BioCompute is not an automation or a new programming language, it is a way of collecting and communicating information between two entities. Rather than a latop and a router, it may be between a pharmaceutical company and the FDA, or between two clinicians, or between a clinician and a researcher. In much the same way that WiFi does not standardize the data that’s being transmitted – allowing you to use Apple’s Facetime, Microsoft’s Internet Explorer, or your favorite cell phone app – BioCompute does not standardize the platforms or tools that are used for genome analysis. You continue to use your favorite platforms and tools, whether it’s [https://hive.biochemistry.gwu.edu/dna.cgi?cmd=main HIVE], [https://galaxyproject.org/ Galaxy], [https://www.sevenbridges.com/ Seven Bridges], [https://www.dnanexus.com/ DNAnexus], or others. Also like WiFi, BioCompute can be layered with other privacy or security protocols depending on usage. So clinical trial data can be secured and HIPAA-compliant, while government-funded data sets shared between researchers can be completely open access.&lt;br /&gt;
&lt;br /&gt;
Because BioCompute acts like an envelope for an entire analysis pipeline, it is compatible with other existing standards, including [https://www.hl7.org/fhir/genomics.html FHIR Genomics] and [https://www.ga4gh.org/ GA4GH].&lt;br /&gt;
&lt;br /&gt;
== BioCompute Description ==&lt;br /&gt;
BioCompute is written in [https://json.org/example.html Javascript Object Notation] (JSON), which is simply a set of key:value pairs (meaning that raw files can be read without any knowledge of programming). Information within the BCO is organized into “domains.” The domains within a BCO record are Provenance, Usability, Extension, Description, Execution, Input/Output, and Parametric Domains. For more information on the domains, please see the [https://gitlab.com/IEEE-SA/2791-archived/2791-schema BioCompute Schema].&lt;br /&gt;
&lt;br /&gt;
BioCompute was built through a collaboration between The George Washington University and the FDA to improve communication of bioinformatics pipelines, and has since been expanded and refined through the participation or collaboration of hundreds of participants from throughout the public and private sectors. While we welcome interest and membership from anyone, most users will fall into one of three categories:&lt;br /&gt;
&lt;br /&gt;
*Research Community&lt;br /&gt;
:The Biocompute standard can help substantially improve replicability, making it possible to repeat a pipeline on a different sample with high fidelity and high confidence.&lt;br /&gt;
&lt;br /&gt;
*Clinical Community&lt;br /&gt;
:As BioCompute Objects become tested and validated, they can be applied in the clinic to identify risk factors, flag pharmakogenetic information, and much more.&lt;br /&gt;
&lt;br /&gt;
*Pharma, Biotech and Regulatory Pipeline&lt;br /&gt;
:Protracted communications with the FDA can extend the review process by months. A standardized method of communicating HTS data may help repeat results more quickly and without the need for additional communication.&lt;br /&gt;
&lt;br /&gt;
Research, clinical, and regulatory groups are key drivers of personalized medicine that is based on next generation sequencing, but there are barriers between these groups. BioCompute reduces these hurdles and brings transparency to the workflow, making it more clear what was done, and clearly delineating expectations for data sharing. The BioCompute specification can be layered with other privacy and security protocols to guard sensitive data, or be made open source depending on the needs of the user.&lt;br /&gt;
&lt;br /&gt;
The BioCompute project has generated two publications, three workshops, FDA funding, contributions from over 300 participants, and FDA submissions. The project has worked with individuals from NIH, Harvard, several biotech and pharma companies, EMBL-EBI, Galaxy Project, and many more, and can be integrated with any existing standard for HTS data. The project is expected to be both an IEEE and ISO recognized standard within 8-10 months.&lt;br /&gt;
&lt;br /&gt;
More information about The current BioCompute standard can be found on the [https://osf.io/h59uh/ Open Science Foundation website] (where the standard is developed and maintained), the [https://hive.biochemistry.gwu.edu/htscsrs/biocompute HIVE] website, and the Research Objects discussion of BioCompute.&lt;br /&gt;
[[File:Milestone for BCO.png|800px|thumb|center|'''Milestones in the BioCompute Program'''&lt;br /&gt;
&lt;br /&gt;
The major milestones of the BioCompute Partnership and future goals are paving the way for a consensus-driven, widely adopted standard. The FDA’s Genomics Working Group (GWG) originally articulated the challenges of communicating genomic analysis pipelines in a regulatory context in 2013. Since then, the project has accumulated tremendous momentum, a testament to the GWG’s efforts in describing communication challenges. More recently, the second BioCompute publication has recently been published, the 4th Workshop is scheduled, and the next major goal is the formal launch of the BioCompute Public Private Partnership. The [https://www.biocomputeobject.org/login Executive Committee] will formalize the future roadmap beyond these goals.]]&lt;br /&gt;
&lt;br /&gt;
== Funding Sources ==&lt;br /&gt;
&lt;br /&gt;
* [https://smhs.gwu.edu/news/gw-led-consortium-receives-22m-grant-fund-biocompute-object-specification-project FDA BAA-19-00123]&lt;br /&gt;
* [https://commonfund.nih.gov/dataecosystem Common Fund Data Ecosystem (CFDE) OT2 OD032092]&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=Main_Page/MediaWiki:Sidebar&amp;diff=1088</id>
		<title>Main Page/MediaWiki:Sidebar</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=Main_Page/MediaWiki:Sidebar&amp;diff=1088"/>
		<updated>2025-03-07T15:29:48Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Created page with &amp;quot;Pilot Project&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;[[BCO Pilot Project|Pilot Project]]&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=Main_Page&amp;diff=1086</id>
		<title>Main Page</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=Main_Page&amp;diff=1086"/>
		<updated>2025-03-07T15:13:02Z</updated>

		<summary type="html">&lt;p&gt;Twang9: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{DISPLAYTITLE:&amp;lt;span style=&amp;quot;position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);&amp;quot;&amp;gt;{{FULLPAGENAME}}&amp;lt;/span&amp;gt;}}&lt;br /&gt;
__NOTOC__&lt;br /&gt;
&amp;lt;!-- BANNER ACROSS TOP OF PAGE --&amp;gt;&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw-topbanner&amp;quot; style=&amp;quot;clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;margin:0.4em; text-align:center;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;font-size:160%; padding:.1em;&amp;quot;&amp;gt;Welcome to BioCompute Objects Wiki,&amp;lt;/div&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;font-size:100%;&amp;quot;&amp;gt;The [https://www.mediawiki.org/wiki/MediaWiki MediaWiki] for the BioCompute Objects project. This wiki system provides complementary information to the [https://www.biocomputeobject.org/ BioCompute portal] and is divided into the following main sections: General information for the [https://www.biocomputeobject.org/ BioCompute portal], [[User_guide|Quick Start and User Guide]], [[Faq|FAQ]], [[Sop|Curation SOP]], and [[About|About]] for the [https://www.biocomputeobject.org/ BioCompute portal].&amp;lt;/div&amp;gt;You can also find the BioCompute White paper [[White paper|here]].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;div style=&amp;quot;clear: both;&amp;quot;&amp;gt;&amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;clear: both;&amp;quot;&amp;gt;&amp;lt;br /&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row2&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[User guide|BioCompute Object (BCO) User Guide]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
This document specifies the structure of BioCompute Objects. The specification is split into multiple parts linked to this top-level document and is maintained in a [https://github.com/biocompute-objects/BCO_Specification GitHub repository] where contributions are welcome. This document was created by the [[Main_Page#BioCompute_Object_Consortium_members_(BCOC)|BioCompute Object Consortium members (BCOC)]].&lt;br /&gt;
&lt;br /&gt;
It is offered as support for IEEE-2791-2020: [https://standards.ieee.org/ieee/2791/7337/ IEEE Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication].&lt;br /&gt;
&lt;br /&gt;
Read more: [[Introduction|Introduction to BioCompute Objects]]&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Faq|Frequently Asked Questions]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
The FAQ section contains a list of questions asked by users regarding using the portal, pipeline steps, and extensions as well as questions related to the prerequisite, knowledgebase recommendation, and saving and publishing BCOs.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Faq|Frequently Asked Questions]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Sop|BCO Curation SOP]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
Intended audience: authors and developers&lt;br /&gt;
&lt;br /&gt;
This section is intended to provide guidance on BCO™ creation, versioning, certification and authentication.&lt;br /&gt;
&lt;br /&gt;
Read more: [[Sop|BCO Curation SOP]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
        &amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[BioCompute Conference and Workshop|Workshop]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
We hosted an in-person workshop on May 10, 2024. Learn more [[BioCompute Conference and Workshop|here]].&lt;br /&gt;
For all previous workshop materials, click [https://hive.biochemistry.gwu.edu/publications#Multimedia here].&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[About]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
A BioCompute Object (BCO) is an instance of the BioCompute standard and is a computational record of a bioinformatics pipeline. A BCO is not an analysis but is a record of which analyses were executed and in exactly which ways. In this way, a BCO acts as an interface for existing standards. A BCO contains all of the necessary information to repeat an entire pipeline from FASTQ to result and includes additional metadata to identify provenance and usage.&lt;br /&gt;
&lt;br /&gt;
Read more: &lt;br /&gt;
*[[About|What is BioCompute?]]&lt;br /&gt;
*[[About|Wifi Analogy]]&lt;br /&gt;
*[[About|BioCompute Description]]&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;div id=&amp;quot;ggw_row3&amp;quot; style=&amp;quot;display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;&amp;quot;&amp;gt;&lt;br /&gt;
    &amp;lt;div style=&amp;quot;flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;&amp;quot;&amp;gt;&lt;br /&gt;
        &amp;lt;h3&amp;gt;[[Publications|Publication]]&amp;lt;/h3&amp;gt;&lt;br /&gt;
        &amp;lt;div style=&amp;quot;border-top: 1px solid #CCC; padding-top: 0.5em;&amp;quot;&amp;gt;&lt;br /&gt;
'''For Citation Purpose:''' Simonyan, V., Goecks, J., &amp;amp; Mazumder, R. (2017). Biocompute Objects — A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA Journal of Pharmaceutical Science and Technology, 71(2), 136–146. doi: 10.5731/pdajpst.2016.006734&lt;br /&gt;
&lt;br /&gt;
See also full list of [[publications]] about BioCompute Object.&lt;br /&gt;
&lt;br /&gt;
=== Other links ===&lt;br /&gt;
# [[CDISC]]&lt;br /&gt;
# [[Galaxy]]&lt;br /&gt;
# [[RO-Crate]]&lt;br /&gt;
# [[CWL|Common Workflow Language (CWL)]]&lt;br /&gt;
# [https://fairsharing.org/4293 FAIRsharing]&lt;br /&gt;
&amp;lt;/div&amp;gt;&lt;br /&gt;
    &amp;lt;/div&amp;gt;&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=SOP&amp;diff=1084</id>
		<title>SOP</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=SOP&amp;diff=1084"/>
		<updated>2025-03-07T14:34:19Z</updated>

		<summary type="html">&lt;p&gt;Twang9: Twang9 moved page Sop to SOP: Nicer title&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main_Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
= BCO Curation SOP =&lt;br /&gt;
&lt;br /&gt;
Intended audience: authors and developers&lt;br /&gt;
&lt;br /&gt;
The following recommendations are intended to provide guidance on BCO™ creation, versioning, certification, and authentication.&lt;br /&gt;
&lt;br /&gt;
== BCO IDs and Versioning ==&lt;br /&gt;
&lt;br /&gt;
Intended Audience: BCO authors&lt;br /&gt;
&lt;br /&gt;
*[[Main Page|BioCompute]] IDs are used as persistent URLs. A novel usability domain must result in the creation of a new BCO with a new BCO ID. BCO IDs are immutable upon creation and are never deleted or retired. If the usability domain (UD) remains unchanged, this results in a new version of the BCO. BCO ID example: OMX_000001&lt;br /&gt;
*BCO major and minor versions can be incremented based on project/institution documented policies.&lt;br /&gt;
*The BioCompute consortium maintains a database of registered authorities. Registered authorities are able to assign their reserved prefixes to their own IDs in the object_id field, such as OMX_000001. We encourage everyone to register a prefix at biocomputeobject.org.&lt;br /&gt;
&lt;br /&gt;
== BioCompute Certification(s) and Authentication ==&lt;br /&gt;
&lt;br /&gt;
Intended Audience: commercial or academic entities looking for additional BCO support&lt;br /&gt;
&lt;br /&gt;
'''Platform certification:''' A BioCompute “audit” will be conducted by the BioCompute Consortium. Requirements include:&lt;br /&gt;
&lt;br /&gt;
*IEEE-2791 conformant BCOs can be created&lt;br /&gt;
*Security (ex: immutable upon creation, secure sharing, platform security)&lt;br /&gt;
*Data QC processes on input/output&lt;br /&gt;
&lt;br /&gt;
'''Syntactical certification:''' Code is available on GitHub for download and use to ensure standard compliance.&lt;br /&gt;
&lt;br /&gt;
'''Scientific certification:''' BCO consortium members will participate in the certification process; each certification process is projected to take ~ 3 months to 1 year to develop pipelines. Verification Kit: Input+output file(s) (in-silico generated), and Template BCO (tBCO) that includes error domain).&lt;br /&gt;
&lt;br /&gt;
'''Template and Run Authentication:''' The Template BCO (tBCO) is created once along with a Verification Kit. Verification Kit usually includes in silico generated input files, BCO (with error domain) and output files. Run BCOs (rBCO) uses the tBCOs, and the only changes allowed are in the input (excluding reference files/databases) and output files field. tBCOs and rBCOs can be authenticated using secure blockchain technology.&lt;br /&gt;
&lt;br /&gt;
*Template certification requirements: Input + output files&lt;br /&gt;
*Run certification requirements: certified template + run BCO (to confirm that parameters and error domain is within range etc.)&lt;br /&gt;
[[File:Certification requirements.png|800px|thumb|center]]&lt;br /&gt;
&lt;br /&gt;
== BCO Metadata ==&lt;br /&gt;
The three metadata fields are filled out at the time of submission. Validity check fills in the spec_version with the IEEE URL, an option to run a SHA256 (or just input your own hash value) for etag, and object_id is assigned (with the option to choose from any prefix associated with the account).&lt;br /&gt;
&lt;br /&gt;
== Domain-specific guidance ==&lt;br /&gt;
=== Execution domain ===&lt;br /&gt;
&lt;br /&gt;
When recording manual curation, the script field of the execution_domain should link to a Google Document or GitHub markdown that describes the steps, either programmatically or in a stepwise fashion. Manual curation steps should ALSO be properly documented in the description_domain. An easy way to conceptualize this is: Description domain is for people, Execution domain is for machine (or programmers).&lt;br /&gt;
&lt;br /&gt;
=== Extension domain ===&lt;br /&gt;
&lt;br /&gt;
Format of how the schema would be defined: [[Execution-domain|Execution domain]]&lt;br /&gt;
&lt;br /&gt;
=== Error domain ===&lt;br /&gt;
&lt;br /&gt;
This domain can support a “QA/QC rules” subdomain which provides rules that, if the output file does not pass the appropriate criteria, then it is flagged as an error.&lt;br /&gt;
&lt;br /&gt;
=== BCO Form-based portal ===&lt;br /&gt;
&lt;br /&gt;
Intended Audience: BCO tool developers and authors&lt;br /&gt;
&lt;br /&gt;
BCOs can be created using any bioinformatics platform that has BCO read and writes functionalities. For users who do not have access to a bioinformatics platform they can use the [https://biocomputeobject.org/builder BCO Builder] in the [https://biocomputeobject.org/ BCO Portal] which has some of the basic API functionalities:&lt;br /&gt;
&lt;br /&gt;
*Create a BCO that is conformant to IEEE-2791.&lt;br /&gt;
*Download and install an instance within an organization’s firewall&lt;br /&gt;
*View videos and documentation on tool use&lt;br /&gt;
&lt;br /&gt;
=== Versioning ===&lt;br /&gt;
&lt;br /&gt;
Any version previous to the current version of a BCO is considered immutable and should not be edited. For example: Once an analysis has been recorded as a BCO, and has undergone several versioning changes, v1.0 of that BCO cannot be edited.&lt;br /&gt;
&lt;br /&gt;
This documentation is currently in the commenting phase until Sept. 15, 2020. Please send your comments to Jonathon Keeney.&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1083</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1083"/>
		<updated>2024-11-21T17:25:05Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Inputs and Outputs */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and I/O Domain? Does input list in I/O domain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and I/O Domain? Does output list in I/O domain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available for this pilot phase.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data for the pilot project. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing  and identification. In addition, provide the shipping company name, transit number and  expected delivery date when available to DCC (DCCEDR@fda.hhs.gov). &lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is not a minimum requirement, it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?'''  Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
# '''Is software used required to submit for the purpose of the pilot project?'''  Software used is not required to be submitted for the pilot. However, some divisions would want software details, this is very much depended on where the submission goes but for the pilot project, we would simplify the process by not requiring software detail submission.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fda.go]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the prom'''''&amp;lt;nowiki/&amp;gt;'''''pts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machine).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. Based on pilot testing with Industry volunteers, the FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1082</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1082"/>
		<updated>2024-11-21T17:12:16Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Knowledgebases */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and input_subdomain? Does input_subdomain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and output_subdomain? Does output_subdomain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== BCO for Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available for this pilot phase.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data for the pilot project. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing  and identification. In addition, provide the shipping company name, transit number and  expected delivery date when available to DCC (DCCEDR@fda.hhs.gov). &lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is not a minimum requirement, it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?'''  Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
# '''Is software used required to submit for the purpose of the pilot project?'''  Software used is not required to be submitted for the pilot. However, some divisions would want software details, this is very much depended on where the submission goes but for the pilot project, we would simplify the process by not requiring software detail submission.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fda.go]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the prom'''''&amp;lt;nowiki/&amp;gt;'''''pts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machine).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. Based on pilot testing with Industry volunteers, the FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1081</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1081"/>
		<updated>2024-11-21T17:11:49Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Submitting BCOs to FDA */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and input_subdomain? Does input_subdomain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and output_subdomain? Does output_subdomain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
=== Submission Process and Requirements ===&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available for this pilot phase.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?''' eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
&lt;br /&gt;
=== Dataset and File Submission Details ===&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data for the pilot project. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing  and identification. In addition, provide the shipping company name, transit number and  expected delivery date when available to DCC (DCCEDR@fda.hhs.gov). &lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is not a minimum requirement, it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?'''  Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
# '''Is software used required to submit for the purpose of the pilot project?'''  Software used is not required to be submitted for the pilot. However, some divisions would want software details, this is very much depended on where the submission goes but for the pilot project, we would simplify the process by not requiring software detail submission.&lt;br /&gt;
&lt;br /&gt;
=== Tools and Technical Details ===&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fda.go]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the prom'''''&amp;lt;nowiki/&amp;gt;'''''pts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machine).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. Based on pilot testing with Industry volunteers, the FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to the FAQ above.&lt;br /&gt;
&lt;br /&gt;
=== Regulatory Applications and Use Cases ===&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
&lt;br /&gt;
=== Communication and Support ===&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
	<entry>
		<id>https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1080</id>
		<title>FAQs</title>
		<link rel="alternate" type="text/html" href="https://wiki.biocomputeobject.org/index.php?title=FAQs&amp;diff=1080"/>
		<updated>2024-11-15T17:07:18Z</updated>

		<summary type="html">&lt;p&gt;Twang9: /* Submitting BCOs to FDA */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;'''Go back to [[Main Page|BioCompute Objects]].'''&lt;br /&gt;
&lt;br /&gt;
== General ==&lt;br /&gt;
1. '''How can I build a BioCompute Object (BCO)?'''&lt;br /&gt;
&lt;br /&gt;
You have several options for building a BCO. You can use the standalone &amp;quot;builder&amp;quot; tool available [https://biocomputeobject.org/builder here]. Alternatively, if you're using a platform that supports BioCompute, you can utilize tools built into that platform such as DNAnexus/precisionFDA, Galaxy, or Seven Bridges/Cancer Genomics Cloud. You may also choose to build an output into your workflow as a JSON file conforming to the standard.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimum requirements for conformance with the BioCompute standard?''' &lt;br /&gt;
&lt;br /&gt;
The minimum requirements include inputs, outputs, data transformation steps, environment details, individuals involved in pipeline development or execution, and a plain text description of the pipeline's objectives. The standard allows for much greater detail if needed, and is extensible to include substantially more. The standard is organized into 8 domains, 5 of which are required and 3 are optional.&lt;br /&gt;
&lt;br /&gt;
3. '''How can I ensure my submission validates against the BioCompute schema?''' &lt;br /&gt;
&lt;br /&gt;
Your submission should validate against the schema, which you can reference directly at the top level domain provided [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads here].&lt;br /&gt;
&lt;br /&gt;
4. '''Where can I find more information about the BioCompute standard and its organization?''' The official repository for the standard is open access and can be found [https://opensource.ieee.org/2791-object/ieee-2791-schema/ here].&lt;br /&gt;
&lt;br /&gt;
5. '''Can you provide an example of a completed BioCompute Object (BCO)?''' &lt;br /&gt;
&lt;br /&gt;
Yes, you can view an example of a completed BCO [https://biocomputeobject.org/viewer?https://biocomputeobject.org/BCO_000452/1.0 here]. You can explore both table and raw JSON views.&lt;br /&gt;
&lt;br /&gt;
6.     '''Where would information regarding data sources and standard operating procedures be? Which specific domain?'''&lt;br /&gt;
&lt;br /&gt;
Data sources should be recorded as described by the input_subdomain in the “[[Iodomain|io_domain]]” and the input_list in the “[[Description-domain|description_domain]]”. Standard operating procedures and any other information about data transformations SHOULD be elaborated upon in the “[[Usability-domain|usability_domain]]”.&lt;br /&gt;
&lt;br /&gt;
7.     '''How can a third-party access URIs in a BCO?'''&lt;br /&gt;
&lt;br /&gt;
URIs can be directed to local paths. In these cases, the necessary files are shared with the parties that will require access. If it is a link to a public domain, it will be easily accessible for all. &lt;br /&gt;
&lt;br /&gt;
8.     '''What is a SHA1 Checksum?''' &lt;br /&gt;
&lt;br /&gt;
A SHA-1 checksum, or Secure Hash Algorithm 1 checksum, is a fixed-size output (160 bits) generated from input data to uniquely identify and verify the integrity of files or documents. In BioCompute Objects (BCOs), it serves to ensure the unchanged state of computational workflows by comparing calculated and original checksums. This allows for accuracy in viewing and downloading BCOs.  &lt;br /&gt;
&lt;br /&gt;
9.     '''How do I sign in with an ORCID/What is an ORCID?''' &lt;br /&gt;
&lt;br /&gt;
[https://orcid.org/ ORCID] stands for Open Researcher and Contributor ID, and is a free, unique identifier assigned to researchers, providing a standardized way to link researchers to their scholarly activities. To sign in with your ORCID,  create an account at: https://orcid.org/. Using the credentials associated with your ORCID account you can log in to view and edit BCOs.  &lt;br /&gt;
&lt;br /&gt;
== Pipeline Questions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Do pipeline steps have to represent sequentially run steps? How can you represent steps also run in parallel?'''&lt;br /&gt;
&lt;br /&gt;
The standard does not mandate any particular numbering schema, but it’s best practice to pick the most logically intuitive numbering system. For example, a user may run a somatic SNV profiling step at the same time as a structural CNV analysis. So if in the example I mentioned, the alignment is step #2, then you might (arbitrarily) call the SNV profiling step #3, and the CNV analysis step #4. The fact that they pull from the output of the same step (#2) can easily be detected programmatically and represented in whatever way is suitable (e.g. graphically).&lt;br /&gt;
&lt;br /&gt;
2.    '''What is the nf-core plugin and how can I test it?'''&lt;br /&gt;
&lt;br /&gt;
The nf-core plugin, designed to facilitate Nextflow workflows, is now available for testing. To enable the BCO (BioCompute Object) format within the plugin, follow these instructions:&lt;br /&gt;
&lt;br /&gt;
* Ensure you have the latest version of the plugin installed.&lt;br /&gt;
&lt;br /&gt;
* Add the following code snippets to your Nextflow configuration file:&lt;br /&gt;
&lt;br /&gt;
plugins {&lt;br /&gt;
&lt;br /&gt;
    id 'nf-prov'&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
prov.enabled = true&lt;br /&gt;
&lt;br /&gt;
prov {&lt;br /&gt;
&lt;br /&gt;
    formats {&lt;br /&gt;
&lt;br /&gt;
        bco {&lt;br /&gt;
&lt;br /&gt;
            file = 'bco.json'&lt;br /&gt;
&lt;br /&gt;
            overwrite = true&lt;br /&gt;
&lt;br /&gt;
        }&lt;br /&gt;
&lt;br /&gt;
    }&lt;br /&gt;
&lt;br /&gt;
}&lt;br /&gt;
&lt;br /&gt;
These settings will enable the BCO format and specify the output file as &amp;quot;bco.json&amp;quot;. Ensure you include these snippets in your configuration file to activate the BCO format.&lt;br /&gt;
&lt;br /&gt;
For any questions related to Nextflow environment, please ask [https://github.com/nextflow-io/nf-prov/issues here]&lt;br /&gt;
&lt;br /&gt;
== Inputs and Outputs ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the relationship and difference between input_list in description_domain and input_subdomain? Does input_subdomain contain all the input files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes. The Input Domain is for global inputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline inputs.&lt;br /&gt;
&lt;br /&gt;
2.   '''What is the relationship and difference between output_list in description_domain and output_subdomain? Does output_subdomain contain all the output files of all the pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
The Output Domain is for global outputs. The input_list/output_list in the pipeline_steps is specific to individual steps and is used to trace data flow if granular detail is needed. If not needed, a user can simply look at the IO domain for the overall view of the pipeline outputs.&lt;br /&gt;
&lt;br /&gt;
3.   '''There is an access_time property for uri, which is referenced by input_list, output_list, input_subdomain, and output_subdomain. What does access_time mean for output files? Aren’t output files generated by pipeline steps?'''&lt;br /&gt;
&lt;br /&gt;
Yes they are, the timestamp is used for creation in those cases.&lt;br /&gt;
&lt;br /&gt;
4.    '''Can a script from the execution domain also be considered an input?'''&lt;br /&gt;
&lt;br /&gt;
This is not usually the case, but it is possible for the script to be assessed as an input if it is used in the workflow to bring about an output.&lt;br /&gt;
&lt;br /&gt;
== Extensions ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the role of extension_domain? How does it relate to other domains? Is it required in some pipeline steps? Or does it affect the execution? Or something else?'''&lt;br /&gt;
&lt;br /&gt;
Extension Domain is never required, it is always optional. It is a user-defined space for capturing anything not already captured in the base BCO. To use it, one generates an extension schema (referenced in the extension_schema), and the associated fields within the BCO. For example, if a user wants to include a specialized ontology with definitions, it can be added here. It’s meant to capture anything idiosyncratic to that workflow not already captured in the standard and is very flexible.&lt;br /&gt;
    &lt;br /&gt;
2.    '''How can BCOs be used for knowledgebases?'''&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Prerequisites ==&lt;br /&gt;
&lt;br /&gt;
1.    '''What is the difference between software_prerequisites in execution_domain and prerequisites in the description_domain? Is the former global, while the latter only applies to one specific pipeline step?'''&lt;br /&gt;
&lt;br /&gt;
Correct, Execution Domain is for anything related to the environment in which the pipeline was executed, and the Description Domain is specific to the software in those steps. So if I’ve written a shell script to run the pipeline, and in one step it includes myScript.py to comb through results and pick out elements of interest, myScript.py might be an Execution Domain prerequisite, and any packages or dependencies called from within the script are Description Domain level prerequisites. Alternatively, if I’m using the HIVE platform, any libraries needed to run HIVE are Execution Domain level.&lt;br /&gt;
&lt;br /&gt;
== BCO Scoring System ==&lt;br /&gt;
&lt;br /&gt;
1.    '''How is the score calculated?'''&lt;br /&gt;
&lt;br /&gt;
The score is computed based on a few key factors:&lt;br /&gt;
&lt;br /&gt;
* '''Usability Domain''': The length of the ''usability_domain'' field contributed to the base score&lt;br /&gt;
* '''Field Length Modifier''': A multiplier (1.2) is applied to the base score to account for field length&lt;br /&gt;
* '''Error Domain''': If the ''error_domain'' exist and is inserted correctly, 5 points are added&lt;br /&gt;
* '''Parametric Objects''': A multiplier (1.1) is applied to the score for each parametric object in the ''parametric_objects'' list&lt;br /&gt;
* '''Reviewer Objects''': Up to 5 points are added, one for each correct ''reviewer_object''&lt;br /&gt;
&lt;br /&gt;
2.   '''What happens if the ''usability_domain'' is missing?'''&lt;br /&gt;
&lt;br /&gt;
If the ''usability_domain'' or other required fields are missing the BCO score is immediately set to 0, and the function returns the BCO instance without further calculations.&lt;br /&gt;
&lt;br /&gt;
3. '''What is the purpose of the ''bco_score'' function'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function calculates and assigns a unique score to each BioCompute Object (BCO) based on specific criteria in its contents. The score is influenced by the presence of characteristics of certain fields like the ''usabiliy_domain'', ''error_domain'', ''parametric_objects'', and ''reviewer_objects''.&lt;br /&gt;
&lt;br /&gt;
4. '''What is the purpose of the ''field_length_modifier'' and ''parametric_object_multiplier''?'''&lt;br /&gt;
&lt;br /&gt;
* ''field_length_modifier'' (1.2): This modifier adjusts the base score according to the length of the usability_domain field.&lt;br /&gt;
* ''parametric_object_multiplier'' (1.1): This multiplier increases the score based on the number of parametric objects present in the BCO, reflecting the complexity of the object.&lt;br /&gt;
&lt;br /&gt;
5. '''What is the expected output of the bco_score function?'''&lt;br /&gt;
&lt;br /&gt;
The ''bco_score'' function modifies the BCO instance by assigning a ''score'' attribute based on the criteria mentioned above, the updated BCO instance, with the score added, is then returned following the saving of the BCO draft.&lt;br /&gt;
&lt;br /&gt;
6. '''How does the reviewer count affect the score?'''&lt;br /&gt;
&lt;br /&gt;
For each ''reviewer_object'' present in the BCO (up to maximum of 5 reviewers), the score increases by 1 point. This incentivizes the inclusion of peer review and validation within the object.&lt;br /&gt;
&lt;br /&gt;
7. '''What is the significance of ''entAliases'' in the ''convert_to_ldh'' function?'''&lt;br /&gt;
&lt;br /&gt;
The ''entAliases'' field is a list that stores multiple identifiers for the BioCompute Object. These include the ''object_id,'' its full URL (entIri), and its entity type (entType), ensuring that the object can be referenced in different contexts.&lt;br /&gt;
&lt;br /&gt;
8. '''How and Where does the score appear on the BCO Builder?'''&lt;br /&gt;
&lt;br /&gt;
The score is calculated by the ''bco_score'' function and is displayed within the BioCompute Object (BCO) metadata section of the BCO Builder interface, following the saving of a BCO draft. &lt;br /&gt;
&lt;br /&gt;
== Knowledgebases ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Can BCOs be used for curating databases?'''&lt;br /&gt;
&lt;br /&gt;
Yes. BCOs have been used in this capacity, such as in the [https://data.argosdb.org/ FDA’s ARGOS database of infectious diseases] and the [https://data.glygen.org/ GlyGen database of glycosylation sites]. The following recommendations are compiled from these use cases. Although these recommendations are built from practical experience, they may not address the needs of every database. Users are free to make modifications at their own discretion.&lt;br /&gt;
&lt;br /&gt;
Using BioCompute’s pre-defined fields and standards, knowledgebases can generate a BioCompute Object (BCO) to document the metadata, quality control, and integration pipelines developed for different workflows. BCOs can be used to document each release. The structured data in a BCO makes it very easy to identify changes between releases (including changes to the curation/data processing pipeline, attribution to curators, or datasets processed), or revert to previous releases.&lt;br /&gt;
&lt;br /&gt;
BCOs can be generated via a user-friendly instance of a BCO editor and can be maintained and shared through versioned, stable IDs stored under a single domain of that knowledgebase. BCOs not only provide complete transparency to their data submitters (authors, curators, other databases, etc.), collaborators, and users but also provide an efficient mechanism to reproduce the complete workflow through the information stored in different domains (such as description, execution, io, error, etc.) in the machine and human-readable formats.&lt;br /&gt;
&lt;br /&gt;
The most common way of adapting BCOs for use in knowledgebases is by leveraging the Extension Domain. In this example, the Extension Domain is used for calling fields based on column headers. Note that the Extension Domain identifies its own schema, which defines the column headers and identifies them as required where appropriate. Because the JSON format of a BCO is human and machine-readable (and can be further adapted for any manner of display or editing through a user interface), BCOs are amendable to either manual or automatic curation processes, such as the curation process that populates those fields in the above example.&lt;br /&gt;
&lt;br /&gt;
== Saving and Publishing a BCO ==&lt;br /&gt;
&lt;br /&gt;
1.    '''Why is my BCO not saved after clicking '''SAVE'''?'''&lt;br /&gt;
&lt;br /&gt;
The '''SAVE''' only saves the entry on the website but it's not saving to the server. For a new draft, after editing, go to '''Tools''', first select a BCODB, then click on '''GET PREFIXES''' to choose a prefix, and lastly, click on '''SAVE PREFIX'''. For an existing draft, to save properly, click on '''SAVE''' first and then under '''Tools''', select '''UPDATE DRAFT'''.&lt;br /&gt;
&lt;br /&gt;
2. '''What are the minimal requirements for validation and publishing with the BioCompute Objects (BCO) standard?'''&lt;br /&gt;
&lt;br /&gt;
A submission simply needs to validate against the [https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/2791object.json?ref_type=heads schema]. The minimal requirements include inputs, outputs, data transformation steps, environment details, person(s) who wrote or executed the pipeline, and a plain text description of the pipeline and its objectives.&lt;br /&gt;
&lt;br /&gt;
== BCO Validation and Error messages ==&lt;br /&gt;
&lt;br /&gt;
The BCO Portal uses a JSON validator to validate the BCOs, and because of the error messages returned may be a little confusing. Below are some common validation results and an explanation of what they mean and how to address them.&lt;br /&gt;
&lt;br /&gt;
1.     '''&amp;quot;[description_domain][pipeline_steps][0][step_number]&amp;quot;: &amp;quot;'1' is not of type 'integer'&amp;quot;'''&lt;br /&gt;
&lt;br /&gt;
The '''step_number''' in the BCO JSON needs to be an INTEGER. &lt;br /&gt;
&lt;br /&gt;
This means it can not be in quotes like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: &amp;quot;1&amp;quot;,'''&lt;br /&gt;
Instead, it must be represented like this:&lt;br /&gt;
    ''' &amp;quot;step_number&amp;quot;: 1,'''&lt;br /&gt;
&lt;br /&gt;
You may not be able to see this difference in the '''COLOR-CODED''' view, and will have to look in the '''TREE VIEW JSON''' or '''RAW JSON VIEW'''.&lt;br /&gt;
&lt;br /&gt;
== Submitting BCOs to FDA ==&lt;br /&gt;
&lt;br /&gt;
# '''How should I submit a BCO with a regulatory submission?'''  Both JSON (the original format of BCO) and plain text (&amp;quot;.txt&amp;quot;) documents are accepted by the FDA. BCO files can be included as a JSON file under Module 5.3.5.4 and submitted to the FDA as supporting documents in the Electronic Common Technical Document (eCTD) for the submission of bioinformatics workflow data to both CDER (Center for Drug Evaluation and Research) and CBER (Center for Biologics Evaluation and Research) for regulatory reviews. CFSAN also accepts BCOs. Please check with your reviewer or review division for logistical details to submit a BCO.  BCOs can contain links to files that are submitted via hard drive. File sharing via the FDA-HIVE portal is not currently available for this pilot phase.&lt;br /&gt;
# '''What is the minimum content requirement for a Sample eCTD Submission to CDER?'''  Module 1 and Module 5 (Module 5.3.5.4 especially where the  BCO is located) are required for the pilot project. A cover letter ( states that the submission is a test for the BCO Pilot and is intended for the CBER HIVE) and FDA Form (1571 for IND and 356h for NDA/BLA/ANDA), and BCO file.&lt;br /&gt;
# '''How to include or indicate dataset information in the BCO and/or ESG submission?''' There are a few options to include the dataset information in the BCO or ESG submission: (Note: it is mandatory to include dataset information in the Cover Letter, however, if you would like to add more clarity, you may choose from the option 2-4 listed below)&lt;br /&gt;
## Include in the dataset information in the Cover Letter: State how the datasets are submitted (via ESG or hard drive), the tracking number, estimated delivery date. This option is mandatory for BCO submission to the FDA to help reviewers to track down related datasets.&lt;br /&gt;
##Globally, suggest to include datasets information in the Usability Domain and refer to the root of the hard drive, see example below:[[File:Screenshot 2024-11-11 at 16.14.20.png|center|thumb|591x591px]]&lt;br /&gt;
##If you prefer to mention the file structure and names in each step, then the datasets information can be included in description domain, see example below:[[File:Screenshot 2024-11-11 at 16.14.05.png|center|thumb|620x620px]]&lt;br /&gt;
##If you would like to use the file structure and names from an existing schema, you may enter the schema URL in the extension domain, using the Figure 1 from this [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424 paper] as an example, the JSON schema defines the file structure and names: &lt;br /&gt;
````&lt;br /&gt;
{&lt;br /&gt;
  &amp;quot;$schema&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;$id&amp;quot;: &amp;quot;http://json-schema.org/draft-07/schema#&amp;quot;,&lt;br /&gt;
  &amp;quot;title&amp;quot;: &amp;quot;Computational Biology Project Structure&amp;quot;,&lt;br /&gt;
  &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
  &amp;quot;properties&amp;quot;: {&lt;br /&gt;
    &amp;quot;level 1&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;msms&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Main directory for project data and scripts.&amp;quot;&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;level 2&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;doc&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Project documentation&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;paper&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Documents related to the project.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;data&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Directory for data files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;src&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Source code directory.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;bin&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Executable files.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;results&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Results directory with analysis outputs.&amp;quot;,&lt;br /&gt;
              &amp;quot;properties&amp;quot;: {&lt;br /&gt;
                &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-15.&amp;quot;&lt;br /&gt;
                },&lt;br /&gt;
                &amp;quot;2009_01_23&amp;quot;: {&lt;br /&gt;
                  &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
                  &amp;quot;description&amp;quot;: &amp;quot;Data from analysis on 2009-01-23.&amp;quot;&lt;br /&gt;
                }&lt;br /&gt;
              }&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    },&lt;br /&gt;
    &amp;quot;level 3&amp;quot;: {&lt;br /&gt;
      &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
      &amp;quot;properties&amp;quot;: {&lt;br /&gt;
        &amp;quot;2009_01_14&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Initial analysis on 2009-01-14.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;yeast&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Yeast dataset.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;worm&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Worm dataset.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        },&lt;br /&gt;
        &amp;quot;2009_01_15&amp;quot;: {&lt;br /&gt;
          &amp;quot;type&amp;quot;: &amp;quot;object&amp;quot;,&lt;br /&gt;
          &amp;quot;description&amp;quot;: &amp;quot;Follow-up analysis and summary on 2009-01-15.&amp;quot;,&lt;br /&gt;
          &amp;quot;properties&amp;quot;: {&lt;br /&gt;
            &amp;quot;split1&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;First data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split2&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Second data split.&amp;quot;&lt;br /&gt;
            },&lt;br /&gt;
            &amp;quot;split3&amp;quot;: {&lt;br /&gt;
              &amp;quot;type&amp;quot;: &amp;quot;string&amp;quot;,&lt;br /&gt;
              &amp;quot;description&amp;quot;: &amp;quot;Third data split.&amp;quot;&lt;br /&gt;
            }&lt;br /&gt;
          }&lt;br /&gt;
        }&lt;br /&gt;
      }&lt;br /&gt;
    }&lt;br /&gt;
  }&lt;br /&gt;
}&lt;br /&gt;
````&lt;br /&gt;
# '''Can I submit a BCO without data files?''' Yes, but if the sponsor is submitting a BCO without the data they should seek agreement with the review division prior to submission.&lt;br /&gt;
# '''For the pilot project, which center should the eCTD (contains BCO file(s)) be submitted to?'''  Ideally, pilot participants should send their sample submissions to both CDER and CBER centers so that both centers can try viewing the BCO file and determine if there are issues with reviewing.&lt;br /&gt;
# '''How to submit eCTD?'''eCTD portion of the pilot (which contains BCO file) should be submitted via Test Electronic Submission Gateway (ESG) to both CBER and CDER. In order for both centers to receive the submission, sponsors would need to make a submission to each center via the ESG Test Gateway.&lt;br /&gt;
## '''CDER:''' Participants should contact [[Mailto:ESUB-Testing@fda.hhs.gov|ESUB-Testing@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The subject line of the email should be “BCO Pilot”. Once the submission is sent through the ESG Test Gateway, the submitter will receive two gateway acknowledgements. The submitter will need to forward the second gateway acknowledgment which contains the “COR id” number to the ESUB-Testing team so they can locate the submission and notify the FDA Pilot point of contact.&lt;br /&gt;
## '''CBER''': Participants should contact [[Mailto:ESUBPREP@fda.hhs.gov|ESUBPREP@fda.hhs.gov]] to request a sample application number to submit a BCO pilot submission. The ESUBPREP team should also be notified when the submission is inbound.  The subject line of any email related to the pilot should contain “BCO Pilot.” Once the submission is sent through the ESG Test Gateway, the submitter will receive up to three acknowledgments.  The submitter will need to forward the second gateway notification acknowledgment, containing the Core ID number, to the ESUBPREP team (also referencing “BCO Pilot” in the subject line) so the submission can be located and shared with the FDA Pilot point of contact.  Please note that if a third acknowledgment is generated containing a rejection notification, it should be ignored by the submitter.&lt;br /&gt;
# '''What is Electronic Submissions Gateway (ESG)?'''  The Electronic Submissions Gateway (ESG) is the FDA's primary way to receive electronic regulatory submissions. The Test ESG is in a pre-production environment and will be used for this pilot.&lt;br /&gt;
# '''What materials are required to register for an ESG account?'''  FDA ESG provides two methods, WebTrader and AS2 for making submissions to FDA.  WebTrader is a web-based user interface to send documents and receive receipts and acknowledgments from the FDA with minimal technical expertise. To set up WebTrader, several preparatory steps are needed. First, prepare an electronic Letter of Non-Repudiation Agreement; Second, generate or obtain a free personal digital certificate. These two documents are needed during the account registration step. Other optional preparatory steps include preparing a guidance compliant test submission and a load test submission. For more details, review the formal FDA documentation [https://www.fda.gov/industry/create-esg-account/setting-webtrader-account-checklist here]. To register the WebTrader account, go to the ESG Account Management Portal at  '''''[https://esgportal.fda.gov/ https://esgportal.fda.go]&amp;lt;nowiki/&amp;gt;[https://esgportal.fda.gov/ v/].''''' Then select &amp;quot;New Account Registration&amp;quot; and follow the prom'''''&amp;lt;nowiki/&amp;gt;'''''pts. Please refer to the [https://www.fda.gov/industry/about-esg/esg-account-management-portal-user-guide ESG Account Management Portal User Guide] for instructions. After account registration, users need to set up the local machine. Download the required WebTrader Client Installer (Note: only compatible with Windows machine).  AS2 (System-to-System) allows industry partners to have the option to access the Gateway via system-to-system communication. It provides an automated connection to the FDA for submissions, receipts, and acknowledgments, generally used by sponsors that have a high volume of submissions. However, this system requires AS2-compliant software and technical expertise. For more information regarding AS2, refer to the [https://www.fda.gov/industry/create-esg-account/setting-as2-account-checklist Setting up an AS2 Account Checklist].&lt;br /&gt;
# '''How to submit large I/O files to the FDA?'''  Please refer to the [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 FDA site] for the definition of large I/O files. Large I/O files need to be sent on a hard drive to CBER, which FDA-HIVE is nested under CBER. All data will be uploaded/downloaded to HIVE. CDER reviewers will use the CBER HIVE to receive and review this type of data for the pilot project. Please use the following address for the hard drive: &amp;lt;u&amp;gt;U.S. Food and Drug Administration&amp;lt;/u&amp;gt; &amp;lt;u&amp;gt;Center for Biologics Evaluation and Research&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Document Control Center&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;10903 New Hampshire Avenue&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;WO71, G112&amp;lt;/u&amp;gt;  &amp;lt;u&amp;gt;Silver Spring, MD 20993-0002.&amp;lt;/u&amp;gt; Also, please add information of the dataset submission plan or details in the Cover Letter so that the reviewer knows it is coming and when to expect it.&lt;br /&gt;
#'''Are there any specific notes or memos that should be included with the hard drive?'''  Yes, please ensure that the application number is attached to the hard drive for easier processing  and identification. In addition, provide the shipping company name, transit number and  expected delivery date when available to DCC (DCCEDR@fda.hhs.gov)&lt;br /&gt;
# '''Can I submit BCOs on a portable hard drive if requested by the FDA?'''  BCOs can also be stored on a portable&amp;lt;ins&amp;gt; &amp;lt;/ins&amp;gt;hard drive and referenced in the eCTD. This allows for easy access and verification of the BCO files during the review process'''.''' The hard drive submitted to HIVE (CBER), CDER would also have access to the data.&lt;br /&gt;
# '''How much data needs to be submitted?'''  There is not a minimum requirement, it depends on the goal of the submission and the scope of the submission.&lt;br /&gt;
# '''Is software used required to submit for the purpose of the pilot project?'''  Software used is not required to be submitted for the pilot. However, some divisions would want software details, this is very much depended on where the submission goes but for the pilot project, we would simplify the process by not requiring software detail submission.&lt;br /&gt;
# '''Are intermediate datasets/files required for the purpose of the pilot project?'''  Currently, the intermediate files are not required to be submitted at the initial phase of the pilot project.&lt;br /&gt;
# '''How much data can ESG (Electronic Submission Gateway) handle?'''  The maximum file size for a single file (non-folder) is 100 GB of uncompressed data. The maximum file size for a multi-file (folder) is 100 GB of uncompressed data that contains single files (non-folder) no larger than 6 GB of uncompressed data. ESG recommends that you send an email to [[Mailto:ESGHelpDesk@fda.hhs.gov|ESGHelpDesk@fda.hhs.gov]] for all submissions over 10 GB of uncompressed data. Based on pilot testing with Industry volunteers, the FDA recommends that submissions greater than 15 GB and less than 25 GB in size be sent overnight starting at 5PM EST to ensure receipt by the targeted FDA Center during the next business day. For large datasets, they need to be submitted via hard drive to CBER, for more information, refer to question 4.&lt;br /&gt;
# '''For which types of regulatory submissions can BCOs be used?'''  BCOs can be applied to the following types of regulatory submission:&lt;br /&gt;
#* Biologics license applications (BLAs);&lt;br /&gt;
#* Investigational new drug applications (INDs);&lt;br /&gt;
#* New drug applications (NDAs);&lt;br /&gt;
#* Abbreviated new drug applications (ANDAs): Note: ANDAs are not recommended for the pilot project submissions&lt;br /&gt;
# '''Where should BCO files be placed within the eCTD?'''  We recommend including BCO files as part of a study, referenced under a Study Tagging File, under Module 5.3.5.4 (Other Study Reports).&lt;br /&gt;
# '''How should sponsors contact the FDA regarding BioCompute Object submissions?'''   We do have points of contact at both CDER and CBER centers. If you have general submission and review questions regarding BCO submissions, please contact [[Mailto:cber-edata@fda.hhs.gov|cber-edata@fda.hhs.gov]] if submitted to CBER; [[Mailto:edata@fda.hhs.gov|edata@fda.hhs.gov]] for CDER.&lt;br /&gt;
# '''What should sponsors do if they have general questions about BioCompute Object submissions but do not have a submission in-house?'''   If sponsors have general questions about BioCompute Object submissions and do not currently have a submission in-house, they can reach out to the email address industry.biologics@fda.hhs.gov managed by OCOD (Office of Computational and Data Sciences). The request will be triaged and directed to the appropriate individuals to provide assistance and address inquiries.&lt;br /&gt;
# For more ESG-related questions, refer to the official FDA ESG FAQ site [https://www.fda.gov/industry/create-esg-account/frequently-asked-questions#_Q19 here]. If you have questions for CBER, please contact CBER ESUB at esubprep@fda.hhs.goc; if the questions are for CDER, please contact CDER ESUB at esub@fda.hhs.gov; if general ESG-related questions, please contact ESG Help Desk at esghelpdesk@fda.hhs.gov.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Publications==&lt;br /&gt;
To explore our publications, please visit [https://hive.biochemistry.gwu.edu/publications this link].&lt;/div&gt;</summary>
		<author><name>Twang9</name></author>
	</entry>
</feed>