SOP - Revision history

Lorikrammer: /* Extension domain */

2026-04-14T21:20:47Z

Extension domain

← Older revision		Revision as of 21:20, 14 April 2026
Line 45:		Line 45:
	=== Extension domain ===		=== Extension domain ===

	Format of how the schema would be defined: [[~~Execution~~ Domain]]		Format of how the schema would be defined: [[Extension Domain]]

	=== Error domain ===		=== Error domain ===

Lorikrammer: /* Domain-specific guidance */

2026-04-14T21:20:21Z

Domain-specific guidance

← Older revision		Revision as of 21:20, 14 April 2026
Line 45:		Line 45:
	=== Extension domain ===		=== Extension domain ===

	Format of how the schema would be defined: [[Execution~~-domain\|Execution domain~~]]		Format of how the schema would be defined: [[Execution Domain]]

	=== Error domain ===		=== Error domain ===

Twang9: Twang9 moved page Sop to SOP: Nicer title

2025-03-07T14:34:19Z

Twang9 moved page Sop to SOP: Nicer title

← Older revision

Revision as of 14:34, 7 March 2025

Twang9 at 18:04, 10 August 2022

2022-08-10T18:04:21Z

← Older revision		Revision as of 18:04, 10 August 2022
Line 1:		Line 1:
			'''Go back to [[Main_Page\|BioCompute Objects]].'''

	= BCO Curation SOP =		= BCO Curation SOP =

Twang9: /* BCO IDs and Versioning */

2022-08-09T22:25:55Z

BCO IDs and Versioning

← Older revision		Revision as of 22:25, 9 August 2022
Line 9:		Line 9:
	Intended Audience: BCO authors		Intended Audience: BCO authors

	*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		*[[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
	*BCO major and minor versions can be incremented based on project/institution documented policies.		*BCO major and minor versions can be incremented based on project/institution documented policies.
	*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.		*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.

Twang9: Created page with "= BCO Curation SOP = Intended audience: authors and developers The following recommendations are intended to provide guidance on BCO™ creation, versioning, certification, and authentication. == BCO IDs and Versioning == Intended Audience: BCO authors *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..."

2022-08-04T21:08:04Z

Created page with "= BCO Curation SOP = Intended audience: authors and developers The following recommendations are intended to provide guidance on BCO™ creation, versioning, certification, and authentication. == BCO IDs and Versioning == Intended Audience: BCO authors *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..."

New page

= BCO Curation SOP =

Intended audience: authors and developers

The following recommendations are intended to provide guidance on BCO™ creation, versioning, certification, and authentication.

== BCO IDs and Versioning ==

Intended Audience: BCO authors

*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
*BCO major and minor versions can be incremented based on project/institution documented policies.
*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.

== BioCompute Certification(s) and Authentication ==

Intended Audience: commercial or academic entities looking for additional BCO support

'''Platform certification:''' A BioCompute “audit” will be conducted by the BioCompute Consortium. Requirements include:

*IEEE-2791 conformant BCOs can be created
*Security (ex: immutable upon creation, secure sharing, platform security)
*Data QC processes on input/output

'''Syntactical certification:''' Code is available on GitHub for download and use to ensure standard compliance.

'''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).

'''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.

*Template certification requirements: Input + output files
*Run certification requirements: certified template + run BCO (to confirm that parameters and error domain is within range etc.)
[[File:Certification requirements.png|800px|thumb|center]]

== BCO Metadata ==
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).

== Domain-specific guidance ==
=== Execution domain ===

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).

=== Extension domain ===

Format of how the schema would be defined: [[Execution-domain|Execution domain]]

=== Error domain ===

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.

=== BCO Form-based portal ===

Intended Audience: BCO tool developers and authors

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:

*Create a BCO that is conformant to IEEE-2791.
*Download and install an instance within an organization’s firewall
*View videos and documentation on tool use

=== Versioning ===

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.

This documentation is currently in the commenting phase until Sept. 15, 2020. Please send your comments to Jonathon Keeney.