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The BioCompute Standard
Because of the many different ways to organize data, a major goal of the BioCompute project is to build and maintain a formal standard through recognized, accredited standards setting organizations like the Institute for Electrical and Electronics Engineers (IEEE) and the International Standards Organization (ISO). A formal, consensus-based standard builds predictability and even more stability into the way in which bioinformatic methods are communicated.
The standard, officially known as 2791-2020, has two parts: the standards document and the schema, which is maintained in an open source repository:
- The current version of the standard can be found [here](https://standards.ieee.org/standard/2791-2020.html)**.
- The schema can be found [here](https://opensource.ieee.org/2791-object/ieee-2791-schema)**.
Since the base BioCompute schema is maintained as an open source repository, it can be cloned and integrated into an organization in unique ways, which allows organizations to build off of this schema to create dependent standards for specific applications. This is similar to the different versions of WiFi based on usage, such as the 802.11a standard for fast speed, but high cost and shorter range, or the 802.11b for slower top speed, but lower cost, etc. --- all of which are built on the 802.11 base standard. It can also be used to further extend the schema, such as for handling proprietary, internal content, while still being compatible with the base standard. The open source schema also enables individuals or organizations to suggest changes to be incorporated into future versions the standard.
Citation
This standard was originaly prepared by [The BioCompute Object working group](/BCO_Spec_V1.2.md#biocompute-object-consortium-members-bcoc) during preparation for the [2017 HTS Computational Standards for Regulatory Sciences Workshop](https://hive.biochemistry.gwu.edu/htscsrs/workshop_2017).
To reference the BCO standards, please use the following citation inclusive of the DOI:
Simonyan, V., Goecks, J., & 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](http://doi.org/10.5731/pdajpst.2016.006734)
Support, Community and Contributing
To suggest changes to [this repository](https://github.com/biocompute-objects/BCO_Specification) we welcome contributions as a [pull request](https://github.com/biocompute-objects/BCO_Specification/pulls) or [issue](https://github.com/biocompute-objects/BCO_Specification/issues) submission.
BCO_Specification is licensed under the [BSD 3-Clause "New" or "Revised" License](https://github.com/biocompute-objects/BCO_Specification/blob/main/LICENSE.md)
A permissive license similar to the BSD 2-Clause License, but with a 3rd clause that prohibits others from using the name of the project or its contributors to promote derived products without written consent.
Mailing List
As a subscriber to the BCO mailing list, you can post to it by sending a message tobiocomputels@hermes.gwu.edu (using the email address that is subscribed). This list is semi-automated and will send your message for review.
To subscribe or unsubscribe, please visit https://hermes.gwu.edu/cgi-bin/wa?A0=BIOCOMPUTELS and click `Subscribe` or `Unsubscribe` on the lower right. You can also unsubscribe from the list at any time by sending an email to listserv@hermes.gwu.edu, in which the body says: `unsubscribe biocomputes`
This repository is in support of [2791-2020](https://standards.ieee.org/standard/2791-2020.html) - IEEE Approved Draft Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication. Please also see our [OSF page](https://osf.io/h59uh/) or our [main page](https://biocomputeobject.org/)
BioCompute Object (BCO) User Guide
This document was created by the BioCompute Object Consortium members (BCOC).
It is offered as support for IEEE-2791-2020: IEEE Standard for Bioinformatics Computations and Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication.[1]
Introduction
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 GitHub repository where contributions are welcome.
Read more: Introduction to BioCompute Objects
BioCompute Domains
BCOs are represented in JSON (JavaScript Object Notation) formatted text, adhering to JSON schema draft-07. The JSON format was chosen because it is both human and machine-readable/writable. For a detailed description of JSON see www.json.org.
BioCompute data types are defined as aggregates of the critical fields organized into the following domains: the provenance domain, the usability domain, the extension domain, the description domain, the execution domain, the parametric domain, the input and output domains, and the error domain. At the time of creation with actual values compliant to the schema the BCO should be assigned a unique identifier, a [[2]]. The object could then be assigned a unique digital etag.