Version 1.3.0
BioCompute Partnership: https://biocomputeobject.org
GitHub repository for BioCompute Objects: https://github.com/biocompute-objects/
The US Food and Drug Administration (FDA) and George Washington University (GW) have partnered to establish a framework for community-based standards development and harmonization of HTS computations and data formats. Standardized HTS data processing and data formats will promote interoperability and simplify the verification of bioinformatics protocols. To do this, a schema has been developed to represent instances of computational analysis as a BCO. A BCO includes:
- Information about parameters and versions of the executable programs in a pipeline
- Reference to input and output test data for verification of the pipeline
- A usability domain
- Keywords
- A list of agents involved along with other important metadata, such as their specific contribution
Knowledge of input data is intended to be captured according to existing efforts, including MIRAGE, MIAPE, and STRENDA, and to be in accordance with Minimum Information Standards. In addition to all the information captured in the BCO, the BCO itself must be independent of the execution environment, whether it is a local high-performance or a cloud-based infrastructure. To facilitate a means for different stakeholders in the HTS communities to provide input on the BioCompute standard we follow the Open-Stand.org principles for collaborative open standards development.
A functional example of a BCO with associated input and output files, and including the optional empirical error domain:
The BioCompute Objects user guide provides an introduction to implementing/writing a BCO for a pipeline and/or a workflow, and is taken from the BioCompute Objects Specification Document.
Note that unless you are viewing a release this is a draft subject to change.
Table of content:
For developers and advanced users, the BCO specification (1.3.0) provides authoritative documentation on the construction of BioCompute Objects using JSON schema.
For developers and advanced users, the BCO specification (v1.2) provides authoritative documentation on the construction of BioCompute Objects before the implementation of JSON schema.
See releases for all releases of BCO object specification since moving to GitHub.
This standard was originaly prepared by The BioCompute Object working group during preparation for the 2017 HTS Computational Standards for Regulatory Sciences Workshop.
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
To suggest changes to this repository we welcome contributions as a pull request or issue submission.
BCO_Specification is licensed under the BSD 3-Clause "New" or "Revised" License
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.
As a subscriber to the BCO mailing list, you can post to it by sending a message [email protected] (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 [email protected], in which the body says: unsubscribe biocomputels