Best Practices
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 that everyone registers a prefix at biocomputeobject.org.
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 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
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 write functionalities. For users who do not have access to a bioinformatics platform they can use the BCO Builder in the 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