The Bioregistry is a community-driven registry of semantic spaces and their metadata. When I learned about BiomarkerKB at the International Society for Biocuration’s 18th Annual International Biocuration Conference, I was excited to curate new records (and prefixes) in the Bioregistry to cover BiomarkerKB’s semantic spaces on biomarkers. This post summarizes the discussions I’ve had with its maintainers, Jeet and Raja, throughout the Bioregistry curation process and also gives insight into how databases can benefit from being represented in the Bioregistry.

How to Contribute to the Bioregistry

The Bioregistry follows the open data, open code, open infrastructure (O3) guidelines, meaning that anyone can make suggestions or additions either by creating an issue or a pull request on its GitHub repository. Both maintainers of ontologies, controlled vocabularies, databases, etc. and proactive community members can request new prefixes (i.e., add new records that represent a semantic space) by following the project’s contribution guidelines (TL;DR, watch this tutorial).

Contributing New Prefixes for BiomarkerKB

Most importantly, I coordinated with its maintainers Raja and Jeet to make a pull request to the Bioregistry’s GitHub repository and add two new prefixes. I was also able to explain the relationship between the records in the Bioregistry and their resource. I recorded part of our discussion that is generally useful for anyone who’s making a resource, and want to think about some of the benefits:

As a follow-up, Jeet and Raja requested a summary of this discussion that they could incorporate into BiomarkerKB’s FAQ. Below is a draft of that text, which could be easily adapted for any resource.

Text for BiomarkerKB’s FAQ

The Bioregistry is a community-driven registry of semantic spaces and their metadata. It contains records for three semantic spaces created for BiomarkerKB:

  1. obci for the Ontology for Biomarkers of Clinical Interest
  2. biomarkerkb.biomarker for condition-specific biomarkers
  3. biomarkerkb.canonical for condition-agnostic biomarkers

The Bioregistry enables BiomarkerKB to unambiguously communicate how its entities should be written as URIs and compact URIs (CURIEs) for use in semantic web and linked (open) data settings. This supports many kinds of scientists, including:

  • biocurators, to identify BiomarkerKB’s semantic spaces as high quality resources for use in annotating their own data
  • data providers, to make their data and knowledge more FAIR before and during publication
  • data scientists, to validate biomarker data annotated with BiomarkerKB semantic spaces against an actionable
  • data stewards, to reference the Bioregistry records as components of research data management plans (DMPs)
  • web developers, to resolve identifiers from BiomarkerKB’s semantic spaces to human-readable web pages

If you’re a database maintainer and would like some specific attention given to representing your resource in the Bioregistry, or explainaning how the Bioregistry could be used for your project, please reach out! My contact information is at the bottom of my website.