Request to include the Ontology of Bacterial Gene Regulation (OBAGER) in the OBO Foundry

[Citlalli Mejía Almonte]

Dear OBO Foundry team,

I am writing to request the inclusion of the Ontology of Bacterial Gene Regulation (OBAGER) in the OBO Foundry.

OBAGER is an ontology designed to provide a formal and transparent framework for the conceptualization of bacterial gene regulation. It translates expert-vetted natural language definitions into OWL axioms at the TBox level, with the goal of capturing the necessary and sufficient conditions that define promoters, transcription units, transcription factors, and related entities. The ontology currently includes all entities represented in RegulonDB, the database of transcriptional regulation in E.coli  (https://regulondb.ccg.unam.mx/) but with refined ontological distinctions.

Key aspects of OBARE include:

• A theory-informed approach: provisional, expert-based definitions that are documented in detail and will be described in an upcoming publication to ensure conceptual transparency.

• Explicit modeling of regulatory entities and relations that are often implicit in databases.

• Future alignment with existing OBO ontologies, once our internal definitions are stable.

The ontology is available here:

https://github.com/ontology-of-bacterial-gene-regulation/Ontology-Of-Bacterial-Gene-Regulation

We believe OBARE fills a gap in the representation of bacterial regulatory biology within the OBO ecosystem and will facilitate data integration, ontology-based reasoning, and FAIRification of resources such as RegulonDB.

Please let us know the next steps for consideration and review. We would be very grateful for your feedback and guidance on aligning OBARE with OBO Foundry principles.

Sincerely,

Citlalli Mejía
Computational Biology Lab
Center for Genomic Sciences, UNAM

[Chris Mungall]

Hi Citlali

See the instructions for submission, and for making an issue in the repo

https://obofoundry.org/faq/how-do-i-register-my-ontology.html

My first impression is that this looks well thought out and serves an important use case, but there is a lot of overlap with SO. I'd recommend reaching out to the SO developers, and putting some of your terms in the SO tracker, details here: https://obofoundry.org/ontology/so

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