Request for new ontology OBCI

[nataled]

Title

Ontology for Biomarkers of Clinical Interest

Short Description

The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects.

Description

OBCI is a reference ontology for biomarkers that formalizes biomarker-centric knowledge (terms, definitions, synonyms) under a unified framework, enriched with objects imported from related reference ontologies and designed to aid clinicians seeking to identify biomarkers useful to their purpose. Construction of OBCI observes recommendations concerning accurate formal representation of biomarkers as proposed by the FDA-NIH Biomarker Working Group and in accordance with the principles of the Open Biomedical and Biological Ontologies (OBO) Foundry to ensure ontological rigor and interoperability.

Identifier Space

OBCI

License

CC-BY 4.0

Domain

health

Source Code Repository

https://github.com/clinical-biomarkers/OBCI

Homepage

https://github.com/clinical-biomarkers/OBCI

Issue Tracker

https://github.com/clinical-biomarkers/OBCI/issues

Contribution Guidelines

https://github.com/clinical-biomarkers/OBCI/blob/main/CONTRIBUTING.md

Ontology Download Link

https://proteininformationresource.org/staff/nataled/OBCI/obci.owl

Contact Name

Darren A. Natale

Contact Email

[email protected]

Contact GitHub Username

nataled

Contact ORCID Identifier

0000-0001-5809-9523

Formats

• [X] OWL RDF/XML (.owl)
• [ ] OBO (.obo)
• [ ] OBO Graph JSON (.json)

Dependencies

• chebi
• cido
• cl
• doid
• ecto
• gno
• go
• iao
• ncbitaxon
• ncit
• pato
• pr
• ro
• so
• uberon

Related

There is currently no active OBO Foundry ontology that covers the same domain. There is, however, a newly-submitted ontology (BMONT) that is being considered for inclusion, and we are aware of at least one other group developing a biomarker ontology. We have looked at BMONT and determined that the approach taken by the developers is inconsistent with our approach. It can best be described as an application ontology (it makes use of axiom injection). OBCI is purely a reference ontology. Indeed, by our criteria, BMONT does not have any biomarkers (the few exceptions being the upper-level-most terms). BMONT contains only what we term 'biomarker assessed entities', nearly all of which (in OBCI) are imported terms. Thus, OBCI could not fit under the umbrella of BMONT without radically changing that ontology. It is unclear as yet how OBCI and the other not-yet-submitted ontology relate in terms of scope or approach, but our two groups will be initiating discussions in the near future.

Usages

No response

Intended Use Cases and/or Related Projects

The NIH CFDE funded BiomarkerKB (https://glygen.ccrc.uga.edu/frontend/home/) was built using early versions of OBCI as a guide for approach and organization. In turn, OBCI will largely--but not solely--ontologically represent many of the biomarkers collected there.

Data Sources

The main definition source for upper level terms in OBCI is the FDA-NIH Biomarker Working Group (see NCBI:books/NBK402285 and PMID:29405771). Many of the specific biomarkers in OBCI will derive from the collected data found in the aforementioned BiomarkerKB.

Additional comments or remarks

• Approach: Many current and previous treatments of biomarkers use the term 'biomarker' to refer to what we call an 'assessed entity'. For example, some particular gene would be called a biomarker for some disease if a perturbation of the gene (such as a sequence variant) is found to cause or correlate with that disease. Thus, one often sees 'BRCA1' called a biomarker. This is not the case in OBCI. Instead, the presence of the variant is a biomarker, or overexpression of the gene is a biomarker (after all, everyone has a copy of some form of 'BRCA1'). Another example is 'blood sugar'. By itself, 'blood sugar' is not a biomarker--its level above or below normal (for an individual, or using a population average) is what indicates some condition of interest.
• Reasoning: OBCI was built to take extensive advantage of reasoning for proper placement of terms within the hierarchy. We recommend the Hermit reasoner for this purpose.
• Relations: It is possible that there are relations proposed here that have existing analogs elsewhere, or that can be composed using property chains. We are partway through the process of identifying these and will make additional replacements as necessary. Any relations not covered elsewhere will be submitted to the Relations Ontology.
• Repository: Ultimately the ontology will be available via GitHub. For now, however, it is publicly available in a folder managed by the submitter.
• ID space registration: In anticipation of this submission, we submitted this prefix to the Bioregistry already: https://bioregistry.io/registry/obci. It later came to our attention that this is not the preferred method, but mentioning it here because the existing Bioregistry term is NOT a different resource, it is this ontology being submitted.
• Axiom injection: There is a single case of axiom injection, on an NCIt term ("Expired air"). There are currently no terms in UBERON that represent the same entity. There are, however, two related terms in UBERON ("bodily gas" and "air in respiratory system"), but the definitions of those terms rule out their use for our case. We will be requesting addition of the needed term (likely to be termed "exhaled breath") and will replace the NCIt term with the new one upon its availability.
• Scope: While it is very likely that many of the biomarker terms pertain to humans, this is not a taxonomic restriction. That is, biomarkers pertinent to the clinical care of animals are in scope. Markers that identify foods (such as presented in FOBI) are not in scope.
• COB alignment: It is likely that the best upper level term for this ontology will be COB:characteristic. However, we have not made that assertion for two reasons: 1) COB:characteristic is not yet undefined; 2) as COB is greatly in flux, there is a possibility that another upper level term will be a better fit; and 3) for the initial visualization we have left 'biomarker' as the top term.
• Top level term: We have it as 'biomarker' since that is the official terminology of the FDA-NIH Biomarker Working Group. However, we would be willing to change it to something like 'clinical biomarker' if other types of entities are commonly called 'biomarkers'. However, to our knowledge, that term is already restricted solely to the clinical domain.

OBO Foundry Pre-registration Checklist

• [X] I have read and understood the registration process instructions and the registration checklist.
• [X] There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.
• [X] My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
• [X] My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy
• [X] My term labels are in English and conform to the OBO Foundry Naming Conventions
• [X] I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the IAO:0000115 property.
• [X] For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
• [X] For all relationship properties (Object and Data Property), I checked whether the Relation Ontology (RO) includes an appropriate one. I understand that aligning with RO is an essential part of the overall alignment between OBO ontologies!
• [X] For the selection of appropriate annotation properties, I looked at OMO first. I understand that aligning ontology metadata and term-level metadata is essential for cross-integration of OBO ontologies.
• [X] If I was not sure about the meaning of any of the checkboxes above, I have consulted with a member of the OBO Foundry for advice, e.g., through the obo-discuss Google Group.
• [X] The requested ID space does not conflict with another ID space found in other registries such as the Bioregistry and BioPortal, see here for a complete list.