=Paper=
{{Paper
|id=Vol-3805/ICBO-2022_paper_899
|storemode=property
|title=COB: A Core Ontology for Biology and Biomedicine
|pdfUrl=https://ceur-ws.org/Vol-3805/ICBO-2022_paper_899.pdf
|volume=Vol-3805
|authors=James A. Overton,Rebecca Jackson,Nico Matentzoglu,William Duncan,Randi Vita,Nomi L. Harris,OBO Operations Committee members,Christopher J. Mungall,Bjoern Peters
|dblpUrl=https://dblp.org/rec/conf/icbo/OvertonJMDVHMP22
}}
==COB: A Core Ontology for Biology and Biomedicine==
https://ceur-ws.org/Vol-3805/ICBO-2022_paper_899.pdf
COB: A Core Ontology for Biology and Biomedicine
James A. Overton1, Rebecca Jackson2, Nicolas Matentzoglu3, William D. Duncan4, Randi
Vita5, Nomi L. Harris6, OBO Operations committee members, Christopher J. Mungall6,
Bjoern Peters5
1
Knocean, Inc., Toronto, Ontario, M6P 2T3, Canada
2
Bend Informatics LLC, Bend, OR 97701, USA
3
Semanticly Ltd, Athens 10563 ΓΕΜΗ 160976003000, Greece
4
University of Florida, Gainesville, FL 32610, USA
5
La Jolla Institute for Immunology, La Jolla, CA 92037, USA
6
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Abstract
The OBO Foundry is a community organization of ontology developers that aims to support
the development, harmonization, application, and sharing of an interoperable set of ontologies.
The OBO Foundry principles are a defined set of guidelines that enable these aims. The OBO
operations group has steadily worked towards making these principles (or parts thereof)
computationally operational. The outcome of the computationally enforceable translation of the
OBO principles saves a great deal of expert volunteer time and promotes greater adherence by
individual ontologies (Jackson et al., 2021). However, the OBO principle for ‘interoperability’
is not easy to computationally check for. While it is possible to check for logical compatibility
between ontologies, that is insufficient, as different ontologies can simply avoid ‘talking to each
other’ and falsely seem compatible, by using distinct relations and classes.
To address this issue, we created the Core Ontology for Biology and Biomedicine (COB), which
provides a set of classes and relations that all OBO ontologies should be built upon and
compatible with. COB extends on BFO, which provides a domain-neutral high-level set of
classes. Specifically, COB was designed to 1) provide a direct parent to every top-level OBO
ontology class; 2) be anchored in Basic Formal Ontology (BFO), but hide its complexity from
end-users; and 3) include logical axioms that make inconsistencies within and between OBO
ontologies apparent through reasoning. Here we report on our current progress on COB, the
methods used to test for COB compatibility of an OBO ontology, and the remaining gaps in
COB class coverage that reveal existing inconsistencies between OBO ontologies. COB is
available from https://obofoundry.org/COB/.
Keywords 1
ontology, interoperability, reasoning
1. References Ruttenberg A, Schriml LM, Smith B,
Stoeckert CJ Jr, Vasilevsky NA, Walls RL,
Zheng J, Mungall CJ, Peters B. OBO
[1] Jackson R, Matentzoglu N, Overton JA,
Foundry in 2021: operationalizing open data
Vita R, Balhoff JP, Buttigieg PL, Carbon S,
principles to evaluate ontologies. Database
Courtot M, Diehl AD, Dooley DM, Duncan
Oct 26;2021. doi:10.1093/database/baab069
WD, Harris NL, Haendel MA, Lewis SE,
Natale DA, Osumi-Sutherland D,
ICBO 2022, September 25-28, 2022, Ann Arbor, MI, USA
EMAIL: cjmungall@lbl.gov (A. 1); bpeters@lji.org (A. 2)
ORCID: 0000-0002-6601-2165 (A. 1); 0000-0002-8457-6693 (A.
2)
©️ 2022 Copyright for this paper by its authors. Use permitted under Creative
Commons License Attribution 4.0 International (CC BY 4.0).
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