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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