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Publications

NCOR affiliates publish research on ontology development, implementation, and theory in leading journals and conferences.

Each records below includes the publication title, authors, year, a brief one-sentence summary of its content, and a direct URL when available. This list covers academic papers, books, conference proceedings, technical reports, and white papers related to NCOR, BFO, CCO, and key contributors Barry Smith, John Beverley, and Alan Ruttenberg, to provide a comprehensive overview of NCOR's ontological research contributions across the years.

National Center for Ontological Research (NCOR)​

Basic Formal Ontology (BFO)​

(Note: BFO is also now an ISO standard, ISO/IEC 21838-2:2021, which codifies BFO 2.0 officially.)

Common Core Ontologies (CCO) – Related Publications​

(Note: The Common Core Ontology suite was developed initially by CUBRC, Inc. under an IARPA project and is maintained by NCOR. The ontologies are available on GitHub: https://github.com/CommonCoreOntology/CommonCoreOntologies.)

(Barry Smith has authored 700+ publications. The above is a selection emphasizing those tied to NCOR's ontological work. For a full list, see his CV (BARRY SMITH - LIST OF PUBLICATIONS) (BARRY SMITH - LIST OF PUBLICATIONS) or Google Scholar.)

By John Beverley​

  • ARGO: Arguments Ontology (John Beverley, Neil Otte, Francesco Franda, Brian Donohue, Alan Ruttenberg, Jean-Baptiste Guillion & Yonatan Schreiber) – Abstract: Although the last decade has seen a proliferation of ontological approaches to arguments, many of them employ ad hoc solutions to representing arguments, lack interoperability with other ontologies, or cover arguments only as part of a broader approach to evidence. To provide a better ontological representation of arguments, we present the Arguments Ontology (ArgO), a small ontology for arguments that is designed to be imported and easily extended by researchers who work in different upper-level ontology frameworks, different logics, and different approaches to argument evaluation. Unlike most ontological approaches to arguments, ArgO utilizes Basic Formal Ontology (BFO) as an upper-level ontology, and may be used alongside other commonly used ontologies in the BFO framework, including both the Information Artifact Ontology (IAO), and the Information Entity Ontology (INFO). Critically, our proposal is principled, based on rigorous definitions and formal axioms out of which characterizations of arguments naturally fall. It is our hope that ArgO may assist researchers in many projects, including: integrating heterogeneous sources of evidence, structuring the content of semantic wikis, and enhancing semantic reasoning. URL: https://philarchive.org/rec/BEVAAO

  • The Common Core Ontologies (Mark Jensen et al., 2024) – [See listing under CCO above] Co-authored by John Beverley, this FOIS 2024 paper is the definitive description of CCO's structure and contents, reflecting Beverley's work in mid-level ontology development.

  • CIDO: A Community-Based Ontology for Coronavirus Disease Knowledge and Data Integration, Sharing, and Analysis (Yongqun "Oliver" He, Brian Athey, John Beverley, Barry Smith et al., 2020) – A paper in Scientific Data 7:181 that introduces the Coronavirus Infectious Disease Ontology (CIDO). Beverley is a co-author; the paper describes CIDO's scope in representing COVID-19 data (pathogens, vaccines, drugs, clinical features) and how it extends the Infectious Disease Ontology (CIDO-He-ICBO2022.pptx) (CIDO-He-ICBO2022.pptx). URL: https://doi.org/10.1038/s41597-020-0513-8

  • The Infectious Disease Ontology in the Age of COVID-19 (Shane Babcock, John Beverley, Lindsay G. Cowell, Barry Smith, 2021) – [See Barry Smith's section] Beverley co-authored this work on updating IDO. It provides a case study of applying ontologies (BFO-based) to model a novel infectious disease outbreak, and includes Beverley's contributions to the Virus Infectious Disease Ontology (VIDO) and IDO-COVID-19 extensions (The Infectious Disease Ontology in the age of COVID-19 | Journal of Biomedical Semantics | Full Text).

  • Referent Tracking for Vaccine Data (John Beverley, 2020) – Talk/abstract (OGMS group, June 2020): Beverley presented on applying rigorous referent tracking (an NCOR technique) to vaccine and infectious disease data, leveraging BFO/IDO to ensure consistent reference to entities like viruses, hosts, and symptoms (not a formal publication, but indicative of his research projects (Applied Ontology — John Beverley) (Applied Ontology — John Beverley)).

  • Blogic: Ontology & AI Blog (John Beverley, 2020–2024) – Beverley's personal blog where he occasionally posts informal write-ups of ontology work (e.g., NCOR projects, CCO updates, event summaries) (Recent NCOR Accepted Work - John Beverley) (Recent NCOR Accepted Work — John Beverley). For instance, in "Recent NCOR Accepted Work" (June 2024) he summarizes NCOR team papers (including the CCO FOIS paper) (Recent NCOR Accepted Work — John Beverley) (Recent NCOR Accepted Work — John Beverley). URL: https://johnbeverley.com/blogic

(John Beverley, PhD, is Co-Director of NCOR and an assistant professor at University at Buffalo. His work focuses on applied ontology (CCO, infectious disease, etc.), and many of his publications are collaborations under NCOR initiatives.)

By Alan Ruttenberg​

  • The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration (Barry Smith et al., 2007) – [See under Barry Smith] Allen Ruttenberg is among the co-authors of this seminal paper establishing principles for open biomedical ontologies (The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration - PubMed), reflecting his role in ontology community building.

  • MIREOT: The Minimum Information to Reference an External Ontology Term (Mélanie Courtot, Alan Ruttenberg et al., 2009) – A proposal (Nature Precedings, Aug 2009) for a lightweight mechanism to import specific terms from external ontologies. Ruttenberg and colleagues outline guidelines (later widely adopted in OBO) to avoid importing entire ontologies when only a few terms are needed, thereby enabling reuse while managing complexity (MIREOT: the Minimum Information to Reference an External Ontology Term | Nature Precedings) (MIREOT: the Minimum Information to Reference an External Ontology Term | Nature Precedings). URL: https://doi.org/10.1038/npre.2009.3576.1 (Open Access)

  • Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates (B. Peters, Alan Ruttenberg, Jason Greenbaum et al., 2009) – A Nature Precedings article (Nov 2009) introducing "Quick Term Templates" – simple spreadsheet templates for rapidly adding new terms to ontologies in a controlled way. This method, co-devised by Ruttenberg, was aimed at speeding up ontology extension (particularly for the Vaccine Ontology and others) by engaging domain experts with user-friendly templates (Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates | Nature Precedings) (Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates | Nature Precedings). URL: https://doi.org/10.1038/npre.2009.3970.1

  • Advancing Translational Research with the Semantic Web (Alan Ruttenberg et al., 2007) – A community paper in BMC Bioinformatics 8(Suppl 3):S2 resulting from the W3C Healthcare and Life Sciences initiative. Ruttenberg and 20+ co-authors demonstrate how Semantic Web technologies (RDF/OWL) and shared ontologies can facilitate data sharing in translational medicine, showcasing use cases that foreshadow later NCOR work on interoperability (Advancing translational research with the Semantic Web) ([PDF] Advancing translational research with the Semantic Web). URL: https://doi.org/10.1186/1471-2105-8-S3-S2

  • Life Sciences on the Semantic Web: The Neurocommons and Beyond (Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall, 2009) – An article in Briefings in Bioinformatics 10(2):193-204 discussing the Neurocommons project. It reviews how ontologies and RDF were used to integrate life science knowledge, highlighting challenges in publishing, linking, and reasoning over large-scale biomedical data – an effort to which Ruttenberg contributed significantly. URL: https://doi.org/10.1093/bib/bbp004

  • The SWAN Biomedical Discourse Ontology (Paolo Ciccarese et al., including Alan Ruttenberg, Tim Clark, 2008) – A paper in Journal of Biomedical Informatics 41(5):739-751 describing the SWAN ontology, which models scientific discourse (papers, claims, hypotheses) in Alzheimer's research. Ruttenberg's contribution here was in developing an ontology that links scientific publications to data and arguments, an early example of applying ontology to knowledge representation in science. URL: https://doi.org/10.1016/j.jbi.2008.03.002

  • The Ontology for Biomedical Investigations (Anita Bandrowski et al., 2016) – A PLOS ONE 11(4):e0154556 article presenting OBI, an ontology for describing biological and clinical investigations. Ruttenberg, as part of the OBI consortium, is acknowledged for contributions to OBI's development; the paper covers OBI's scope (instrument, protocol, study design terms, etc.) and its role in standardizing metadata for experiments (The Ontology for Biomedical Investigations - NASA/ADS) (‪Alan Ruttenberg‬ - ‪Google Scholar‬). URL: https://doi.org/10.1371/journal.pone.0154556

  • Uberon: An Integrative Multi-Species Anatomy Ontology (Chris Mungall et al., 2012) – A paper in Genome Biology (13:R5) for which Ruttenberg provided personal communications or input on ontology design. Uberon is not authored by Ruttenberg, but as a founding member of OBO, he influenced its development. (This highlights Ruttenberg's broader impact on the OBO library beyond his direct authorships.) URL: https://doi.org/10.1186/gb-2012-13-1-r5

  • OWL: Experiences and Directions – Third International Workshop (OWLED 2007) (Alan Ruttenberg et al., eds., 2007) – Ruttenberg co-edited the proceedings of OWLED 2007, reflecting his involvement in bridging the OWL community with ontology users. These proceedings include discussions relevant to BFO/OBO adoption in OWL and issues like modularity and reasoning, which informed later technical work on BFO 2.0. URL: http://ceur-ws.org/Vol-258/

  • ICBO 2012 Proceedings (Alan Ruttenberg, Mélanie Courtot, Amar Das, eds., 2012) – Ruttenberg co-edited the published proceedings of the International Conference on Biomedical Ontology 2012 (CEUR Workshop Proceedings 897). This volume contains many short papers and posters (including some of Ruttenberg's co-authored abstracts on adverse event ontology and vaccine ontology) and serves as a snapshot of ontology research circa 2012. URL: http://ceur-ws.org/Vol-897/

(Allen "Alan" Ruttenberg is an ontologist known for his work on the Semantic Web in life sciences and for co-founding the OBO Foundry and OBI. Many of his publications above are collaborative efforts setting standards for ontology development and data integration in biomedicine.)