From BFO to IAO

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From Basic Formal Ontology to the Information Artifact Ontology

Wednesday and Thursday, July 22-23, 2009

Venue: Norton 112, UB North Campus

Two-day Course organized in conjunction with the International Conference on Biomedical Ontology.

Now available in streaming video format here.

Slides: Smith Ceusters Ruttenberg

Ontologies provide controlled structured representations of what is general in any given domain of scientific research. Referent tracking is an approach to the controlled structured representation of the corresponding particular entities, for example to particular patients, or particular disorders, as they change through time.

Session 1: Wednesday 9am to 12.30pm

  • Barry Smith: introduction to Basic Formal Ontology, the top-level ontology that has been developed to serve integration of domain-level scientific ontologies, particularly within the context of the Open Biomedical Ontologies (OBO) Foundry] initiative,

Session 2: Wednesday 1.30pm to 5pm

  • Werner Ceusters: introduction to Referent Tracking, and its applications to the task of relating ontologies to instance data in ways useful to healthcare and biomedical research

Session 3: Thursday 9am to 12.30pm

  • Alan Ruttenberg: Introduction to the Ontology for Biomedical Investigations (OBI) and the Information Artifact Ontology (IAO). OBI is a BFO-based integrated ontology for the description of life-science and clinical investigations. Its domain encompasses materials made and produced in investigations, research objectives, experimental protocols, roles of people in investigations, and processing and publication of data gathered in investigations. We will discuss both entities that are unique to investigations as well as the ways OBI bridges the world of the investigation to the natural world as represented in other OBO ontologies.
  • IAO, a spinoff of OBI, is a BFO-based ontology representing entities such as documents, measurement results, URIs, IDs, names, serial numbers, datatypes, databases, and ontologies, and the processes in which they are created and consumed. The session will discuss the motivation for creating this ontology and the unique perspective it takes among ontologies of information.
  • Attendees will finish these sessions with an understanding of upper level entities essential to read (and review) the ontologies in more detail, examples of how they can be applied, a picture of the current state of the ontology and of future work and be cognizant of issues that need to be resolved and perhaps primed to help solve them.

Session 4: Thursday 1.30pm to 5pm

  • Discussion session (addressing a list of open questions and action items generated by the first 3 sessions)

Literature and Links


Werner Ceusters is Professor in the Psychiatry Department of the University at Buffalo (UB), Director of the Ontology Research Group of the New York State Center of Excellence in Bioinformatics and Life Sciences, and Coordinator of Bioinformatics for the UB Health Science Faculties.

Alan Ruttenberg is a Principal Scientist at Science Commons. His project, the Neurocommons, prototypes the use of Semantic Web technology for integrating and querying biomedical knowledge.working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a chair of the OWL Working Group.

Barry Smith is SUNY Distinguished Professor in the University at Buffalo (New York, USA). His primary research focus is the application of ontology in biomedicine and other fields. He is one of the principal scientists in the National Center for Biomedical Ontology, a member of the Scientific Advisory Board of the Gene Ontology Consortium, a Coordinating Editor of the OBO Foundry, and a PI of the NIH-funded Protein Ontology and the Infectious Disease Ontology projects.