2013 ICBO OBO tutorial
Date
July 7th 2013
Venue
This tutorial will take place in association with the ICBO conference taking place in Montreal, Canada. Registration details are provided here.
Schedule
TBD
Abstract
With the increase in use of ontologies, specifically in the biomedical domain, more and more resources are being developed ad-hoc rather than following a concerted action. This can result in resources that can be used only within a specific project, and will often die when funding runs out. The OBO Foundry is a consortium of ontology developers which aims to address this issue by implementing a set of best practices for ontology development, including open access, collaborative work, and technical resources supporting them. This introductory tutorial will provide:
- 1. a brief introduction to the rationale behind the OBO consortium effort, and a short update as to its status,
- 2. a guideline of becoming a member of OBO foundry ontologies including OBO foundry ontology requirements and registration,
- 3. an overview of the current best practices pertaining to development of OBO foundry ontologies such as ID policy, naming convention, deprecation policy, ontology metadata, importing selected terms from external resources using the Minimum Information to Reference an External Ontology Term (MIREOT) mechanism,
- 4. An introduction to the use of Protege to build OWL format ontologies
- 5. A description of tools that have been implemented to support OBO foundry resources, such as the unique URI generation tool (URIgen,) the obo2owl pipeline, the OBO Ontology Release Tool (OORT), the MIREOT web tool, OntoFox.
We will provide small exercises for attendees to follow along during the discussions. At the end of the tutorial, attendees will have a better understanding of the importance of collaborative and open development and will be aware of various tools available to support them in their daily activities.
Format
We will host a full day event. Morning will consist in a theoretical session, aimed at people wanting to better understand the OBO Foundry and its place within the semantic web. Afternoon will be geared towards developers of resources with a practical session and hands-on exercises.
Faculty
Mélanie Courtot
- BC Cancer Agency
- email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting in the context of the Public Health Agency of Canada - Canadian Institutes of Health Research Influenza Research Network (PCIRN). She has actively contributed to several biomedical ontologies, including the Ontology for Biomedical Investigations (OBI), the Information Artifact Ontology (IAO), the Vaccine Ontology (VO) and the Influenza Ontology. She co-developed the Minimum Information to Reference an External Ontology Term (MIREOT), increasing their interoperability. She co-founded and organizes the Semantic Web Meetup group in Vancouver, which currently counts more than 140 members. She is an elected steering committee member of the OWL Experiences and Directions (OWLED) workshop series since 2008, and chaired the OWLED 2011 workshop.
Alan Ruttenberg
- University at Buffalo School of Dental Medicine
- email: alanruttenberg@gmail.com
Alan Ruttenberg’s research interest is in structuring and using biological and clinical knowledge to enable computational interpretation of clinical and experimental data, and the scope of his current work spans technical, medical, and organizational aspects of improving access to essential knowledge. In that context, he has been an active member in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that forms the upper level ontology for the OBO Foundry, of which he is a coordinating editor, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), and the Information Artifact Ontology (IAO). He has been an active participant in W3C Semantic Web activities, and was chair of the OWL working group, developing the Neurocommons project as a prototype of how to deploy biomedical knowledge using Semantic Web technologies.
Barry Smith
- University at Buffalo Department of Philosophy
- email:phismith@buffalo.edu
Barry Smith is Professor of Philosophy, Neurology and Computer Science and Director of the National Center for Ontological Research at the University at Buffalo. He is also one of the principal scientists of the National Center for Biomedical Ontology (NCBO), an NIH Roadmap National Center for Biomedical Computing, a member oft he Scientific Advisory Board of the Gene Ontology Consortium, and a PI of the Protein Ontology and Infectious Disease Ontology projects. He is a Coordinating Editor of the OBO Foundry initiative, and plays a guiding role in Basic Formal Ontology and the Ontology for General Medical Science, the Environment Ontology, and the Plant Ontology initiatives.
