How to Develop and Use OBO Foundry Ontologies

Date

July 21, 2012, Morning

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Venue

This tutorial will take place in association with the ICBO conference taking place in Graz, Austria. Registration details are provided here.

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Schedule

08:00 Tea/Coffee

08:30 Introduction: Background, Rationale and Current Structure of the OBO Foundry (BS) Slides

09:30 How to Build an Ontology in Conformity with OBO Foundry Best Practice Principles (BS) Slides1 Slides2

10:30 Break

10:45 OBO Foundry and the Semantic Web (MC, AR) Slides

11:45 Next Steps (BS, MC) Slides

12:30 Lunch

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Abstract

Biological research is being revolutionized by an explosion of data. Ontologies are increasingly being used to bring order to this plethora of data and to promote reasoning for information extraction from these data and thereby infer new information and inform new hypotheses. The Open Biomedical Ontologies (OBO) Foundry has played a pivotal role in coordinating and standardizing ontology development in the biomedical domain. In order for ontologies to successfully serve their intended purposes and bring together data to address new hypotheses, the ontologies must be constructed consistently so that both researchers and software can understand and use them in an interoperable manner.

This tutorial aims to bring together consumers and developers of ontologies with the aim of forging community partnership. We will review the list of OBO Foundry core principles, and provide guidance on their usage. This will help both existing and new OBO consortium ontology developers conform to these principles, as well as contribute new requirements. We will address the present and future use of the OBO Format and interoperability with OWL (http://purl.obolibrary.org/obo/oboformat/spec.html) and the use of new tools to facilitate format conversion.

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Rationale

Biomedical ontologies are widely used to index biomedical data and as such it is important to develop and use them in an orthogonal and interoperable way in support of maximal data use, reuse, and hypothesis generation. The OBO Foundry was created in support of this goal and provides a set of guiding principles that are used in the evaluation of ontologies. Ontologies that meet these criteria are members of the OBO Foundry. As the OBO consortium has grown, there have been a diversity of design patterns and variable adherence to these community standards. The goal of this tutorial is to provide guidance towards the application of the OBO principles to facilitate the consistency and orthogonality, and the promotion of OBO Library ontologies into the Foundry. As Foundry ontology development relies on parties working collaboratively, we will emphasize interoperability between different ontologies and community participation in the review process. Further, there is a need to promote interoperability between OBO format and OWL, and we provide guidance on the use of tools and metadata conversion for this purpose.

We hope to draw from the community ontology success stories and needs analysis, towards the end of developing requirements for ontology editing tools and ontology design principles and standards that can further their interoperability within the Foundry framework.

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Format

This half-day ICBO introductory tutorial aims to bring together consumers and developers of OBO ontologies with the aim of forging community partnership in the application of standards. The first section of the tutorial will provide guidance to current and future submitters as to how they can ensure that they conform to OBO principles. Attendees will participate in a short version of applying the OBO review process. The second section of the tutorial will address the current use of the OBO Format, its future, and interoperability with OWL. A short third section will be used to gather requirements for the OBO ontology portal to best suit the needs of OBO ontology consumers in support of interoperability and orthogonality in development practices.

The tutorial requires little background and is suitable for creators or clients of ontologies. The following links provide information for those who would like to read about the Foundry and related tools and resources before attending the workshop:

• http://obofoundry.org/

• http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Principles

• http://www.ontobee.org/

• http://code.google.com/p/oboformat/

• http://www.obofoundry.org/id-policy.shtml

• http://obi-ontology.org/page/MIREOT

• http://code.google.com/p/owltools/wiki/OortIntro

Participants who attend the workshop will leave with an understanding of the OBO Foundry process including:

- The benefits of re-using existing ontologies

- How to reserve a namespace and make your ontology available in the OBO Library

- What the OBO Foundry principles are, how they came to be, and how they change

- The difference between OBO Library and OBO Foundry ontologies

- Assessing whether to submit your ontology to the OBO Foundry

- How to initiate and participate in ontology review

- Ontology formats (OBO and OWL) and how to convert between them

- Release tools and process

- How to use Foundry tools to make your ontology available as Linked Open Data

- How to participate in the future development of the Foundry

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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.