View source for 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 [http://www.kr-med.org/icbofois2012/ ICBO conference] taking place in Graz, Austria. Registration details are provided [http://kr-med.org/icbofois2012/registration.htm here].
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'''Schedule'''

:08:00 Tea/Coffee
:08:30 Introduction: Background, Rationale and Current Structure of the OBO Foundry (BS) [http://ontology.buffalo.edu/obofoundry/Graz2012/1-The_OBO_Foundry.ppt Slides]
:09:30 How to Build an Ontology in Conformity with OBO Foundry Best Practice Principles  (BS) [http://ontology.buffalo.edu/obofoundry/Graz2012/OBO%20Foundry%20Principles.pptx Slides1] [http://ontology.buffalo.edu/obofoundry/Graz2012/BestPractices.ppt Slides2]
:10:30 Break
:10:45 OBO Foundry and the Semantic Web (MC, AR) [http://ontology.buffalo.edu/obofoundry/Graz2012/OBO_SemanticWeb.pdf Slides]
:11:45 Next Steps (BS, MC) [http://ontology.buffalo.edu/obofoundry/Graz2012/3-Future.ppt 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 [http://obofoundry.org/wiki/index.php/Category:Principles 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'''
C-BRASS project manager at The University of British Columbia
Software engineer - Ontologist at BCCRC

'''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.