How to Develop and Use an OBO Foundry Ontology: Difference between revisions

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'''Rationale'''
'''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
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.
OWL, and we provide guidance on the use of tools and metadata conversion for this purpose.
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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.
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.


'''Presenters'''
'''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.
 
'''Requirements'''
 
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
 
'''Deliverables'''
 
Participants who attend the workshop will leave with an understanding of the OBO Foundry process including:
 
:- 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
 
'''Faculty'''


The workshop proposers are coordinating members of the OBO Foundry and are all actively
'''Melissa Haendel'''
involved in the biomedical ontologies community, and will rely on existing dissemination
:Oregon Health & Science University
resources to circulate the workshop, such as mailing lists. They have been and will continue to
:email haendel@ohsu.edu
directly contact colleagues that should be interested in participating, encouraging them to
 
prepare relevant presentations. Outreach will also be made to consumers of ontologies who will
Dr. Haendel has co-lead several previous ontology workshops and has participated in  
want to have this chance to directly engage the Foundry and influence future work. Finally, a
website will be set up with details of the workshop, that can be linked from and will link to the
main ICBO webpage, increasing visibility.
Proposed 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 workshop will consist providing 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 workshop 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.
Requirements
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
Deliverables
Participants who attend the workshop will leave with an understanding of the OBO Foundry
process including:
- 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
- What ontologies are currently available as part of the OBO Foundry
- How to participate in the future development of the Foundry
Proposers
Melissa Haendel
Oregon Health & Science University
Assistant professor, OHSU Library and Dept. of Medical Informatics
3181 Southwest Sam Jackson Park Road
Portland, OR 97239-3079
email haendel@ohsu.edu
Dr. Haendel has co-lead several previous ontology workshops and has participated in
development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO,
development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO,
Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI). She is
Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI). She is
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organism data, and to infer experimental details relating to the use of organismally derived
organism data, and to infer experimental details relating to the use of organismally derived
research resources.
research resources.
Chris Mungall
 
Genomics Division, Lawrence Berkeley National Laboratory
'''Chris Mungall'''
Building 64, 1 Cyclotron Road
:Genomics Division, Lawrence Berkeley National Laboratory
Berkeley, CA 94720
:email cjmungall@lbl.gov
email cjmungall@lbl.gov
 
Chris Mungall is a computer scientist at LBNL with an interest in applications of biological
Chris Mungall is a computer scientist at LBNL with an interest in applications of biological
ontologies. He is part of the Gene Ontology Consortium, where he leads the software group and
ontologies. He is part of the Gene Ontology Consortium, where he leads the software group and
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models to human diseases using a diversity of OBO ontologies. One aspect of this work was
models to human diseases using a diversity of OBO ontologies. One aspect of this work was
integrating multiple vertebrate anatomy ontologies through a bridging ontology (Uberon).
integrating multiple vertebrate anatomy ontologies through a bridging ontology (Uberon).
Alan Ruttenberg
 
University at Buffalo
'''Alan Ruttenberg'''
School of Dental Medicine
:University at Buffalo School of Dental Medicine
Squire Hall, Buffalo, NY 14215
:email: alanruttenberg@gmail.com
email: alanruttenberg@gmail.com
 
Alan Ruttenberg’s research interest is in structuring and using biological and clinical knowledge
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
to enable computational interpretation of clinical and experimental data, and the scope of his
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developing the Neurocommons project as a prototype of how to deploy biomedical knowledge
developing the Neurocommons project as a prototype of how to deploy biomedical knowledge
using Semantic Web technologies.
using Semantic Web technologies.
Barry Smith
 
University at Buffalo
'''Barry Smith'''
Department of Philosophy
:University at Buffalo Department of Philosophy
126 Park Hall, Buffalo NY 14260
:email:phismith@buffalo.edu
email:phismith@buffalo.edu
 
Barry Smith is Professor of Philosophy, Neurology and Computer Science and Director of the
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
National Center for Ontological Research at the University at Buffalo. He is also one of the
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projects. He is a Coordinating Editor of the OBO Foundry initiative, and plays a guiding role in
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
Basic Formal Ontology and the Ontology for General Medical Science, the Environment
Ontology, the Vaccine Ontology, and the Plant Ontology initiatives.
Ontology, and the Plant Ontology initiatives.
Suggested reviewers
Colin Batchelor, Royal Society of Chemistry, UK
Judith Blake, The Jackson Laboratory, US
Lindsay Cowell, University of Texas

Revision as of 17:05, 10 February 2012

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.

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.

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.

Requirements

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:

Deliverables

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

- 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

Faculty

Melissa Haendel

Oregon Health & Science University
email haendel@ohsu.edu

Dr. Haendel has co-lead several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI). She is currently working on the ontology driven eagle-i research resource discovery platform. Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.

Chris Mungall

Genomics Division, Lawrence Berkeley National Laboratory
email cjmungall@lbl.gov

Chris Mungall is a computer scientist at LBNL with an interest in applications of biological ontologies. He is part of the Gene Ontology Consortium, where he leads the software group and works on the maintenance of the GO and the cell type ontology. He is also involved in a number of other Open Bio-Ontology (OBO) efforts, and with the organization of the OBO Foundry. His research is in applying phenotype ontology based algorithms for linking animal models to human diseases using a diversity of OBO ontologies. One aspect of this work was integrating multiple vertebrate anatomy ontologies through a bridging ontology (Uberon).

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.