NCOR Wiki - User contributions [en]

BFO 2.0 Meeting

2013-07-11T13:27:42Z

Mcourtot:

*Location: Montreal, site of ICBO
*Date: July 10, 2013

See the [https://docs.google.com/document/d/1Yp8vrO-lHf_vieryKFSQQxi_E7cN2IvMw2_-0KgTaO0/edit google doc]

'''Schedule'''

*Session 1: 2pm - 3:30 pm
**Use cases
:::Jie Zheng, Islet Cells
:::Oliver He, Process Patterns; BFO Software issues
**Release process (Alan Ruttenberg, 10 min)
**Interconnections
**BFO specification (Barry, 10 min)
**BFO-FOL (Barry Smith, 10 min)
*Coffee Break
*Session 2: 4:00 - 5:30
**Time-related issues
**Temporalized relations (Alan, 45 min)
**Temporally qualified continuants (Stefan, 45 min)

2013 ICBO OBO tutorial

2013-07-08T13:35:59Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. It is '''FREE'''! 
----

[http://storify.com/kerfors/icbo2013 Links and Tweets] from Kerstin Forsberg (@kerfors)

'''Schedule'''

'''08:30-12:00 - theoretical session'''

:8:30 to 9:45 - Introduction (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9:45 to 10:30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk (Melissa Haendel)
::Technical and Outreach groups - 15 min talk (Melanie Courtot)

:10.15 to 10.45 - coffee break

:10:45 to 11:45 - OBO Foundry, OWL, and the Semantic Web (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)

:11.45 to 12.00 - Discussion - help Protege installation available

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13:30-17:00 afternoon - application session'''

:13:30 to 14:30 - Basic Knowledge of Ontology (focusing on OWL) and Protégé (Alan Ruttenberg/Melanie Courtot)
::Including how to use OBO Foundry ontologies and starting to develop an ontology

:14:30 to 15:00 - Protégé plugins and ontology tools (Jie Zheng)
::Including Protégé plugins: URI Entity (show URI of a selected term), Obsolete terms, OBO style graph view, and URIgen (assign URI), and OWL difference tools

:15:00 to 15:30 - coffee break

:15:30 to 16:00 - Ontology quality checking and usage (James Overton)
::Including ontology consistency checking, reasoning, and querying (DL and SPARQL queries), obo2owl, OORT

:16:00 to 16:30 - Reuse existing terms defined in external resources: MIREOT and OntoFox (Jie Zheng)

:16:30 to 17:00 - Add a set of terms into ontology: QTT and Ontorat (James Overton)

'''Recommended installation before the tutorial'''

:Protégé 4.3
::http://protege.stanford.edu/download/protege/4.3/installanywhere/Web_Installers/
:OBO style graph view
::http://code.google.com/p/obographview/
:Obsolete terms (installation can follow instruction of ‘OBO style graph view’ installation)
::https://github.com/balhoff/obo-actions/downloads

:ELK (OWL EL reasoner)
::http://code.google.com/p/elk-reasoner/downloads/detail?name=elk-distribution-0.3.2-protege-plugin.zip

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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
[http://ontology.buffalo.edu/smith 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 of the 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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-07-06T18:42:45Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. It is '''FREE'''! 
----

'''Schedule'''

'''08:30-12:00 - theoretical session'''

:8:30 to 9:45 - Introduction (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9:45 to 10:30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk (Melissa Haendel)
::Technical and Outreach groups - 15 min talk (Melanie Courtot)

:10.15 to 10.45 - coffee break

:10:45 to 11:30 - OBO Foundry, OWL, and the Semantic Web (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)

:11.30 to 11.45 - OBO, obo2owl, OORT (Melissa Haendel)

:11.45 to 12.00 - Discussion - help Protege installation available

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13:30-17:00 afternoon - application session'''

:13:30 to 14:30 - Basic Knowledge of Ontology (focusing on OWL) and Protégé (Alan Ruttenberg/Melanie Courtot)
::Including how to use OBO Foundry ontologies and starting to develop an ontology

:14:30 to 15:00 - Protégé plugins and ontology tools (Jie Zheng)
::Including Protégé plugins: URI Entity (show URI of a selected term), Obsolete terms, OBO style graph view, and URIgen (assign URI), and OWL difference tools

:15:00 to 15:30 - coffee break

:15:30 to 16:00 - Ontology quality checking and usage (James Overton)
::Including ontology consistency checking, reasoning, and querying (DL and SPARQL queries)

:16:00 to 16:30 - Reuse existing terms defined in external resources: MIREOT and OntoFox (Jie Zheng)

:16:30 to 17:00 - Add a set of terms into ontology: QTT and Ontorat (James Overton)

'''Recommended installation before the tutorial'''

:Protégé 4.3
::http://protege.stanford.edu/download/protege/4.3/installanywhere/Web_Installers/
:OBO style graph view
::http://code.google.com/p/obographview/
:Obsolete terms (installation can follow instruction of ‘OBO style graph view’ installation)
::https://github.com/balhoff/obo-actions/downloads

:ELK (OWL EL reasoner)
::http://code.google.com/p/elk-reasoner/downloads/detail?name=elk-distribution-0.3.2-protege-plugin.zip

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-07-04T17:06:49Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. It is '''FREE'''! 
----

'''Schedule'''

'''08:30-12:00 - theoretical session'''

:8:30 to 9:45 - Introduction (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9:45 to 10:30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk (Melissa Haendel)
::Technical and Outreach groups - 15 min talk (Melanie Courtot)

:10.15 to 10.45 - coffee break

:10:45 to 11:30 - OWL format (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)
::Including Semanticweb

:11.30 to 11.45 - OBO, obo2owl, OORT (Melissa Haendel)

:11.45 to 12.00 - Discussion - help Protege installation available

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13:30-17:00 afternoon - application session'''

:13:30 to 14:30 - Basic Knowledge of Ontology (focusing on OWL) and Protégé (Alan Ruttenberg/Melanie Courtot)
::Including how to use OBO Foundry ontologies and starting to develop an ontology

:14:30 to 15:00 - Protégé plugins and ontology tools (Jie Zheng)
::Including Protégé plugins: URI Entity (show URI of a selected term), Obsolete terms, OBO style graph view, and URIgen (assign URI), and OWL difference tools

:15:00 to 15:30 - coffee break

:15:30 to 16:00 - Ontology quality checking and usage (James Overton)
::Including ontology consistency checking, reasoning, and querying (DL and SPARQL queries)

:16:00 to 16:30 - Reuse existing terms defined in external resources: MIREOT and OntoFox (Jie Zheng)

:16:30 to 17:00 - Add a set of terms into ontology: QTT and Ontorat (James Overton)

'''Recommended installation before the tutorial'''

:Protégé 4.3
::http://protege.stanford.edu/download/protege/4.3/installanywhere/Web_Installers/
:OBO style graph view
::http://code.google.com/p/obographview/
:Obsolete terms (installation can follow instruction of ‘OBO style graph view’ installation)
::https://github.com/balhoff/obo-actions/downloads

:ELK (OWL EL reasoner)
::http://code.google.com/p/elk-reasoner/downloads/detail?name=elk-distribution-0.3.2-protege-plugin.zip

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-07-04T16:50:47Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. It is '''FREE'''! 
----

'''Schedule'''

'''08:30-12:00 - theoretical session'''

:8:30 to 9:45 - Introduction (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9:45 to 10:30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk (Melissa Haendel)
::Technical and Outreach groups - 15 min talk (Melanie Courtot)

:10.15 to 10.45 - coffee break

:10:45 to 11:30 - OWL format (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)
::Including Semanticweb

:Discussion 30 min - help Protege installation available

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13:30-17:00 afternoon - application session'''

:13:30 to 14:30 - Basic Knowledge of Ontology (focusing on OWL) and Protégé (Alan Ruttenberg/Melanie Courtot)
::Including how to use OBO Foundry ontologies and starting to develop an ontology

:14:30 to 15:00 - Protégé plugins and ontology tools (Jie Zheng)
::Including Protégé plugins: URI Entity (show URI of a selected term), Obsolete terms, OBO style graph view, and URIgen (assign URI), and OWL difference tools

:15:00 to 15:30 - coffee break

:15:30 to 16:00 - Ontology quality checking and usage (James Overton)
::Including ontology consistency checking, reasoning, and querying (DL and SPARQL queries)

:16:00 to 16:30 - Reuse existing terms defined in external resources: MIREOT and OntoFox (Jie Zheng)

:16:30 to 17:00 - Add a set of terms into ontology: QTT and Ontorat (James Overton)

'''Recommended installation before the tutorial'''

:Protégé 4.3
::http://protege.stanford.edu/download/protege/4.3/installanywhere/Web_Installers/
:OBO style graph view
::http://code.google.com/p/obographview/
:Obsolete terms (installation can follow instruction of ‘OBO style graph view’ installation)
::https://github.com/balhoff/obo-actions/downloads

:ELK (OWL EL reasoner)
::http://code.google.com/p/elk-reasoner/downloads/detail?name=elk-distribution-0.3.2-protege-plugin.zip

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-07-04T16:49:45Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. It is '''FREE'''! 
----

'''Schedule'''

'''08:30-12:00 - theoretical session'''

:8:30 to 9:45 - Introduction (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9:45 to 10:30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group (Melissa Haendel) - 15 min talk (Melanie Courtot)
::Technical and Outreach groups - 15 min talk (Melanie Courtot)

:10.15 to 10.45 - coffee break

:10:45 to 11:30 - OWL format (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)
::Including Semanticweb

:Discussion 30 min - help Protege installation available

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13:30-17:00 afternoon - application session'''

:13:30 to 14:30 - Basic Knowledge of Ontology (focusing on OWL) and Protégé (Alan Ruttenberg/Melanie Courtot)
::Including how to use OBO Foundry ontologies and starting to develop an ontology

:14:30 to 15:00 - Protégé plugins and ontology tools (Jie Zheng)
::Including Protégé plugins: URI Entity (show URI of a selected term), Obsolete terms, OBO style graph view, and URIgen (assign URI), and OWL difference tools

:15:00 to 15:30 - coffee break

:15:30 to 16:00 - Ontology quality checking and usage (James Overton)
::Including ontology consistency checking, reasoning, and querying (DL and SPARQL queries)

:16:00 to 16:30 - Reuse existing terms defined in external resources: MIREOT and OntoFox (Jie Zheng)

:16:30 to 17:00 - Add a set of terms into ontology: QTT and Ontorat (James Overton)

'''Recommended installation before the tutorial'''

:Protégé 4.3
::http://protege.stanford.edu/download/protege/4.3/installanywhere/Web_Installers/
:OBO style graph view
::http://code.google.com/p/obographview/
:Obsolete terms (installation can follow instruction of ‘OBO style graph view’ installation)
::https://github.com/balhoff/obo-actions/downloads

:ELK (OWL EL reasoner)
::http://code.google.com/p/elk-reasoner/downloads/detail?name=elk-distribution-0.3.2-protege-plugin.zip

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-06-27T22:51:50Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

'''08:30-12:00 - theoretical session'''

:8:30 to 9:45 - Introduction (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9:45 to 10:30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group (Melissa Haendel)
::Technical and Outreach groups - 30 min talk (Melanie Courtot)

:10.15 to 10.45 - coffee break

:10:45 to 11:30 - OWL format (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)
::Including Semanticweb

:Discussion 30 min - help Protege installation available

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13:30-17:00 afternoon - application session'''

:13:30 to 14:30 - Basic Knowledge of Ontology (focusing on OWL) and Protégé (Alan Ruttenberg/Melanie Courtot)
::Including how to use OBO Foundry ontologies and starting to develop an ontology

:14:30 to 15:00 - Protégé plugins and ontology tools (Jie Zheng)
::Including Protégé plugins: URI Entity (show URI of a selected term), Obsolete terms, OBO style graph view, and URIgen (assign URI), and OWL difference tools

:15:00 to 15:30 - coffee break

:15:30 to 16:00 - Ontology quality checking and usage (James Overton)
::Including ontology consistency checking, reasoning, and querying (DL and SPARQL queries)

:16:00 to 16:30 - Reuse existing terms defined in external resources: MIREOT and OntoFox (Jie Zheng)

:16:30 to 17:00 - Add a set of terms into ontology: QTT and Ontorat (James Overton)

'''Recommended installation before the tutorial'''

:Protégé 4.3
::http://protege.stanford.edu/download/protege/4.3/installanywhere/Web_Installers/
:Entity URI (shows the URI of the last selected entity)
::http://code.google.com/p/co-ode-owl-plugins/wiki/URITools
:Obsolete terms
::https://github.com/balhoff/obo-actions/downloads
:OBO style graph view
::http://code.google.com/p/obographview/
:URIgen - assign URI to terms
::http://code.google.com/p/urigen/wiki/ProtegePlugin
:Pellet (OWL reasoner)
::http://clarkparsia.com/pellet/download/
:ELK (OWL EL reasoner)
::http://code.google.com/p/elk-reasoner/downloads/list

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-06-26T22:32:29Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

'''08.30-12.00 - theoretical session'''

:8.30 to 9.45 - Intro (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9.45 to 10.30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group, Technical and Outreach groups - 30 min talk (Melissa Haendel/Melanie Courtot)
::Discussion 15 min

:10.30 to 11.00 - coffee break

:11.00 to 11.45 - OWL format (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)
::Including Semweb

:Discussion 15 min

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13.30-17.00 afternoon - application session'''
:Protege setup (Melanie Courtot/Alan Ruttenberg)
::minimum import (BFO, IAO) with brief explanation of hierarchies/properties
:MIREOT/OntoFox
:Ontology view
:Testing tool
:Programmatic usage ( OWL API, LSW, Python, OWLTools, tawny-owl...)

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-06-24T21:17:45Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

'''08.30-12.00 - theoretical session'''

:8.30 to 9.45 - Intro (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9.45 to 10.30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk (Melissa Haendel)
::Technical group - 15 min talk (Melanie Courtot)
::Discussion (for both groups) 15 min

:10.30 to 11.00 - coffee break

:11.00 to 11.45 - OWL format (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)
::Including Semweb

:Discussion 15 min

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13.30-17.00 afternoon - application session'''
:Protege setup (Melanie Courtot/Alan Ruttenberg)
::minimum import (BFO, IAO) with brief explanation of hierarchies/properties
:MIREOT/OntoFox
:Ontology view
:Testing tool
:Programmatic usage ( OWL API, LSW, Python, OWLTools, tawny-owl...)

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-06-24T21:17:20Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

'''08.30-12.00 - theoretical session'''

:8.30 to 9.45 - Intro (1h) - 60 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk (Barry Smith)
::Being a Foundry/Library member - 30 min talk (Melissa Haendel)
::Discussion (for both groups) 15 min

:9.45 to 10.30 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk (Melissa Haendel)
::Technical group - 15 min talk (Melanie Courtot)
::Discussion (for both groups) 15 min

:10.30 to 11.00 - coffee break

:11.00 to 11.45 - OWL format (45 min) 30 min talk, 15 min discussion (Alan Ruttenberg)
::Including Semweb

:Discussion 15 min

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13.30-17.00 afternoon - application session'''
:Protege setup
::minimum import (BFO, IAO) with brief explanation of hierarchies/properties
:MIREOT/OntoFox
:Ontology view
:Testing tool
:Programmatic usage ( OWL API, LSW, Python, OWLTools, tawny-owl...)

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-06-20T23:39:56Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

'''08.30-12.00 - theoretical session'''

:8.30 to 9.30 - Intro (1h) - 45 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk
::Being a Foundry/Library member - 15 min talk
::Discussion (for both groups) 15 min

:9.30 to 10.15 - OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk
::Technical group - 15 min talk
::Discussion (for both groups) 15 min

:10.15 to 10.45 - coffee break

:10.45 to 11.30 - OWL format (45 min) 30 min talk, 15 min discussion
::Including Semweb

:Discussion 30 min

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13.30-17.00 afternoon - application session'''
:Protege setup
::minimum import (BFO, IAO) with brief explanation of hierarchies/properties
:MIREOT/OntoFox
:Ontology view
:Testing tool
:Programmatic usage ( OWL API, LSW, Python, OWLTools, tawny-owl...)

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-06-14T20:27:42Z

Mcourtot:

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

'''08.30-12.00 - theoretical session'''

:Intro (1h) - 45 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk
::Being a Foundry/Library member - 15 min talk
::Discussion (for both groups) 15 min

:OWL format (45 min) 30 min talk, 15 min discussion
::Including Semweb

:OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk
::Technical group - 15 min talk
::Discussion (for both groups) 15 min

:Discussion 30 min

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13.30-17.00 afternoon - application session'''
:Protege setup
::minimum import (BFO, IAO) with brief explanation of hierarchies/properties
:MIREOT/OntoFox
:Ontology view
:Testing tool
:Programmatic usage ( OWL API, LSW, Python, OWLTools, tawny-owl...)

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-06-14T16:31:57Z

Mcourtot: added agenda /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

[[File:[[File:Example.jpg]]]]== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

'''08.30-12.00 - theoretical session'''

:Intro (1h) - 45 min talk, 15 min discussion
::Goal and status of the Foundry - 30 min talk
::Being a Foundry/Library member - 15 min talk
::Discussion (for both groups) 15 min

:OWL format (45 min) 30 min talk, 15 min discussion
::Including Semweb

:OBO Foundry working groups (45 min) 30 min talk, 15 min discussion
::Editorial group - 15 min talk
::Technical group - 15 min talk
::Discussion (for both groups) 15 min

:Discussion 30 min

LUNCH BREAK - check your installation of Protege/plugins. No help available later!

'''13.30-17.00 afternoon - application session'''
:Protege setup
::minimum import (BFO, IAO) with brief explanation of hierarchies/properties
:MIREOT/OntoFox
:Ontology view
:Testing tool
:Programmatic usage ( OWL API, LSW, Python, OWLTools, tawny-owl...)

----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-06-14T16:20:55Z

Mcourtot: added James /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

08.30-12.00 - morning session
13.30-17.00 - afternoon session
----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''James Overton'''
:[http://knocean.com Knocean.com], Toronto, Ontario, Canada
:email:james@overton.ca
James Overton is a philosopher of science and an ontology development consultant. He contributes to the Basic Formal Ontology, has written code for OWLTools, and is an active developer of the Ontology for Biomedical Investigations (OBI). His current projects include working with the Immune Epitope Database and the Chemical Effects on Biological Systems database to develop ontology-based software tools and applications, writing automated build and testing software for OBI, and coordinating the OBI Core review process.

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-05-22T17:45:59Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial is collocated with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

08.30-12.00 - morning session
13.30-17.00 - afternoon session
----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-05-21T16:53:42Z

Mcourtot: /* OBO Foundry 101: Collaborative ontology development, tool support and semantic web */

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial will take place in association with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html here].
----

'''Schedule'''

08.30-12.00 - morning session
13.30-17.00 - afternoon session
----

'''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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-04-26T20:47:04Z

Mcourtot:

== OBO Foundry 101: Collaborative ontology development, tool support and semantic web ==

A tutorial from and about the Open Biological and Biomedical Ontologies Foundry

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial will take place in association with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html 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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-04-26T19:03:39Z

Mcourtot: added faculty

'''Date'''

July 7th 2013
----

'''Venue'''

This tutorial will take place in association with the [http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO conference] taking place in Montreal, Canada. Registration details are provided [http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/registration.html 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''' ''(in alphabetical order)''

'''Mélanie Courtot'''
:BC Cancer Agency
:email: mcourtot@gmail.com
Mélanie Courtot is a PhD student whose research focuses on improving vaccine adverse events reporting with the goal of classifying them automatically. 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 organized 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. She chaired the workshop session at ICBO 2012 and participated in several of them.

'''Melissa Haendel'''
:Oregon Health & Science University, Portland, OR
: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, Berkeley, CA
: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).

'''Bjoern Peters'''
:La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
:email:bpeters@liai.org
Bjoern Peters is working at the interface of computational and experimental biology. He is
Principal Investigator or Co-Investigator on multiple projects ranging from leading the
bioinformatics component of the Immune Epitope Database to designing and analyzing
clinical and basic studies of immune responses in the context of allergy, Dengue fever,
Tuberculosis and Smallpox vaccination. He is the elected representative of OBI in the OBO
foundry, and is actively contributing to several other ontologies. He has led several
workshops for users of the IEDB.

'''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.

'''Carlo Torniai'''
:Oregon Health & Science University, Portland, OR
:email:torniai@ohsu.edu
Carlo Torniai is currently working as ontologist and semantic architect in several projects such http://ctsaconnect.org , http://eagle-i.net where uses ontologies and semantic web technologies to integrate clinical and research data. He is an active developer of the eagle-i resource ontology (ERO), the Ontology for Biomedical Investigation (OBI), the Agent, Resources and Grants (ARG) ontology. He is member of the OBO Foundry operations Committee. Throughout his work experience he has been developing and using ontologies in several domains (multimedia, e-learning, biomedicine).

'''Jie Zheng'''
:Penn Center for Bioinformatics, Philadelphia, PA
:email:jiezheng@pcbi.upenn.edu
Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in ontology development (e.g. Ontology for Biomedical Investigation (OBI), Ontology for Parasite Lifecycle (OPL)) and making releases of new ontology versions (e.g. OBI, OPL). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations. She initiated and organized discussions among developers of OBO Foundry (candidate) ontologies (e.g. OBI, Evidence Code Ontology, Cell Ontology, Cell Line Ontology, Software Ontology, etc.) to align shared high level concepts to make ontologies interoperable and facilitate biomedical data integration.

2013 ICBO OBO tutorial

2013-04-26T18:58:25Z

Mcourtot: created page ICBO 2013 OBO tutorial

Main Page

2013-04-26T18:53:53Z

Mcourtot: /* Events */

The goal of the National Center for Ontological Research is to advance ontological investigation within the United States. NCOR serves as a vehicle to coordinate, to enhance, to publicize, and to seek funding for ontological research activities. It lays a special focus on ontology training and on the establishment of tools and measures for quality assurance of ontologies. NCOR provides ontology services to multiple organizations, including the US Department of Defense.

==Events==

*April 18, 2013 - Thursday, 9am-5pm
'''[http://ncor.buffalo.edu/oi2/ Ontologies for Information Integration]''', Buffalo, April 18, 2013. Please write to [mailto:jillian.pugliese@cubrc.org Jillian Pugliese] for registration details.
'''Press coverage of this event'''
:[https://www.buffalo.edu/news/releases/2013/04/012.html The challenges of big data for military, security and intelligence domains]
:[http://www.informationweek.com/government/security/military-intelligence-tries-to-tame-data/240152675 Military Intelligence Tries To Tame Data 'Monster']

*May 13-14, 2013
'''[http://ncorwiki.buffalo.edu/index.php/2013_BFO_Meeting Basic Formal Ontology Meeting]''', Buffalo. Please write to [mailto:phismith@buffalo.edu Barry Smith] for registration details.

*May 15-16, 2013
'''[http://wiki.plantontology.org/index.php/PRO-PO-GO_Meeting PRO-PO-GO Ontology Workshop]''', Buffalo. Please write to [mailto:phismith@buffalo.edu Barry Smith] for registration details.

*June 10-14, 2013
'''[http://www.bu.edu/computationalimmunology/summerschool/index.html Summer School for Quantitative Systems Immunology], Institute for Computing and Computational Science and Engineering, Boston University, Boston, MA.
For session on Immunology Ontology by Lindsay Cowell and Barry Smith, Tuesday June 11, 2013 see [[Immunology Ontology | here]].

*July 7-9, 2013
'''[http://ncorwiki.buffalo.edu/index.php/2013_ICBO_OBO_tutorial OBO Foundry 101: Collaborative ontology development, tool support and semantic web]''', Montreal. Co-located with the Fourth International Conference on Biomedical Ontologies ([http://www.unbsj.ca/sase/csas/data/ws/icbo2013/ ICBO2013])

== [[Past Events]] ==

==News==

[http://xbrl.squarespace.com/journal/2013/2/23/advantages-of-financial-report-ontology-in-accounting-resear.html Advantages of Financial Report Ontology in Accounting Research]

[http://ontology.buffalo.edu/IMMPORT/UB-Press-Release-2013.pdf UB Ontologists Win Bioinformatics Integration Award to Support National Institutes of Health]

[[Announcing Clinical and Translational Science Ontology Affinity Group]]

[http://www.sciencedaily.com/releases/2012/08/120820161058.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+(ScienceDaily%3A+Latest+Science+News) Information Overload in the Era of Big Data]

[http://www.kurzweilai.net/botanists-building-ontologies-to-cope-with-information-overload Botanists building ontologies to cope with information overload]

[[UB Applied Informatics Portal]] unveiled.

==Tutorials and Courses==

[[How to Develop and Use OBO Foundry Ontologies]], Tutorial and Workshop at ICBO, Graz, Austria, July 21, 2012

[[Basic Formal Ontology 2.0: Tutorial at ICBO/FOIS]], Graz, Austria, July 25, 2012

[[Introduction to Protégé]], Tutorial, Buffalo, NY, August 11-12, 2012

[[Basic Formal Ontology 2.0]], Tutorial, Buffalo, NY, August 18-19, 2012

[[Problems in Ontology]], Class, Buffalo, NY, Mondays from 4-6pm, August 29 - December 5, 2012

[[Ontological Engineering]], Class, Department of Industrial and Systems Engineering, University at Buffalo, NY, Mondays from 4-7pm, August 26 - December 2, 2013

==Defining Ontology==

An ontology is a representation of some part of reality, (e.g. medicine, social reality, physics, etc.). Smith states that: “Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality…Ontology seeks to provide a definitive and exhaustive classification of entities in all spheres of being.”1 To be an accurate representation of reality an ontology includes the types of entities and events in a given domain (along with their definitions) arranged in a hierarchical structure, along with relations (such as part-of, depends-on, caused-by, etc. where necessary). Ontologies enable the formulation of robust and shareable descriptions of a given domain by providing a common controlled vocabulary for doctrine writers, IT Developers, and war-fighters alike, thereby allowing these disparate communities to communicate with each other. An ontology should be a shared resource between communities, and its continued collaborative development should support the integration of information and facilitate knowledge discovery.2 These two goals are realized by ensuring wide dissemination of the ontology, so that it will be used by many stakeholders, and its terms will be correspondingly familiar and readily used for search.

==Documents==

Semantic Enhancement: [[Distributed Development of a Shared Semantic Resource]]

== Suggested Reading ==

[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]

[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Coordinated Evolution of Biomedical Ontologies]

[[Avoiding Perspective-Relative Silos]]

[http://ceur-ws.org/Vol-555/paper5.pdf Universal Core Semantic Layer]

== Ontology Videos by William Mandrick ==

[http://www.youtube.com/watch?v=fB6BjF4lAQ4&feature=related A Repeatable Process for Ontology Development]

[http://www.youtube.com/v/Z5o1SpPqNrA Avoiding Semantic Stovepipes: Five Ontological Principles for Interoperability]

[http://www.youtube.com/watch?v=JkQG1_gsXtc War-Fighter Ontology]

[http://ncorwiki.buffalo.edu/index.php/Mandrick_Vita William Mandrick]

User:Mcourtot

2013-04-26T18:50:47Z

Mcourtot:

More information [http://purl.org/net/mcourtot here]

User:Mcourtot

2013-04-26T18:50:23Z

Mcourtot:

More information at [http://purl.org/net/mcourtot]

User:Mcourtot

2013-04-26T18:50:02Z

Mcourtot: added user page

More information at [[http://purl.org/net/mcourtot]]

How to Develop and Use OBO Foundry Ontologies

2012-07-25T16:36:24Z

Mcourtot: adding personal details

'''Date'''

July 21, 2012, Morning
----

'''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].
----

'''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

----

'''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.

----
'''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.

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

----
'''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.

ICBO Conference Logistics

2011-07-20T15:42:02Z

Mcourtot:

'''Logistics Links'''

*[http://www.marriott.com/hotels/travel/bufny-buffalo-marriott-niagara/ Conference venue]
*[http://icbo.buffalo.edu/AreaHotels.pdf Area hotels]
*[http://www.buffaloairport.com/ Buffalo airport]
*[http://www.cse.buffalo.edu/restaurant.guide/ Buffalo restaurants]
*[http://www.google.com/search?q=niagara+falls&hl=en&prmd=ivnsbm&tbm=isch&tbo=u&source=univ&sa=X&ei=MJHaTdPMB5PEgAes4YxY&ved=0CHQQsAQ&biw=1280&bih=647 Niagara Falls]

'''Registration Desk'''
Badges, Programs and Proceedings may be picked up at the Registration desk located near the Ballroom (1st floor) of the Marriott (Conference) Hotel. Registration desk hours are as follows:

*Tuesday, July 26: 8:00am – 2:00pm
*Wednesday, July 27: 8:00am – 2:00pm
*Thursday, July 28: 7:15am – 12:00pm

'''Special Topic Sessions'''

A block of 2 hours, from 3.30 to 5.30pm, has been set aside on Day 2 of the ICBO program - Friday July 29th - to allow scheduling of parallel sessions on special topics.
Persons wishing to organize special topic sessions at this or other times within the course of the meeting are invited to post announcements here:

*1. Day 2 3.30-4.30pm: '''Working Session on IAO''', the Information Artifact Ontology. Convener: Melanie Courtot <mcourtot@gmail.com>. Please check the agenda and register on the [http://code.google.com/p/information-artifact-ontology/wiki/WorkingSessionICBO2011 IAO wiki]
*2. Day 2 4.30-5.30pm: '''Working Session on OGMS''', the Ontology for General Medical Science. Convener: Albert Goldfain <agoldfain@blue-highway.com>. Venue