2013 ICBO OBO tutorial

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

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Venue

This tutorial is collocated with the ICBO conference taking place in Montreal, Canada. Registration details are provided here.

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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, 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 Semanticweb

Discussion 15 min

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)

Including how to use OBO Foundry ontologies and getting start 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

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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.

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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.

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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

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.