2014 ICBO OBO Tutorial

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A tutorial at the 5th International Conference on Biomedial Ontologies in Houston, October 6-9 2014.

Getting Things Done with Open Biological and Biomedical Ontologies

In this hands-on tutorial participants will learn about the tools, techniques, and best practices available for developing and working with OBO projects. We will cover three main topics: the use and reuse of ontologies; processing data with ontologies; and development workflows, including updates, testing, and managing releases. Participants will work with us through a range of real-world examples using OBO Foundry and Library ontologies.

Summary

The Open Biological and Biomedical Ontologies (OBO) provide a suite of interoperable ontologies for biology and medicine. Close collaboration between diverse projects brings many benefits to ontology users, but it also requires commitment to standards and disciplined development practices. In this hands-on half-day tutorial we will cover a wide range of best practices for using and contributing to OBO projects. Participants will be asked to bring their laptops and work with us through a series of real-world examples of ontology development focused on OBO Foundry and Library ontologies, covering these topics:

  • A brief introduction to the OBO Library and to the OBO Foundry
  • Using and Reusing Ontologies
    • assessing ontologies for reuse
    • importing single terms with MIREOT
    • importing sets of terms using OntoFox
    • importing lists of terms with Quick Term Templates
    • importing full ontologies in Protégé
    • extracting and importing ontology modules
  • Processing Data with Ontologies
    • converting relational data to RDF
    • using SPARQL with OWL ontologies
    • converting instance data to OWL
    • querying instance data with DL Query and SPARQL
    • best practises for reasoning over large data sets
  • Updating, Testing, and Releasing Ontologies
    • tracking changes with ontology diff tools
    • filing effective term requests and bug reports with issue trackers and TermGenie
    • best practices for committing changes to an ontology
    • quality checking for ontologies
    • unit testing for ontologies
    • continuous integration with Jenkins
    • release workflows with OWLTools
    • publishing ontologies
    • managing PURLs

Organizers

Mélanie Courtot

BC Cancer Agency
mcourtot@gmail.com

Mélanie Courtot is a PhD Candidate 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 co-organized the OBO tutorial at ICBO 2013.

Melissa Haendel

Department of Medical Informatics and Epidemiology, Oregon Health and Science University
haendel@ohsu.edu

Melissa Haendel has led 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, ERO). 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.

James A. Overton

Knocean.com, Toronto, Canada
james@overton.ca

James Overton is a philosopher of science and an ontology development consultant. He is also the release manager for the Ontology for Biomedical Investigations (OBI) and contributor to several other OBO ontologies. James has built ontology testing and release tools for OBI and contributed to OWLTools development. 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.

Bjoern Peters

La Jolla Institute for Allergy and Immunology
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
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
phismith@buffalo.edu

Barry Smith is Professor of Philosophy, Biomedical Informatics, 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, a PI of the Protein Ontology and Infectious Disease Ontology projects, and head of the ontology team for the NIAID Bioinformatics Integrating Support Contract (BISC). He is a Coordinating Editor of the OBO Foundry initiative, and plays a guiding role in Basic Formal Ontology, the Ontology for General Medical Science, the Environment Ontology, and the Plant Ontology initiatives.

Jie Zheng

Department of Genetics, Perelman School of Medicine, University of Pennsylvania
jiezheng@upenn.edu

Jie Zheng is interested in ontology-based approaches to biomedical metadata analysis and biomedical data integration including ontology development and data modeling. She has contributed to the development of several ontologies such as the Ontology for Biomedical Investigations (OBI), the Ontology of Biological and Clinical Statistics (OBCS) and application ontologies based on OBI (Beta Cell Genomics Ontology (BCGO) and biobank ontology). She has taken responsibility for making releases of several ontologies, such as OBI, OBCS, and BCGO. She has been involved in the development of ontology subset extraction and Basic Formal Ontology version conversion tools. She is currently working on biosample metadata standardization and biomedical data integration from different resources with various representations and annotations based on OBI semantic framework.