2014 ICBO OBO Workshop

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

Hands-On with Open Biological and Biomedical Ontologies

OBO developers use online development workflows every day, but there is no substitute for face-to-face communication. This participant-driven workshop is open to developers and users of any OBO project. We will focus on technical problems we are facing, aiming for concrete solutions that we can begin to implement during the session. The primary topic will be improving OBO development workflows, but participants will be invited to suggest their own topics and benefit from the collective experience of the workshop attendees.

Summary

The Open Biological and Biomedical Ontologies (OBO) embrace open source development practices and the online tools that support them, including public mailing lists, issue trackers, wikis, teleconferences, etc. Despite all these tools, there is no substitute for face-to-face meetings and the rich communication they allow. The OBO Technical Workshop is an opportunity for developers and users of any OBO project to meet face-to-face, discuss technical problems, and start solving them. By sharing experience, advice, code, and best practices with a group of like-minded developers, we aim to generate small breakthroughs that push projects forward, and to build foundations for future collaboration.

The agenda for this workshop will be driven by the participants. While we hope to have both experts and beginners present, we expect all attendees to be active participants in the workshop. Proposed topics will be shared in advance and goals will be set at the beginning of the workshop. The focus will be on problems (1) with a technical element, and (2) for which we can make concrete progress during the session. By the end of the session we will have deliverables such as requirement documents, new code, new or enhanced ontologies, tracker items, etc.

The primary topic for the workshop is improving development workflows for OBO projects. The outcome will be a list of requirements and a plan for improvements. We will also discuss and create tracker items for current tools. Other topics may include:

  • getting started with a new application ontology
  • improving reasoner or query performance for an ontology project
  • improving domain modelling using OBO ontologies
  • improving OBO tools, such as OWLTools
  • improving OBO infrastructure
  • debugging software installation and configuration problems
  • tackling tricky tracker items

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.

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.