OBI: A shared ontology for representing biomedical studies and resources

A tutorial at the International Conference on Biomedical Ontology (ICBO 2011)

27 July 2011, Buffalo, USA,
12:30 - 4:00 pm

Instructors:
Bjoern Peters
Jie Zheng
Philippe Rocca-Serra
Carlo Torniai
Melissa Haendel

Overview

The Ontology for Biomedical Investigations (OBI) aims to represent all elements of investigations such as assays, instruments or subject enrollment criteria. This tutorial will provide training on how to use OBI in specific applications and contribute to OBI development. We will present the following current applications for OBI: 1) representation of experiments mapping targets of immune responses in IEDB 2) EuPathDB annotation of genomic-scale datasets associated with eukaryotic pathogens 3) eagle-i representation of research resources 4) ISA tools and annotation of functional genomics experiments 5) Cross references to OBI within the Evidence Code Ontology. While going through these use cases, we will discuss: OBI design principles and the underlying Basic Formal Ontology, the Minimum Information to Reference an External Ontology Term (MIREOT) methodology, how to use the QuickTerm Template, how to edit OBI and submit term requests. This tutorial will start with a general overview of OBI followed by a presentation of practical applications leading to a hands-on session where attendees can practice using tools and applying principles introduced in the use cases. Attendees are encouraged to bring their own issues that can be addressed, working directly with the OBI developers.

This half-day tutorial will demonstrate real-world applications of OBI to

Coordinate large scale knowledge base creation and management across biomedical communities
Add semantic capabilities to existing databases
Drive data collection from experimentalists
Coordinate the development of existing ontologies

Tutorial requirements and preparation

Participants are expected to have their own laptop in order to actively participate in the hands-on session. Shortly before the workshop, a list of suggested reading material and software that should be installed prior to the tutorial will be provided.