OBI Tutorials


 * 1) OBI Tutorial at ICBO 2012, Graz, Austria
 * 2) OBI Tutorial at ICBO 2011, Buffalo, NY
 * 3) OBI Tutorial at ICBO 2009, Buffalo, NY
 * 4) OBI core
 * 5) Technique Tutorials

Tutorial_ICBO2012
All the slides and related documents are available under the OBI SVN: OBI tutorial July 2012 ICBO

Abstract

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. The application use cases will cover various biological and medical investigations of interest to different communities, such as those performing functional genomics or clinical investigations. 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 Quick Term Template (QTT), how to submit term requests, and how to generate an OBI view for specific applications. 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.

Introduction To OBI

Presenter: Christian Stoeckert

Content: Overview of OBI including details of OBI core (Reference 1)

Hands-on Exercises: Accessing and browsing OBI and associated resources.

Representation Of Biomedical Investigations Using OBI

Presenter: Jie Zheng

Content: The ontology-base modeling of investigation will aid understanding of each step of an experiment. This modeling also provides a map of biomedical data to Resource Description Framework (RDF) triples which in turn facilitates data integration and enables SPARQL queries. A biomedical investigation about host and parasite interactions will be used as an example (Reference 2).This part will also cover the relationship between OBI and the Evidence Code Ontology (ECO).

Hands-on Exercises: Generate a community view of OBI for a specific application using Ontodog.

Ontology Development By Using OBI As A Source Ontology

Presenter: Yongqun "Oliver" He

Content: Development of the Vaccine Ontology (VO) will be used to show how to develop an application ontology that is based on OBI. It will cover two strategies, MIREOT (importing external ontology terms) and QTT (adding multiple terms in an ontology), which were developed by OBI developers to facilitate ontology development. Hands-on Exercises: Reuse OBI terms in VO based on MIREOT using OntoFox and add a set of new terms based on QTT using Ontorat.

Tutorial_ICBO2011
All the slides and related documents are available under the OBI SVN: OBI tutorial July 2011 ICBO

Abstract 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

OBI Overview and IEDB

Presenter: Bjoern Peters

Content: Introduction to OBI and representation of experiments mapping targets of immune responses in IEDB (slides)

OBI application: EuPathDB

Presenter: Jie Zheng

Content: EuPathDB annotation of genomic-scale datasets associated with eukaryotic pathogens including ontology driven isolate submission form design (slides)

OBI application: eagle-i

Presenter: Carlo Torniai

Content: eagle-i representation of research resources (slides)

OBI application: ISA Tools

Presenter: Bjoern Peters (present for Philippe Rocca-Serra who prepared the slides)

Content: ISA tools and annotation of functional genomics experiments (slides)

OBI application: Evidence Code

Presenter: Marcus Chibucos

Content: Cross references to OBI within the Evidence Code Ontology (slides)

Hands-on Exercise


 * Editing OBI

Presenter: Bjoern Peters (slides)


 * MIREOT And Ontology Community View

Presenters: Yongqun (Oliver) He & Jie Zheng (slides)


 * QTT And Design Patterns

Presenter: Carlo Torniai (slides)