Welcome to the tutorial website for the tutorial "Bio-ontologies and their role in analyzing personal genome data". The tutorial will initially be presented at ECCB 2016 on 4 September 2016.
Aim
The aim of the tutorial is to introduce recent advances in using biomedical ontologies for data analysis, in particular for the interpretation of personal genome data and identifying causal variants underlying a phenotype or disease.
Target audience
The tutorial is aimed at computational biologists and (bio-)medical informaticians interested in incorporating ontologies, in particular phenotype ontologies, into their analysis pipelines. Clinicians, biologists, and pharmacologists with basic informatics expertise will also find the course accessible and useful.
Presenters
- Dr Paul N Schofield, University Reader in Biomedical Informatics, Department of Physiology, Development and Neuroscience, University of Cambridge
- Prof Robert Hoehndorf, Assistant Professor of Computer Science, Computational Bioscience Research Center, King Abdullah University of Science and Technology
- Mr Luke Slater, College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham
- Ms Imene Boudellioua, PhD student, Computational Bioscience Research Center, King Abdullah University of Science and Technology
Tutorial outline
| Time | Topic | Presenter | Slides | Lecture materials, additional reading |
|---|---|---|---|---|
| 9:00-9:30 | Welcome and introduction; the role of ontologies in biology, biomedicine and disease genetics | Paul Schofield | tbd | The role of ontologies in biological and biomedical research: a functional perspective |
| 9:30-10:00 | Ontology Basics: classes, relations, axioms; relations between ontologies and graphs; the Web Ontology Language (OWL) | Robert Hoehndorf | tbd | Relations as patterns: bridging the gap between OBO and OWL |
| 10:00-10:30 | Finding, building and using ontologies (1): ontology repositories | Luke Slater | tbd | Aber-OWL: a framework for ontology-based data access in biology |
| 10:30-11:00 | Coffee Break | all | ||
| 11:00-11:45 | Finding, building and using ontologies (2): editing ontologies with Protege; reasoning with ontologies | Luke Slater | tbd | Aber-OWL: a framework for ontology-based data access in biology |
| 11:45-12:30 | Phenotype ontologies: PATO and EQ | Paul Schofield | tbd | Building mouse phenotype ontologies |
| 12:30-13:30 | Lunch break | All | Diet and Weight Management | |
| 13:30-14:15 | Informatics of phenotype ontologies, computational analysis of phenotype data | Robert Hoehndorf | Lecture slides | PhenomeNET: a whole-phenome approach to disease gene discovery |
| 14:15-15:00 | The role of ontologies in the analysis of personal genome data | Imene Boudellioua | tbd | Improved exome prioritization of disease genes through cross-species phenotype comparison |
| 15:00-15:30 | Coffee Break | all | ||
| 15:30-16:15 | Complex diseases, physiology, disease modules and networks | Paul Schofield | tbd | |
| 16:15-17:00 | Discussion: discuss problems brought up by the audience; ontologies and the EHR; ontology mapping | all | tbd |
Participant Requirements
All participants must have a laptop with Protege installed and a web browser to access BioPortal and AberOWL.
Materials
Here you will soon find all materials developed for the tutorial, including slides, lecture notes, software tools and reading material.
Slides
Lecture slides are at http://aber-owl.net/aber-owl/diseasephenotypes/phenotype-tutorial/
Software and libraries
Working with ontologies:
Ontology Matching:
Analyzing genomic data with ontologies:
Libraries, mainly for developers (optional, not required for the tutorial):
Additional reading material
Contact
For any questions related to the tutorial, or requests for topics to cover in the course, please send a mail to phenotype-ontology-tutorial@googlegroups.com. The mailinglist will remain active after the tutorial and can be used for post-tutorial discussions.