Disease Ontologies and Information Workshop

19th – 20th June 2008

Workshop Dates: 19th – 20th June 2008

Motivation

Health research generally as well as target driven drug discovery requires researchers in industry¹ to identify those genes which are not only amenable to intervention but also to be disease relevant. Hence, disease information linked to genetic information is of high importance. While gene information is now in good shape and structured, disease information is widespread and diffuse and difficult to access from a bioinformatics point of view. Some databases exist on the web with different scope and content.

Links between genes and diseases are of major interest in industry target identification and also links between compounds and diseases. The workshop will help to shed more light on the disease – gene links.

Scope

The workshop shall focus on the question: where we can find good information about diseases, especially diseases with known or suspected linkage to genes, and integrate this with information available in biomedical informatics data resources. 

Furthermore, how can we best link this information to disease models in animal and in particular mouse phenotypes, where such models are used as a proxy for disease information in humans.

Finally, the outcome from the workshop will be communicated into the ELIXIR WP7 roadmap which is focussed on biomedical standards and ontologies (www.elixir-europe.org).

Discussion topics and areas are:

• What approaches are currently being made in the community to address disease ontologies orchestration?
• What is the linkage between bioinformatics resources and disease/medical information?
• Which genes are involved in a disease and how can this information be accessed?
• Which diseases share common symptoms (hierarchical structure of diseases) or are otherwise related?
• Can animal model systems be ontologised in a meaningful manner to allow cross-platform or cross-species comparisons.
• How can animal model phenotypes be related to human disease information to make them more useful and amenable to automatic interrogation. Can we establish something like “disease ontologies”?
• Most generally, how do we overcome the historical poor linkage between bioinformatics data and disease and medical information?

Organisers and contacts:

The Coordinator of the EBI Industry Programme is Dr. Dominic Clark (EMBL-EBI).

The Scientific Coordinator for this workshop is Prof. Michael Ashburner (University of Cambridge and former joint head of EMBL-EBI).

The programme advisors are Dr. Ian Harrow (Pfizer), Ms. Wendy Filsell (Unilever), Dr. Matt Hall (GSK) and Dr. Bertram Weiss (Bayer Schering Pharma).

Please send any questions regarding the strategic intent and programme to Dominic Clark.

Time	Item	Location (status)
Thursday 19th June 2008
9.30	Registration and Tea/Coffee	Foyer, Wellcome Trust Conference Centre, Hinxton
10:15	Wellcome and Background to Meeting (Prof. Janet Thornton,  & Dr. Dominic Clark, EMBL-EBI)	Francis Crick Auditorium (Open meeting)
10.30	“Ontologies for Biologists – The Promise and the Reality” (Prof. Michael Ashburner, U. Cambridge).
10.50	The OBO (Open Biomedical Ontologies) Foundry and PATO: Phenotype And Trait Ontology (Prof. Michael Ashburner, U. Cambridge.)
11.10	“Towards an Open Source Disease Ontology” Prof. Warren Kibbe (Northwestern University)
11.50	Tea/Coffee
12.20	Mouse Genome Informatics Database: Phenotypes and Phenotype Ontology (Prof. Janan Eppig , Jackson Lab)
12.50	Discussion
13.10	Lunch for workshop attendees	WT Conference Centre Restaurant
14.20	Presentations by Industry Partners, Dr. Bertram Weiss, Bayer Schering Pharma , Dr Ian Harrow Pfizer , Dr. Andrew Garrow, Unilever	IT Training Room, EBI East Wing (by invitation)
15.00	Prof. Giorgio Valle (University of Padua): Gene Ontology of CNS and Disease Ontology.
15.20	The GEN2PHEN Project – Harnessing the Web for Genomics (Prof Anthony Brookes, U. Leicester).
15:40	Discussion
16:00	Tea/Coffee
16:20	Healthgrid, the EU SHARE project and the EMBRACE project (Dr. Vincent Breton, CNRS, Clermont-Ferrand)
16:40	Disease Ontologies and their Relation to Genes (Dr Anita Burgun, University of Rennes)
17:00	Developing an Application Ontology for Annotation of Experimental variables across HTP data sets (Helen Parkinson and James Malone, EMBL-EBI)
17:20	Summary and discussion
17:45	Bus transfer to Alimentum Restaurant, Hills Road, Cambridge
18.30	Pre-dinner drinks followed by dinner at Alimentum Restaurant (please note that the restaurant is only a short walk from Homerton College)
Friday 20th June
09.00	Transport from Homerton College to WT Genome Campus
09.30	Tea/Coffee	IT Training Room, EBI East Wing (by invitation)
09.45	The Influenza Infectious Disease Ontology (I-IDO) (Dr Joanne Luciano, Mitre Corporation)
10.05	UniMed: Mapping Protein Information to Disease Terminologies. (Dr. Anne-Lise Veuthey, Swiss Institute of Bioinformatics)
10.25	Text Mining and Ontologies: an analysis of all gene-disease associations over Medline based on GO terms (Dr. Dietrich Rebholz-Schuhmann, EMBL-EBI)
10.45	Observations on presentations and themes by invited discussants.
11.20	Tea/Coffee
11.45	Discussion led by industry partners and documentation of Actions/Next Steps (Dr. Dominic Clark)
12:30	LUNCH
13:45	Introduction to ELIXIR Project WP7 (Prof. Amos Bairoch)
14.00	Facilitated Discussion (Dr. Dominic Clark)
15.30	Documentation of input from workshop into ELIXIR WP7 Roadmap document (Prof. Amos Bairoch & Prof. Michael Ashburner)
15:45	Tea/Coffee and Departures