Ontologies for the Gene Regulation Knowledge Commons, and Database 'FAIRness'
At the Hinxton workshop, we focus on the ontologies that will underpin the annotation of gene regulation knowledge, and various aspects related to the sharing of the Gene Regulation Knowledge Commons (GRKC) content. The Gene Regulation Ontology, published in 2008, is being carefully assessed for its relevance to the needs of a comprehensive GRKC and will be updated to the Gene Regulation Application Ontology GRAO. For sharing the GRKC content the newly established CausalTab data exchange format will be discussed, as well as an updated PSICQUIC webservice. Finally, we have teamed up with FAIR consortium members and will organize a FAIRness assessment of databases that can be considered as part of the GRKC, with Database engineers testing FAIR aspects using tooling newly developed by the FAIR partners.
- Sandra Orchard
09:00 – 11:00: Management committee meeting – Garden Room/EBI
11:00 – 12:30: Plenary meeting – Workshop presentations of invited speakers – Garden Room/EBI
|09:00 – 11:00||Management Committee meeting||Martin Kuiper|
|11:00 – 12:30||Plenary Workshop|
|11:00 – 11:30||FAIR||Michel Dumontier|
|11:30 – 12:00||Sequence Ontology||Karen Eilbeck|
|12:00 – 12:30||Relation Ontology||Chris Mungall|
Participants: MC members, invited speakers, external experts
12:30 – 13:30: lunch
13:30 – 16:30: Breakout sessions 1, 2: FAIR; GRKC Ontologies – Garden Room EBI; Green Room Hinxton Hall
16:30 – 17:30: Reporting of progress
Workshop sessions continued – Garden Room EBI; Green Room Hinxton Hall
09:00 – 12:30: Breakout sessions 3, 4
12:30 – 13:30: lunch
13:30 – 16:30: Breakout sessions 5, 6
16:30 – 17:30: Reporting of progress, Action points
More details to be announced
The Wellcome Trust Conference Centre, The Wellcome Trust Genome Campus
Hinxton, Cambridgeshire, CB10 1RQ
Tel: +44 (0)1223 495000
Fax: +44 (0)1223 495114
or a location of your choice in Cambridge
- Plans for the development of the Gene Regulation Application ontology were developed.
- The results of a text mining effort from NTNU and BSC were presented, now available as ExTRI data (www.extri.org)
- A series of DNA binding transcription factor cartoons, with proteins and DNA associating in a wide range of regulatory configurations, were discussed for their use in building knowledge models, resulting in a paper for a BBA special issue.