Interoperability and the Gene Regulation Knowledge Commons
At this Workshop, producers and users of Gene Regulation Knowledge Commons resources will assess the state of the art in curation, representation, archiving, and sharing of information about gene regulatory processes; as well as its subsequent use in computational biology applications. Discussions will focus on the breadth of information types that need to be annotated with the help of ontologies, and to what extent ontologies, representation formats and data exchange mechanisms are mature enough to establish one interconnected and interoperable information pipeline that satisfies end users.
- Pedro Monteiro
Monday, 23 October 9:00 – 11:00 Management Committee meeting:
- Review of current activities, future plans
- Mandate of Core Group
- Additional WG Co-leaders
- The website
- The Ljubljana meeting (brief scaffold needed)
- Any other business (based on agenda announcement)
11:30 – 13:00 Workshop Kickoff
- Actions initiated at the Malta meeting and how they set the stage for the Lisbon workshop
- International developments in the area of curation
- Expectations for this workshop
13:00 – 14:00 Lunch 14:00 – 15:30 Needs of Users of the KC: computational biologists, tool builders, systems modellers
- From modelling by reading to modelling by accessing databases
- Core knowledge and contextual knowledge
- Formalizing these types of knowledge
- Sharing knowledge
15:30 – 16:00 Break 15:45 – 17:30 Vision of Producers of the KC: curators, database managers, ontologists, text miners
- What is practiced, what is possible
- How can user demands be met
- What is good, what needs to change
Tuesday, 24 October 09:00 – 13:00 Defining concepts essential to Gene Regulation
- Types of objects used in the domain of gene regulation (TF, TF binding site, target gene, region, peak, cis-regulatory module, motif, …)
- Resources / objects available in existing databases (JASPAR, Hocomoco, RegulonDB, ReMap, EPD, ENSEMBL, UCSC Genome Browser, …).
- Resources / objects produced by existing tools (RSAT, cisTargetX, …).
- Discussion: how to represent the complexity of regulation?
- Context-dependency: cell type, tissue, developmental stage, culture conditions, …
- Combinatorial effects (combinations of factors act on combinations of sites and regulate genes, structural interactions, …)
14:00 – 17:00 Action points
You can find the report of the workshop in the following link