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Sarajevo

Sarajevo Workshop

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Short description:

Goals of the meeting

Discuss the status of the new ontology development initiatives to provide new use cases for the Gene Regulation Knowledge Commons. Ontologies to be discussed include: Sequence Ontology, Gene Regulation Ontology, Gene Regulation Application Ontology, Gene Ontology. In addition, the status of data standards and exchange mechanisms will be discussed: the Minimum Information about a Molecular Interaction Causal Statement (MI2CAST), Causal JSON / MI JSON, and CausalTAB/PSICQUIC.

Local organiser(s):
  • Lejla Kapur Pojskić
Agenda:

Tuesday, 05 November

The Management Committee:

  • 09:00 – 09:15: Welcome and opening of the Workshop
  • 09:15 – 11:00: Management committee meeting
Main Event: Hotel Europe
Plenary 1
  • 11:00 – 11:30: Coffee break
  • 11:30 – 12:00: Setting the stage for the Workshop: what do we want to achieve?
  • 12:00 – 12:30: Plenary discussion. Aims for the remaining period
  • 12:30 – 13:30: lunch
  • 13:30 – 14:15: Joint session WS themes: ontologies and data sharing
  • 13:30: GRO and GRAO
  • 13:45: MI2CAST status
  • 14:00: Data sharing. Case of Signor. Make PSICQUIC dev topic of Training School?
Breakouts
  • 14:15 – 16:30, Bo1: WG1: GRO/GRAO. Status of Ontologies: which ones to take terms from? Which ontology sub=branches should be taken to connect into GRAO? Example Application Ontologies: Gene Expression Knowledge Base; Cell Cycle Ontology; Minutes
  • 14:15 – 16:30, Bo2: WG4: Data exchange and standards. Minutes. Final 30 minutes: MI2CAST paper discussion?
  • 15:00 – 15:30: Coffee break
Plenary 2
  • 16:30: Reporting on Breakouts
  • 17:00 – 17:30: Status GO/SO/MSO
  • 19:00: Workshop dinner

 

Wednesday, 06 November

Plenary 3
  • 09:00 – 09:15: VSM and GO-CAM
  • 09:15 – 09:30: MI CV vs. RO & Signor to GO-CAM
  • 09:30 – 09:45: Summary previous training school – workflows
  • 09:45 – 10:00: TF-TGs from computational prediction
  • 10:00 – 10:15: Automating FAIR Scores and Inferring Semantic Information from text
  • 10:15 – 10:30: Discussion
  • 10:30 – 11:00: Coffee break
Plenary 4
  • 11:00 – 12:30: Bo3: Mobilising GREEKC relevant data: Relevant data resources, plan to approach them.

In this session, we will review resources with data relevant for the Gene Regulation Knowledge Commons, assess to what extent their data is ‘computationally available’, what ontologies are in place to support their querying, and what web service could be devised to improve their data availability.

  • 12:30 – 13:30: lunch
Plenary 5
  • 13:30 – 15:00: Mobilising GREEKC relevant data: Producing a KC for computers: the target for a Training School? For  STSMs? Use cases
  • 15:00 – 15:30: Coffee break
  • 15:30 – 17:00: Wrap-up, next steps
  • 15:30 – 16:15: Next workshops and Training School topics. Writing a joint GREEKC progress paper
  • 16:15 – 17:00: Wrap-up, Action points
Workshop Report:

Summary Results

An overview of the GRKC was created, including some details about the accessibility (See Minutes). Next activities:

  • Organize a dedicated WG1 discussion on GRAO, early 2020.
  • Organize a dedicated WG2 curation session for dbTF work, early 2020
  • Plan the next workshop in Rende, Italy

 

Group work in Sarajevo