February 15, 2011

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Agenda - BioGRID and WB interaction meeting.

item 1 - Overall vision of the collaboration
What are the goals and envisioned data flow. This will be refined over time.
item 2 - Mapping of interaction terms between WB and BioGRID. (Attached Excel and PowerPoint)
Possible mappings – problems and solutions
Development of an Interaction Ontology?
item 3 - Directionality of interactions.
Bait/Hit = effected/effector? or other way?
Non-directional interactions?
More than 2 genes involved?
item 4 - High throughput vs Low throughput?
item 5 - Going forward - work flow.


Notes

item 1 - Overall vision of the collaboration
  1. We envision a pipeline whereby BioGRID and WB can exchange interaction curation information via mapping of the database objects between the two groups.
    • Ideally we would want to minimize overlap in our efforts
item 2 - Mapping of interaction terms between WB and BioGRID. (Attached Excel and PowerPoint)
File:BioGRID-to-WormBase Interaction Mapping.xls
File:Interaction type Venn diagrams.ppt
  1. Physical interactions
    • Going forward, WB will use/incorporate parts BioGRID curation for physical Interactions (Will alter WB data Model)
  2. Genetic interactions
    • Need to map terms between the two groups (see below for list of interactions)
    • Not trival, may need to incorporate new terms into the respective databases.
    • WB will better define the interaction types it uses so BioGRID has a better understanding of how WB uses terms.
    • Ontology information to look at - IMEx and the PSI-MI ontology:
http://www.imexconsortium.org/
http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI
http://psidev.sourceforge.net/mi/psi-mi.obo
WormBase - Interaction Types
Genetic
Regulatory
No_interaction
Predicted_interaction
Physical_interaction
Suppression
Enhancement
Synthetic
Epistasis
Mutual_enhancement
Mutual_suppression
BioGRID - Types of Genetic Interactions:
Dosage Growth Defect
Dosage Lethality
Dosage Rescue
Negative Genetic
Phenotypic Enhancement
Phenotypic Suppression
Positive Genetic
Synthetic Growth Defect
Synthetic Haploinsufficiency
Synthetic Lethality
Synthetic Rescue
item 3 - Directionality of interactions.
  1. Bait/Hit = effected/effector
    • This is not a major hurdle as there is consistent usage of Bait/Hit by BioGRID and effected/effector by WB.
  2. Non-directional interactions?
    • Tag only exists in WB, but can formalize solution later.
item 4 - High throughput vs Low throughput?
  1. Tag not in WB, but could possibly go back and retrocurate? or leave out?
item 5 - Going forward - work flow.
  1. Too premature to discuss work flow per se...will meet next week to start going over definitions for eventual mapping of terms.