February 15, 2011

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.