Difference between revisions of "February 15, 2011"
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;item 2 - Mapping of interaction terms between WB and BioGRID. (Attached Excel and PowerPoint) | ;item 2 - Mapping of interaction terms between WB and BioGRID. (Attached Excel and PowerPoint) | ||
| − | [[File:BioGRID-to-WormBase_Interaction_Mapping.xls]] | + | :::::::[[File:BioGRID-to-WormBase_Interaction_Mapping.xls]] |
| − | [[File:Interaction_type_Venn_diagrams.ppt]] | + | :::::::[[File:Interaction_type_Venn_diagrams.ppt]] |
# Physical interactions | # Physical interactions | ||
#* Going forward, WB will use/incorporate parts BioGRID curation for physical Interactions (Will alter WB data Model) | #* Going forward, WB will use/incorporate parts BioGRID curation for physical Interactions (Will alter WB data Model) | ||
| Line 36: | Line 36: | ||
#* Not trival, may need to incorporate new terms into the respective databases. | #* 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. | #* 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 | ::WormBase - Interaction Types | ||
Latest revision as of 22:13, 22 February 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
- 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)
- Physical interactions
- Going forward, WB will use/incorporate parts BioGRID curation for physical Interactions (Will alter WB data Model)
- 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:
- WormBase - Interaction Types
- Genetic
- Regulatory
- No_interaction
- Predicted_interaction
- Physical_interaction
- Suppression
- Enhancement
- Synthetic
- Epistasis
- Mutual_enhancement
- Mutual_suppression
- WormBase - Interaction Types
- 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
- BioGRID - Types of Genetic Interactions:
- item 3 - Directionality of interactions.
- 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.
- Non-directional interactions?
- Tag only exists in WB, but can formalize solution later.
- item 4 - High throughput vs Low throughput?
- Tag not in WB, but could possibly go back and retrocurate? or leave out?
- item 5 - Going forward - work flow.
- Too premature to discuss work flow per se...will meet next week to start going over definitions for eventual mapping of terms.
