WormBase-Caltech Weekly Calls

2012 Meetings

FlyBase SAB topics

Genome Space - can integrate data in different formats
- Cloud-based data integration
- File conversion done automatically - no need to write scripts
FlyBase talking about joining Genome Space?

Protein-to-GO Tool

Ranjana and Kimberly performing data checks for testing
If file can get to Rachel and Tony, maybe can discuss this weekend (at GO meeting)

GO Annotator Tool

Kimberly looking over
James will make a couple slides to introduce tool and provide demo
- 1-minute demo: can have file in XML/HTML format, can highlight, annotate a sentence, and save annotation as a link
  - Demo: simpler = better
  - Prepare for live feedback and discussion

Curation Status/Statistics Tool

How many papers have given data types?
How many papers have been curated, how many not?
How many objects/connections do we have of a given type?
How many objects per paper (average, distribution?)?
Estimated number of objects/papers exist vs. how many we have curated?
Do we care about types of flagging? Curator first pass, author first pass, etc? Yes
- All flagging types should be shown; combined and individual statistics would be useful
Interactive form vs. static page showing curation/flagging statisitcs
Tracking negatives (true vs false)
Data types in OA vs not (microarray, Protein-to-GO output)
- Microarray data - Wen can write script to generate stats for microarray curation
Curation stats per paper (Raymond): write comments in a remark field; traceable, transparent, available

Process pages

GPML - may be able to automatically map Postgres data to GPML
WikiPathways has color, formatting, labels, etc. so we can define types/views of different relationships (should follow standards)
AWC-ON/AWC-OFF sample page: only single connection type; can be many different types, as we define it
"Too many arrows" editorial?

Physical interaction curation

On interaction OA (Tab2) physical interactions; 'Colocalizes', etc.
Need to establish our data exchange with BioGRID; get BioGRID data in Postgres/OA (daily cronjob?)
Interaction model was modeled to be compatible with BioGRID's data
Revive curator first pass for physical interactions? To tag papers (in the meantime)

Molecules

GO Meeting

How to make GO more expressive/inclusive
How can GO represent more of the biology
GO Extensions: LEGO
Deeper annotations can help develop the "big picture"
Phenotype-2-GO mapping: What is the purpose? How does it work?
- Broad vs specific term mapping; how good is the mapping?