WormBase-Caltech Weekly Calls July 2012

July 12, 2012

Grant Renewal

Like to have rough draft by end of July
Including things we are doing now that are obvious
30 pages total
10 pages for Caltech, likely
Focus on: Gene function, transcriptional networks, pathways
How much have we curated? What is our rate of curation?
What is the backlog? How much left to curate?
Not caught up on RNAi and allele curation by end of this term
Logical extensions to GO (we will discuss next week)
How are we going to measure quality? Metrics?
- Coverage?
- Accuracy?
- What is a/the gold standard? These things aren't generally well defined
Other species
- Automated triage for papers
- Use nematode Textpresso to estimate what's out there?

LEGO (Logical extensions to GO)

Try to use GO annotations to make more expressive statements about gene function, pathways and processes
Prior to this, curators took gene or gene product to describe subcellular localization, molecular function, and processes the product involved in
Looking to create much bigger picture of the biology
LEGO annotations: adding info to typical GO annotation, such as regulation targets
- TF has sequence-specific DNA binding activity; now add what the targets are
- If TF in nucleus, what cell types?
- Now we could start to create pathways and describe processes in more detail
Being done with OWL, web ontology language
Example, the dauer pathway; do more examples to see where the holes are
8 examples from C. elegans: involving cell types, signal transduction pathways, etc.
Build much broader picture of the biology of the worm
Filling in annotation gaps or inconsistencies
Start to build annotation models
Can we integrate with Wikipathways?
Community annotations?

Protein-to-GO

EBI's protein GO annotation system
Data written to UniProt
We agreed that we could clean up our GO annotation files and try this out
Big picture: many groups may buy in to using Protein-to-GO, but will not become our only curation tool
Can we use the OA to modify or create extensions to GO or Protein-to-GO?
What would we have to do to make the OA better than/comparable to Protein-to-GO?
- We need a drop down for the relations
- We need an ontology domain to match to the relations
One benefit/intention of centralized curation system was to have a central quality control system in place
Don't need a central/unified curation system to have a central database, but may help reduce some effort/work
Protein-to-GO has a lot of real time error checking, which is very helpful
Arguably, common/central curation tool and database could speed up curation across different databases
Wormbase can push ahead with a pilot test

CSHace data

Wen will work on merging CSHace data into CITace
We received PCR products before the final CSHace dump, but some were apparently missing
We, collectively, don't remember what the arrangement was
May have been decided that some PCR products remain with Sanger (at the time) to perform mappings
May be problem if we had overwritten data or will overwrite data with new merger; we need to do appropriate comparisons and see what is most up to date

Working with Reactome

At Biocurator meeting, Karen met with Marc Gillespie to figure out how WormBase could best work with Reactome
Disease pathways would be very useful
If we have overlap with their (human) pathway, we could highlight pathway components that human biologists aren't yet aware of
Challenge is to associate worm pathways with human pathways
What is the Reactome data model? Can we port our data to fit into their data model?
Reactome curates in a Protege-based file format (flat files); similar to OWL format
Can base pathway homologies on orthologs and/or Ranjana's disease curation
If we adopt LEGO (Logical Extensions of GO) will we need to use Protege? Initial stages of data modeling using Protege and OWL-like representation, but not for long term
LEGO would liket o develop their own tool

Transgene Pages

Transgenes are being affiliated with gene pages of promoter for over-expression phenotypes
Punc-47::SNB-1 (SNB-1 over-expression) phenotype showing up on unc-47 page; should really be on snb-1 gene page

Grant Writing

Rough draft by end of July
- To include ongoing projects and efforts
In August we can contribute (or any time earlier) new projects and proposals
We can each write about a paragraph(?) on our individual subjects and add it to the Google Doc 'WB12-GrantDraft1'
- Add name and time/date written when adding to Google Doc

Worm Tracking data from Rankin lab

Handling large scale queries

WormMart? On it's way out, not supported; data just getting stale (stuck in WS220)
AQL, requires knowledge of data models and AQL syntax; Also cannot do batch queries
Intermine/WormMine on its way, timeline?
6 months or longer before having something usable?
Do we provide 'one-off' services for users
Do we have a Wiki page for commonly asked questions/pre-canned queries? Maybe Anthony Rogers had set up a page
Wen will look through old e-mails
Chris will check Wiki and e-mail group
Have a button that can run a query script when clicked?
Can we make older (requested) tools available?
CGI-based query tool?

Community annotation of Person info

What if Postgres (as opposed to ACEDB) became main repository of person info?
May be worth considering
Maybe webpages could actively pull person data from Postgres
What about paper objects then?
People (WormBase users) could mess up the data in Postgres if they had direct access/editing rights to Postgres
Special characters in names (e.g. tilda, umlaut)?