WormBase-Caltech Weekly Calls July 2012
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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
July 19 2012
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
July 26, 2012
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
- Large scale data set
- Andrew Giles (Cathy Rankin's lab)
- Worm tracker data, with phenotypes
- They want us to run the server for their data (600GB)
- Movie data/interactive tool
- In what format do we store the data?
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)?