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| | [[WormBase-Caltech_Weekly_Calls_June_2012|June]] | | [[WormBase-Caltech_Weekly_Calls_June_2012|June]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_July_2012|July]] |
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| − | == July 12, 2012==
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| − | Grant Renewal
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| − | *Like to have rough draft by end of July
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| − | *Including things we are doing now that are obvious
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| − | *30 pages total
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| − | *10 pages for Caltech, likely
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| − | *Focus on: Gene function, transcriptional networks, pathways
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| − | *How much have we curated? What is our rate of curation?
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| − | *What is the backlog? How much left to curate?
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| − | *Not caught up on RNAi and allele curation by end of this term
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| − | *Logical extensions to GO (we will discuss next week)
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| − | *How are we going to measure quality? Metrics?
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| − | **Coverage?
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| − | **Accuracy?
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| − | **What is a/the gold standard? These things aren't generally well defined
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| − | *Other species
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| − | **Automated triage for papers
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| − | **Use nematode Textpresso to estimate what's out there?
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| − | LEGO (Logical extensions to GO)
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| − | *Try to use GO annotations to make more expressive statements about gene function, pathways and processes
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| − | *Prior to this, curators took gene or gene product to describe subcellular localization, molecular function, and processes the product involved in
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| − | *Looking to create much bigger picture of the biology
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| − | *LEGO annotations: adding info to typical GO annotation, such as regulation targets
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| − | **TF has sequence-specific DNA binding activity; now add what the targets are
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| − | **If TF in nucleus, what cell types?
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| − | **Now we could start to create pathways and describe processes in more detail
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| − | *Being done with OWL, web ontology language
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| − | *Example, the dauer pathway; do more examples to see where the holes are
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| − | *8 examples from C. elegans: involving cell types, signal transduction pathways, etc.
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| − | *Build much broader picture of the biology of the worm
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| − | *Filling in annotation gaps or inconsistencies
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| − | *Start to build annotation models
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| − | *Can we integrate with Wikipathways?
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| − | *Community annotations?
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| − | Protein-to-GO
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| − | *EBI's protein GO annotation system
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| − | *Data written to UniProt
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| − | *We agreed that we could clean up our GO annotation files and try this out
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| − | *Big picture: many groups may buy in to using Protein-to-GO, but will not become our only curation tool
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| − | *Can we use the OA to modify or create extensions to GO or Protein-to-GO?
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| − | *What would we have to do to make the OA better than/comparable to Protein-to-GO?
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| − | **We need a drop down for the relations
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| − | **We need an ontology domain to match to the relations
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| − | *One benefit/intention of centralized curation system was to have a central quality control system in place
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| − | *Don't need a central/unified curation system to have a central database, but may help reduce some effort/work
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| − | *Protein-to-GO has a lot of real time error checking, which is very helpful
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| − | *Arguably, common/central curation tool and database could speed up curation across different databases
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| − | *Wormbase can push ahead with a pilot test
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| − | == July 19 2012==
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| − | CSHace data
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| − | *Wen will work on merging CSHace data into CITace
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| − | *We received PCR products before the final CSHace dump, but some were apparently missing
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| − | *We, collectively, don't remember what the arrangement was
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| − | *May have been decided that some PCR products remain with Sanger (at the time) to perform mappings
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| − | *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
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| − | Working with Reactome
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| − | *At Biocurator meeting, Karen met with Marc Gillespie to figure out how WormBase could best work with Reactome
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| − | *Disease pathways would be very useful
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| − | *If we have overlap with their (human) pathway, we could highlight pathway components that human biologists aren't yet aware of
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| − | *Challenge is to associate worm pathways with human pathways
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| − | *What is the Reactome data model? Can we port our data to fit into their data model?
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| − | *Reactome curates in a Protege-based file format (flat files); similar to OWL format
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| − | *Can base pathway homologies on orthologs and/or Ranjana's disease curation
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| − | *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
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| − | *LEGO would liket o develop their own tool
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| − | Transgene Pages
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| − | *Transgenes are being affiliated with gene pages of promoter for over-expression phenotypes
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| − | *Punc-47::SNB-1 (SNB-1 over-expression) phenotype showing up on unc-47 page; should really be on snb-1 gene page
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| − | == July 26, 2012 ==
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| − | Grant Writing
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| − | *Rough draft by end of July
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| − | **To include ongoing projects and efforts
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| − | *In August we can contribute (or any time earlier) new projects and proposals
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| − | *We can each write about a paragraph(?) on our individual subjects and add it to the Google Doc 'WB12-GrantDraft1'
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| − | **Add name and time/date written when adding to Google Doc
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| − | Worm Tracking data from Rankin lab
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| − | *Large scale data set
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| − | *Andrew Giles (Cathy Rankin's lab)
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| − | *Worm tracker data, with phenotypes
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| − | *They want us to run the server for their data (600GB)
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| − | *Movie data/interactive tool
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| − | *In what format do we store the data?
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| − | Handling large scale queries
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| − | *WormMart? On it's way out, not supported; data just getting stale (stuck in WS220)
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| − | *AQL, requires knowledge of data models and AQL syntax; Also cannot do batch queries
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| − | *Intermine/WormMine on its way, timeline?
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| − | *6 months or longer before having something usable?
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| − | *Do we provide 'one-off' services for users
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| − | *Do we have a Wiki page for commonly asked questions/pre-canned queries? Maybe Anthony Rogers had set up a page
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| − | *Wen will look through old e-mails
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| − | *Chris will check Wiki and e-mail group
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| − | *Have a button that can run a query script when clicked?
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| − | *Can we make older (requested) tools available?
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| − | *CGI-based query tool?
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| − | Community annotation of Person info
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| − | *What if Postgres (as opposed to ACEDB) became main repository of person info?
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| − | *May be worth considering
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| − | *Maybe webpages could actively pull person data from Postgres
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| − | *What about paper objects then?
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| − | *People (WormBase users) could mess up the data in Postgres if they had direct access/editing rights to Postgres
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| − | *Special characters in names (e.g. tilda, umlaut)?
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