WormBase-Caltech Weekly Calls

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October 2, 2014

ParaSite infrastructure

• Discussion regarding communication/coordination of curation effort (& data display) between WormBase and ParaSite
• What curation/work will ParaSite be taking over that we (WormBase) can stop doing?
• What ParaSite info would a WormBase user be interested in: e.g. synteny/alignments, genetic maps?
• WB has user tracking and feedback features; will we use the same tools for ParaSite? Who handles ParaSite help desk issues?
• Branding? Similarity/differences in look & feel between ParaSite and WB?

WormBase Use Statistics

• 2012 to 2013: page impressions increased ~8%

Last year WB object numbers

• Will compare WS245 numbers to WS239 (~1 year)

Enzyme Widgets & Metabolic Pathway Integration

• Marian Walhout working on metabolic flux analysis project
• Would like to display data for enzymes on WormBase outlining likely reactions that are catalyzed by the gene product
• We could interface with Reactome and/or MetaCyc/BioCyc
• Was an idea to create an enzyme reaction widget on gene page
• GO molecular function has associations with E.C. numbers

October 9, 2014

Citace upload

• Curators should upload data by end of tomorrow (Friday Oct 10th)
• Wen will upload citace to Hinxton on Wednesday (Oct 15th)
• Will be the last upload of the year (next in January?)

BioCurator Meeting

• http://biocuration2015.tilsi.org/
• April 2015 in China
• Michael and Yuling are going
• Abstract deadline in November?
  • Edit by Mary Ann - Paper submission deadline 15th Nov, 2014, Abstract submission deadline 1st Feb, 2015

SAB Review

• Response from SAB
• What are our priorities?
• Expression cluster data mining tools (Wen will work on)
• Community Annotation
  • CANTO tool - Val Wood from Pombase gave a talk about CANTO
  • We could integrate/use CANTO, but we need to decide how we will implement it (probably implement our own type)
  • Used for new, recently released papers only
  • Would be good for users to get immediate feedback for their contributions
    • A widget on user/person pages showing annotation contributions
    • On WormBase homepage, have a very visible widget for top community annotators showing the identities of top users
  • Advisors felt that it would be useful to have a table and/or template that users/authors could fill out for their data
  • Eventually want to coordinate with publishers to get data submissions as part of the publication process
  • Good to have PR in place for the International Worm Meeting

International Worm meeting Workshops

• http://www.genetics-gsa.org/celegans/2015/
• Workshop submission deadline for 2015 meeting is November 13, 2014
• Wen could do workshop on SPELL
• Chris could do WormMine workshop

October 16, 2014

Phenotype annotation

• Phenotype curators regularly have to deal with difficulties of annotating phenotypes to genes
• One issue is the completeness of the ontology and the regular need for new terms
• We may benefit from a PATO-like annotation approach
• We will create a Phenotype Curation working group which can meet regularly to discuss

Community annotation

• We would like to implement a CANTO like tool
• We will establish a Community Annotation working group and a community annotation leader/czar to take charge (can discuss next meeting)
• Would be good to establish a good working connection with PIs and labs with regard to community annotation and pathway curation

Topics name

• Change name to "Pathways"? Back to "Processes"?
• "WormBase Processes"? "Worm Processes"?

http://wiki.wormbase.org/index.php/Topic_pages#Renaming_this_class

Topic images

• Since we already have permission to display images from some publishers, we can pick out some that depict pathways and processes
• Going forward, curators can capture the WBPaper ID and figure title/frame that are useful
• Daniela can then compare to the list of publications we have permissions to and add figures
• Would be fun to have a voting system in which users can (on WormBase Topic pages) vote for the best or most informative pathway images from papers
• Maybe top 3 ranked images could be displayed in full with the remaining images as thumbnails that can be opened/expanded