WormBase-Caltech Weekly Calls October 2014

From WormBaseWiki
Jump to navigationJump to search

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


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


October 23, 2014

CANTO

  • Kim Rutherford, programmer, in New Zealand
  • We can communicate with Kim to determine what we can port over/re-use for WormBase
  • Probably we can focus on phenotype for now
  • We want text-mining with entity prepopulation
    • What is the best Textpresso approach to extract possible phenotypes (CCC approach? categories? ontologies (names & definitions)?)
    • Prepopulating genes and alleles should be (relatively) trivial

Textpresso string searches for Curation Status Form

  • Daniela (Seq features), Ranjana (Disease), Xiaodong, Karen and Mary Ann are ready to add their data types
  • Curators should add notes to the Curation Status Form Wiki page

http://wiki.wormbase.org/index.php/New_2012_Curation_Status#Datatypes_for_Textpresso_String_Searches

International Worm Meeting Outreach

  • Curators can/should reach out, personally, to individual researchers to request community annotation efforts

Journal Outreach

  • We want to reach out to journals to mandate data submission (in standard format) by authors
  • We will try trials with Paul, Paul's lab, worm community
  • Want to reach out to other databases to create a uniform process and consensus
  • Data submission process could be table data entry for each data type
  • Goes hand-in-hand with general community annotation effort
  • We want meta-data, especially sequence data (dsRNA, allele, clone, etc.)

Topics name

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

  • "Pathways & Processes"
  • "Pathways, Overviews, and Processes (POP)"
  • What do other databases use?
  • "Biology"
  • "Pathways"
  • "Biological Topic"
  • "Context", "Biological Context"
  • Want one word in menu


October 30, 2014

Bio Lunch

  • Caltech Bio Lunch talks need speakers
  • WormBase/Textpresso could give one/some


WormBase chapter for WormBook

  • Paul asking for contributions for WormBook chapters on WormBase
  • Good to have several sections done before the 2015 International C. elegans Meeting
  • Paul sent around a putative outline
  • Gene Ontology discussion could go into Gene Function section
  • WormMine, GBrowse, JBrowse?
  • Could integrate WormMine/GBrowse functionality and usage within separate chapters
  • Explaining data models without jargon in context
  • Nomenclature & strains?
  • Drafts by January?


Paper prioritization

  • We can prioritize papers first on current topic, then on those that refer to genes with no phenotype (allele and/or RNAi)


Foot pedal for repetitive keyboard/mouse tasks

  • Daniela ordered a foot pedal to help with repetitive keyboard and mouse tasks
  • She will try out to see if it helps and let people know


Data submission forms/tables for community annotation

  • Relaxed vs. stringent rules? e.g. sequence submission for clones and dsRNA sequences versus clone names or more ambiguous identifiers
  • Some form for journals (more stringent for mandatory submission) and optional (more relaxed community submission requests)


Textpresso string search results in Curation Status Form

  • We will add lists of papers that come up positive for Sequence Feature, for example
  • Juancarlos needs lists of papers per datatype
Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls_October_2014&oldid=25322"