WormBase-Caltech Weekly Calls May 2015

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May 2015

May 7, 2015

Disease variants

  • Ranjana, Karen, and Chris will work out a pipeline to link elegans gene variations and phenotypes to homologous human disease gene variations. This is separate from any automated pipeline that can be set up by Hinxton.
  • Tim Schedl brought up: would be good to connect conserved/syntenic mutations
  • Human disease mutations should be mapped to C. elegans/nematode variants
  • Is there an ortholog? Is the mutation location conserved? Is there a mutation at the site in both orthologs?
  • Authors refer to C. elegans mutations as a model; may or may not be strictly conserved
  • Need to consider what can be done automatically, and what needs to be curated manually
  • We could consider curating connections between mutations and protein domains, and predict affects on function
  • Query use case: what mutations exist in SH3 domains?
  • We could perform two-way mappings: human disease variants to worms/elegans AND elegans/worm mutations to human protein sequence
  • First need to identify all protein sequences of "sufficient" identity/orthology between human and elegans proteins
  • Discuss with Michael Paulini et al

Grant Progress Report

  • Statistics for WS248
  • Want to report progress to data display on web
  • Xiaodong will write section on binding sites, gold-standard regulatory regions, sequence features updates
  • Daniela can write short bit on sequence feature OA

Pathway curation: metabolites

  • Karen talking with Michael Witting
  • Sent Karen list of >2700 (I initially said 4000) metabolites and is curating those verified to be elegans metabolites from publications; wants incorporated into WB with IUPAC names etc.
  • Michael working mostly off of KEGG pathways; metabolites have KEGG IDs
  • Not necessarily an applicable ontology of metabolites, as far as we know
  • Worm-specific vs. general biological metabolites
  • Would be good to connect enzyme commission (EC) numbers to metabolites
  • We can add tag to ?Molecule data model to capture endogenous molecules/metabolites

Community Annotation

  • Biggest backlog: allele-phenotype
  • We want simplest, minimal form necessary
  • We need (minimally): who is curating, allele, phenotype, and reference
  • Need good look-ups for phenotypes, references
  • We can (later) increase the detail
  • Allele names can be entered (ideally) in one field that handles both registered terms, and new terms (with warning)
    • Allele designations must be registered
  • Confirmation screen
  • We want a prominent "Submit Data" button and/or tab (Allele-Phenotype could be a drop down option at top)
    • Users click on this and (at least for now) are redirected to the Allele-Phenotype form (only)
    • Option to submit other data
  • We will accept PubMed IDs for papers (only)
  • We will keep allele data (allele nature, temperature sensitivity, etc. as optional entries)

May 14, 2015

WormBase/ParaSite shopping bag souvenirs for 2015 IWM

  • Daniel looked into costs and styles
  • We can choose from a number of material colors as well as print colors
  • Having two distinct logos will cost more
  • There is a reinforced option that is about 14 cents more per bag
  • We can order locally (saves on shipping costs)
  • Cost break down estimates: base $1.06 per bag, +$0.35 per bag for extra logo, +$0.14 per bag for reinforced
  • What is our budget? How many bags are we going to order?
  • People will draw up potential designs and will send around to the group

Allele-Phenotype User Submission Form

  • Juancarlos is drafting the form now
  • Data entered through form will automatically populate the Phenotype OA, with a "Needs Review" toggle as necessary
  • New fields have been added to the Phenotype OA: Community Curator, Community Curator Email, Unregistered Variation, and Unregistered Paper
  • "Community Curator" WBPerson has been added to the "Curator" drop down list; this will be the default for form entries
  • Whenever form gets filled out an e-mail will be sent to Karen, Chris, and Gary
  • Whenever an unregistered allele is entered Mary Ann will be e-mailed
  • Whenever an unregistered paper is entered Kimberly will be e-mailed
  • Whenever an unregistered phenotype is entered Gary will be e-mailed, as in current pipeline with new_objects.cgi
  • Below each phenotype field (Observed and Not) is a link to browse the phenotype ontology
  • Options to request new phenotypes are hidden by default; user clicks on "Can't find your phenotype?" checkbox to open up fields to enter a new phenotype name and definition, respectively

Concise description form feedback

  • Are the forms written with specific web browsers in mind?
  • Some bugs were seen on Safari

Community Curation Portal

  • Mary Ann set up a GitHub ticket #3867
  • Addressing issues discussed at last weeks CIT call
  • Need to establish the landing page for community curation and easy access from WB home page

Grant Progress Report 2015

  • Curators should fill out table on updated curation numbers
  • We want some text on WOBr, GO annotation changes, automated descriptions, etc.

May 21, 2015

Concise descriptions for Expression Clusters

  • Wen and Ranjana working on

2015 Progress Report: WS244 - WS248

  • Curation numbers that Wen collected are from the full releases not citace

Allele-Phenotype Form

  • http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/allele_phenotype.cgi
  • We would like a way to inform users of data already curated:
    • We could display a notice/warning message in the form (or term info) that indicates that a paper entered in the "PubMed" field has already been curated for allele-phenotype
    • Such a warning message might be best displayed in the form (like allele warnings) next to the field itself, instead of just in the term info, so that users don't miss the message
    • Might be nice to show phenotype data already curated for the paper and/or provide a hyperlink to a page that displays a summary of this data
  • Seems to be consensus that nesting (with inset) associated fields under main fields (e.g. Phenotype Remarks under the associated Phenotype fields) would be most preferable user interface option
  • Do people like having a confirmation to submit the data: "Are you sure you want to submit?"
    • Although useful for micropublication form, probably not necessary (and actually annoying) in the Allele-Phenotype form
  • Some people prefer the "Preview" button to show a static summary table of data to submit on a separate page, without the form included
    • This new page would include options to go back to the form or to submit the data
    • We will leave the "Preview" functionality as is (showing the preview table above the form), unless there is a lot of feedback from users to change it
    • We may want to add some explanation text, pointing out that the form is still displayed below the preview in case the user wants to make edits before submitting
  • We can add a comment next to the "Optional" section header, explaining that the optional data may be pertinent only to specific phenotypes for the allele in question
  • Although real-time chat with WormBase staff has been disabled, if we re-enable it, this form (and others) would likely benefit from having a chat option for users; will need to ask Todd
  • The "X" in the upper right corner of the term info panel will now close the term info box entirely, instead of just clearing the contents and leaving the empty box

May 28, 2015

Picture discrepancy

  • 1000 more picture objects in WS compared to citace or citace minus
  • Paul Davis found them coming from GeneAce
  • Have "pick_me_to_call" tag
  • Represent images from Ian Hope's lab
  • Objects are redundant with what we already have and will be deleted
  • May be generated (unintentionally) by ?Expr_pattern objects; data may need to be cleaned up

Allele-Phenotype Form

  • http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/allele_phenotype.cgi
  • Made changes since last week
  • Added check for prior allele-phenotype curation for a given paper; shows html table summary of results
  • Phenotype remark fields do not show up by default, only after entering a phenotype
  • Phenotype remark and suggested definition fields are now inset, directly under the associated phenotype field
  • Added help text (from green question mark) to various fields

2015 Progress Report