WormBase-Caltech Weekly Calls December 2013

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December 5, 2013

WBPapers sans C. elegans data

  • There are papers in the WormBase collection that are used as paper evidence for some concise descriptions
  • They don't refer to C. elegans experiments, but were used to write descriptions with characterizations in other organisms
  • These papers are lumped in with all the other papers, come up as false positives in flagging pipelines
  • They have a "functional annotation" tag
  • Many of these were coming up in the disease paper pipeline
  • Michael and Kimberly worked to pull out all papers with this problem
  • Some are methods papers, some possibly mistakes, etc.
  • Main question: do we want to take 'functional annotation' papers out of Textpresso/Curation pipelines?
  • Are the 'functional annotation' tags unique or otherwise mutually exclusive? Yes, historically
  • We will change the name of the tag to "non_nematode" and exclude the papers from flagging pipelines (SVM, Textpresso, etc.)
  • Will need to change in Postgres (Paper Display "curation_flags", Paper Editor). Curators need to check their scripts to see if they use this and update it or talk to Juancarlos (search for 'functional_annotation')

Topic Curation

WS241

  • UPR (Unfolded Protein Response)
  • Chris and Karen playing with pathways diagrams on WikiPathways, Google Slides, and Prezi (SVG presentation); will send around
  • May be nice to have a video overview with narration from Prezi presentation, and details (with evidence) captured in WikiPathways

WS242

  • Small/ncRNA pathways?
  • We will stick to miRNA pathways, specifically biogenesis (transcription through to mature miRNA)
  • Chris will send around WBPaper IDs for papers flagged by PubMed Mesh headers for "C. elegans" and "miRNAs"
  • We will get a copy of Alla Grishok's recent (2013) small RNA pathway review
  • We can identify core components of the miRNA biogenesis pathway and filter the WBPaper list based on references to those genes
  • Alternatively (or in parallel), we can break up the ~300 miRNA C. elegans papers into groups and delegate the screening of relevance

LEGO (Logical Extensions of Gene Ontology)

  • Discussions with Paul Thomas on Thursday, January 23, 2014

Topics and Subtopics

  • We don't want to recreate Gene Ontology or a complicated hierarchy of topics
  • We may need to create simple parent/child, topic/subtopic relationships
  • We can show general pathway/topic overview on parent topic, specifics on subtopic pages

Discussions with WikiPathways

  • We may consider inviting Alex Pico to come talk to us about feature requests, discussion of future plans, current WikiPathway features
  • Would be nice to link out to other pathways from inside a pathway (e.g. Link to "Innate Immunity" from "Unfolded Protein Response")

AMIGO development

  • Setting up backend:
    • Juancarlos is learning how to use Catalyst
    • Todd gave Juancarlos access to a development environment
    • Raymond and Juancarlos figuring out web code structure
  • May be good to have Juancarlos visit/meet with web team to determine best integration practices

Database changes to WormBase

  • Discussion/meeting in March 2014
  • Paul Sternberg, Juancarlos, and maybe one curator will join in
  • Need to 'boil down' the candidates to a small number and test things like: data model changes, capturing biological data, scalability, web performance


December 12, 2013

AGENDA

  • Progress on collecting papers for miRNA biogenesis topic

Topic Curation WS242: miRNA pathway

  • Currently have Google Docs for tracking miRNA papers
  • Collected all papers from PubMed with MeSH headers for "micro RNAs" and "Caenorhabditis elegans"
  • Will upload all WBPapers for miRNAs into the Topic Curation OA, under "miRNA Pathway"
  • Will break up remaining "unchecked" papers 5 ways to check for relevance

?Construct Model

  • Need to discuss how the construct model should be structured
  • Incorporation for expression pattern curation, sequence features, Crispr-Cas genome editing alleles, ...
  • Hopefully we can sort out this model for the next upload


December 19, 2013

AGENDA

  • miRNA Pathway topic curation
    • Please continue to add pathway figures from papers here
    • Feel free to play around with ways to diagram the miRNA pathway in Google Slides here
  • Curation of protein complexes?
  • Updated Mitochondrial UPR WikiPathway here

Conference Calls in January 2014

  • January 9th and 23rd
  • Should discuss ?Construct model on the 9th?

WormBase Models meeting: March 9, 2014, Toronto, Canada

  • Which curators should join?
  • What are the important considerations?
  • What system might enable ~real-time annotations or corrections to the database/site?

Life Stages for Burgia malayi

  • Defined by Mark Blaxter et al
  • "Infective Juveniles", "IJs" included

Topic Curation

  • WikiPathways is good but clunky; easier to draw up ideas in other formats (e.g. Google Slides?)
  • Would be good to discuss feature development of WikiPathways (and others?) with respective developers
  • Reactome? LEGO?
  • We can discuss with Alex Pico, for example, about WikiPathways features
    • May be best if we wait until the new WikiPathways layout is released, or maybe we can get access to a Beta version of the new interface
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