WormBase-Caltech Weekly Calls July 2016

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July 21, 2016

Yuling leaving in August

  • Will send out announcements to hire a replacement
  • Will take time to get back up to speed
  • Curators should address concerns before he leaves (documentation, SVM stuff, etc.)

AGR curator call

  • Yesterday we (FlyBase, ZFIN, and WormBase) presented paper curation status tracking
  • Chris Mungall will discuss phenopackets next week


  • Will be good to be able to compare phenotypes across DBs
  • Is there a working list of Phenologs anywhere? See Ed Marcotte's paper
  • Monarch/phenopackets, Chris M talks next week
  • Uberon; phenotype-anatomy associations in WB could be associated with Uberon anatomy terms

GO annotation model

  • Common GAF was an impetus, but were other reasons
  • ACE format couldn't accommodate some aspects of GO annotations
  • Ranjana considering similar model for disease annotations

WBPerson lineage graph

  • Raymond requests that people take a look and send feedback
  • It's not clear right now where this is intended to be displayed

Web Phenote being resurrected

  • We should talk to WebPhenote people to discuss our existing OA features

July 28, 2016


  • Ranjana willing to test out the newest version of WebPhenote for disease annotations
  • WebPhenote is currently being built for human phenotype curation
  • Dan (developer) could give WB a demo at end of August

Paper curation status tracking for WB ParaSite

  • Juancarlos has cloned and modified the curation status form for ParaSite
  • Some paper have both Caltech species as well as ParaSite species; this creates problems in the tool
  • WB Caltech standard SVMs are run on ParaSite papers as well as 3 data types (RNASeq, Proteomics, ...)
  • How should we track papers separately for Caltech/ParaSite species? Add a "Curated for C. elegans" or similar standard remark?
  • We may need to have separate tables for each datatype for Caltech/ParaSite
  • 1094 papers have species from Caltech group and ParaSite set. SELECT joinkey FROM pap_species WHERE pap_species IN ('6239','860376','135651','6238','6239','281687','1611254','31234','497829','1561998','1195656','54126') AND joinkey IN ( SELECT joinkey FROM pap_species WHERE pap_species NOT IN ('6239','860376','135651','6238','6239','281687','1611254','31234','497829','1561998','1195656','54126') );

Dumping data subsets from OA

AGR curator call

Paper supplemental files

  • Most papers have separate files for each supplemental document (separate PDFs, XMLs, Excel docs, Word docs, etc.)
  • Some AGR groups consolidate separate docs into a single file
  • File consolidation could be beneficial to WB curators as well
  • Karen will look into what this would involve; if it's worthwhile

AGR call with NIH

  • NIH happy with supplement proposal; would like more specifics on deliverables
  • Will the MODs continue to have separate SABs? Yes, for now

AGR Working Groups

  • Current proposed working groups:
    • Shared orthology
    • Disease ontology
    • Textpresso central as a common curation tool
    • Noctua as a common curation tool
    • Common web portal(s)


  • Discussed at TAGC
  • Need to fix naming and identification of metabolites
  • There is plan to work together (across organizations) and apply for funding
  • Work with BioCyc? Art Edison (worm researcher) already talking to Peter Karp (BioCyc) about collaborations. Unless they've changed over the years, BioCyc does not use common ontologies - only their in-house ones - this won't work with Alliance-wide databases and collaborations with ChEBI. In addition, BioCyc might not be able to offer the flexibility in visualization and curation that is needed for grand project.