WormBase-Caltech Weekly Calls

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January 2015

January 8, 2015

Community annotation

  • author participation
    • Cecilia: still lots of work, need to manually process data submitted by authors
    • old data kept for history and for comparison
    • people mess up institution names - institution field on submission form being changed to a controlled vocabulary
    • campus addresses also not standardized - will organize/create address fields, e.g., street address, mail-code, etc.,
    • add example address
    • ~10 author submissions a week
    • most curation involves extracting people information from papers (~800 week), as automated as possible right now - people and affiliation are extracted from xml, but information still needs to be parsed
    • can we mine author data from other sources (institution, laboratory); important to get laboratory address for sending strains; two sets of data- (1) easy- people associated with a laboratory, (2) difficult- people not in a registered lab

Cross-product development


  • embarking on cross-product generation- ex., male tail, versus hermaphrodite tail - better to have one 'tail' and add modifiers
  • wants to move to OWL now; comment is that obo relationships are not directly translatable into OWL
  • Uberon has elegans anatomy


  • starting to work with Chris and Karen on developing cross-products, still in exploration phase
  • not looking at OWL yet
  • will get relationships from Raymond

Sequence feature curation

Daniela, Gary, Xiaodong, Mary Ann are validating papers as positive/negative in curation status form. As soon as ready, Mary Ann/Gary will start curating

Rose alleles

  • 150,000 new alleles, Mary Ann done just all bar 12 of them in time for WS247
  • phenotypes were only reported for a small fraction

CGC strains

Mary Ann received latest update, CGC very busy with strains generated through new gene engineering techniques

WB WBook chapters

Main outline here- note this document cannot be edited, people can create their own shared docs for their respective papers

  • Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly)


  • Pathways and Processes (Karen) here
  • Expression (Daniela)


  • Hobert- micropublication for expression = small facts, which are data that will never be published (Daniela working with Hobert on these)
  • Community annotation not linked to a publication
  • a couple models for WB dealing with the micropubs
    • WB captures all submissions blind and posts them
    • WB reviews submission - curators decide which micropubs have value
  • need to establish microattributions to increase the value of submissions
  • involve semi-peer review through automated fact review requests to scientists who've worked on the gene, cell, entity, etc.
  • need to set up a pilot, to get a feel for the amount of participation/work this tool will be

Picture curation

  • for topic curation
    • want to annotate figures with genes - involves model change
    • want dynamic display with slide show, different highlighted figures - need to work with webteam
  • community voting - crowdsourcing - need to work with webteam
  • WB-blessed image represented through wikipathways


Continuing work on the new GO model


  • management of automated descriptions with Ranjana
  • phenotype requests through RNAi and allele phenotype done in december

Automated descriptions

  • playing with pulling out useful data to add to description automation (James and Ranjana)

January 15, 2015

New expression objects and pictures

  • Cross-species comparison of developmental gene expression
  • Have life stage annotation
  • Microarray experiments
  • Do we have data on significant differences from C. elegans? Can we get the analysis or algorithm?

Neuro anatomy

  • 3 ways to access neuro-connectivity data
  • ACEDB, Kris Gunsalus' server at NYU (defunct), Nikhil Bhatla's connectivity browser
  • We would like to adopt Nikhil's browser (for neural connectivity AND the cell lineage browser); we need to act before it disappears

FPKM RNA-Seq data display

  • Should we suggest splitting the data display by tissue, life stage, treatment, etc.?
  • Gary Williams is responsible; need to talk to him

Heavy metal toxicity/response

  • New topic, all papers have been checked
  • Need to send list of relevant genes to Hinxton
  • Curators can now flag figures relevant as topic diagrams

Phenotype picture curation

  • We will begin to collect pictures for phenotypes
  • Will require model changes

Phenotype OA Strain fields

  • "Parental strain" autocomplete field added to TAB 2 of Phenotype OA
  • Plan is to put parental strains in the Phenotype_info hash
  • Natural isolate strains can be directly annotated with phenotype?

BioCuration meeting in April

  • Xiaodong is writing up an abstract, will send around before submission
  • Xiaodong will run a curation tutorial for Chinese speakers

Jan 22, 2014

ad hoc curation of tier III species (Mary Ann)

WBPaper00046176 describes Ctr- genes and alleles (fig 3). Although we do not curate this (and other tier III) species, should we place this information somewhere, on an ad hoc basis? http://tazendra.caltech.edu/~acedb/daniel/00046176_Wei14_temp.pdf

Mins: Curate as much as existing models allow and hopefully expand at later date. The volume of this sort of data will increase as we encourage Community Curation. Don't seek out papers, but add data as they come along. Talk to Hinxton about adding gene models.

Complex Gene Loci (Mary Ann)

e.g. lin-15A/lin-15B


We should use existing Gene_cluster model and add new Type tag to differentiate between e.g. rrn Gene cluster and e.g. lin-15A lin-15B complex loci.

nb. Maybe hard to discuss w/o Paul Davies.


  • Daniela starting to work on author submission forms for expression patterns where people can submit images
  • Requirements? Paul says needs sequence - minimal important stuff, sequence, expression pattern, construct, reporter gene
  • genome coordinates are ok for elegans, but not for other species whose genomes
  • making a micropublication - identifier, research object identifier,