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

Raymond

• 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

Gary

• 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)

here

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

Micropublication

• 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

Kimberly

Continuing work on the new GO model

Juancarlos

• 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)