WormBase-Caltech Weekly Calls February 2019

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February 7, 2019

Automation of curation

  • For paper-by-paper curators (vs. datatype-by-datatype) it's difficult to parse papers into data types
  • MGI and WB curate by datatype, so may have an easier time
  • All MODS still need paper triage

IWM workshop

  • Ranjana replied to Julie about a consolidated WormBase workshop; hasn't heard back

Site-specific outreach

  • Wen has been invited to small RNA meeting in Mexico in April; may go if they offer to pay (waiting to hear back)


  • Raymond and Juancarlos have worked out a way to display top-slicing of the ontology (trimming to higher level nodes)
  • Needs a bit more clean up; will send around a URL when ready

February 21, 2019


  • specific genes, from simple to complex

let-4 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=let-4%20(Caenorhabditis%20elegans,%20WB:WBGene00002282,%20-,%20C44H4.2,%20sym-5)>

let-60 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=let-60%20(Caenorhabditis%20elegans,%20WB:WBGene00002335,%20-,%20ZK792.6,%20lin-34)>

daf-2 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=daf-2%20(Caenorhabditis%20elegans,%20WB:WBGene00000898,%20-,%20Y55D5A.5)>

  • Looks good
  • Some confusion with filled circle legend (half red and half blue) for slim terms; maybe make two separate circles, one red, one blue and possibly indicate each as direct/indirect, respectively
  • May be good to make graph depth options more obvious; we can move it up to the top of the legend, maybe also display all graph depths by default so a user can see them and select one
  • Would it be possible to force display of any AGR/Alliance slim terms on the path from an annotation node to root (not all pertinent slim terms are currently displaying due to the trimming algorithms in place); might be possible but would probably significantly interfere with the current trimming and display algorithm

Moving away from dependency on OBO format files

  • Nico, an ontology developer with the Monarch group, has some suggestions for how we can move away from dependency on OBO files
  • Planning to have a meeting on Monday (Feb 25) at 9am Pacific, 12pm Eastern, 5pm UK to discuss
  • How are we handling OBO for GO? GO OBO is parsed into ACE format
  • This should be a group-wide discussion as we have many OBO dependencies
  • There are several OBO-to-ACE conversion scripts we use
  • What is the trend in the ontology field? Seems to be that OBO will become deprecated and OWL will supersede it
  • We will try to reschedule to Tuesday (same time) to include more people

Phenotype request mass emails

  • 1,820 emails gone out this week (since Monday) for 1,820 papers (957 still in queue; need to wait for Google limit to expire)
  • Have received 217 direct annotations for 49 papers (45 requested papers) from 47 distinct community curators
    • 158 to Phenotype OA
    • 59 to RNAi OA
  • Have received 5 submissions via email (4 worksheets)
    • 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
    • 4 phenotype submissions, 4 curators, 93 phenotype annotations
  • 57 papers flagged as not having phenotypes
  • Total: 310 phenotype annotations from 51 community curators for 53 papers

February 28, 2019

Phenotype request mass emails

  • 2,777 emails gone out (last week) for 2,777 papers
  • Have received 421 direct annotations for 88 papers (81 requested papers; ~3% response rate) from 84 distinct community curators
    • 313 to Phenotype OA
    • 108 to RNAi OA
  • Have received 5 submissions via email (4 worksheets)
    • 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
    • 4 phenotype submissions, 4 curators, 93 phenotype annotations
  • 83 papers flagged as not having phenotypes
  • Total: 514 phenotype annotations from 88 community curators for 92 papers
  • ~6% response rate including negtaive flagging
  • Are annotations accurate? Yes, as far as has been checked
  • What type of depth are we getting? Good depth; although maybe not lots of details or treatment conditions, we often get very specific proposed phenotypes
  • We could visit labs and email them right after the visit
  • What about an undergrad course? Graduate students? Journal club activity?
  • Caltech has a small body of bio majors, may not get much yield, but could focus on specific pool of grad students
  • Community vs WB curator comparison:
    • Chris thoroughly curated one paper also curated by community
    • Community curator submitted four annotations; Chris curated 29
    • On a per annotation basis, processing community annotations is (for this paper) about 3-fold more efficient than manual curation; we probably have higher gains for papers with more annotations
    • Checking involves making sure, for example, that alleles, genes, and phenotypes submitted are referred to in paper; may be able to take advantage of AFP pipeline to automate some of this
  • Bounced emails
    • Out of 2,777 emails total, 150 bounced
    • Of 150, 85 failed to find the address, 32 just failed, 15 said failed but to try resending; "Policy reason"
    • Have sent Cecilia list of bounced addresses; will update records accordingly, although sometimes hard to tell if we should make any updates since it may just be that our email was detected as SPAM and not that the email address is bad

OBO axioms

  • Nico is asking for a list of all OBO axioms needed by WormBase
  • He will then make sure that any OWL-derived OBO files (from ODK pipeline) will include required axioms
  • Collecting list of OBO relations in minutes doc from meeting on Tuesday

SObA update

  • Probably soon going to freeze development of SObA
  • Expand SObA graphs for all applicable ontologies
  • SObA for other species, we need to assess interest