WormBase-Caltech Weekly Calls

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Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1


2019 Meetings

January


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)

SObA

  • 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

SObA

  • 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)>

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