WBConfCall 2022.08.18-Agenda and Minutes

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Additional grant discussion on Aug 25th, 2022

  • Grant doc here: https://docs.google.com/document/d/1gl2NNsb1I4bBwPHP6Z8xs5cff5FrtnFuWJRedR8Uwo0
  • Curators to fill out the section "B. Resource Development Plan"
    • Add why the datatype is important, what has been accomplished and what needs to be done (e.g. backlog) and how we are going to approach it. e.g. Utilize community input, ACKnowledge, jamborees, workshops at in person meetings.
      • Low throughput Expression -> Daniela
      • High throughput Expression -> Wen
      • Phenotype -> Chris
      • Interactions -> Physical Jae, genetic Chris
      • JBrowse -> Scott
        • Usage of track data -> we don't track it but JBrowse may
      • GO -> Kimberly
      • Literature -> Kimberly
      • Disease models and gene descriptions -> Ranjana
      • People Author lineage -> Include or not? Make forms better
      • Reagents -> Antibody -> Daniela; Molecules, transgenes, constructs -> Karen
      • Anatomy function -> focus on site of action -> Raymond
  • Suggest people for LoS -> CenGen, CENDR, Andy G for disease, WormBoard, CGC, Wormatlas, mirBase?, Briggsae, someone for protein protein interaction?, a pathogen person

Aug 18th, 2022

Agenda and Minutes

  • Helpdesk
  • Clone, fosmid and cosmid availability [MZ]
    • links we are sending to users not working correctly.
    • Ticket #
  • WB grant -> due Thursday September 22nd. Full draft by September 1st.
    • PO still thinking about the LOI
    • Same study section as FB
    • Focus on new things we are going to do - include details, numbers and deliverables and milestones
    • Figure out what type of curation we want to do, prioritize, and put down numbers on how long is going to take. Document on why a certain datatype is important (e.g. expression pattern, phenotype).
    • https://docs.google.com/document/d/1gl2NNsb1I4bBwPHP6Z8xs5cff5FrtnFuWJRedR8Uwo0/edit
  • SAB
    • We will have one later on, after the grant will be in
    • Parasite has an expert group (people familiar with the resource), who give more detailed feedback on missing data, how things can be improved on a practical level. Should we consider something like this for WormBase? Paul S.: We can do it
      • Make a doc with a list of focus groups? Tight for the grant, can do for later on.
        • e.g. 6 people (experts in the field) for datatype
        • focus on new data types, neural connectivity, single cell RNAseq
    • What to do with data such as FPKM displays. Todd: more of a generic question. What are we generally keeping for the transition to Alliance and what are we getting rid of (or display as a per se component).
      • Need a list of all widget.

List of widgets & functions https://docs.google.com/spreadsheets/d/12lchr7BIgIPWCfVunhdYKlUSyACqRAMxlnmvXhvRQD4/edit?usp=sharing

    • Need vision on what we are going to do in the next couple of years.
      • Paul S: need to detail as much as possible how we are dealing with the transition, evaluate our 20 years history and how to move on. Then we need to detail on new things that we want to focus on. Innovation on worm specific data can happen later on.
      • Can we do more with cell lineages and single cell genomics? Cell deconvolution network.
      • Regulatory networks? Ensembl is working on it now.
      • Is the cell lineage browser gone? Yes, lost in the Datomic transition. Raymond: info is in the ontology browser (relationship between nuclei and cells).
    • Phenotype vs GO-CAM modeling. We should generate a more useful and connected set of genes and gene products. Get more useful annotations from people.
    • What about other nematode genes that are not characterized. When people do enrichment analysis.
    • Coexpression -> add to the grant that we can build a tool (similar to Simple mine) to analyze genes coexpressed in tissues (to be worked on by Daniela, Wen, Juancarlos). Talk also to Jae, we may want to include interaction data.
    • Mark Blaxter is going to generate much more genome sequences
    • Do more work on noncoding RNAs. The field is growing and we have good relationship with these users.
    • Focus on genes that have no functional information
      • out out a list for the community and alert them we need data on those? Can advertise on website, can add to the grant.
  • 25th Anniversary of the C elegans genome
  • Paper corpora for all species [MM & MZ]
    • How many papers for secondary species -> Michael M pulled out a list, Magda will add to the grant
    • Rearrange Tier Species on WB? Ascaris is big, next T spiralis
    • Can highlight in the grant the synergy with ACKnowledge. We can have community validated entities and make connections to papers.
    • Wormicloud may be useful here
   6532 pmc/Ascaris lumbricoides 
   4973 pmc/Trichinella spiralis
   4813 pmc/Brugia malayi
   4502 pmc/Strongyloides stercoralis
   4472 pmc/Meloidogyne incognita 
   3890 pmc/Trichuris trichiura
   3658 pmc/Ascaris suum
   3624 pmc/Wuchereria bancrofti
   3593 pmc/Haemonchus contortus
   3579 pmc/Onchocerca volvulus