WormBase-Caltech Weekly Calls May 2019

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May 2, 2019

SObA for all ontologies

  • http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
  • SObA graph search for all ontologies
  • Juancarlos and Raymond looking for feedback; let them know
  • Would be good to make it clear to users what the edges/arrows mean; what relations are included for inference? Can we include blurb in the legend?
    • Raymond: thinking of putting blurb on a separate documentation page
  • Can we track who is using this tool (and others)? SObA is hosted by WormBase so we'd have to ask Todd (Google analytics); SimpleMine is Caltech hosted so we'd need to look at Tazendra logs to see who (and how many people) are using the tool (cannot rule out bots etc.)

IWM swag - screen cloth

  • Need to finalize design
  • Put Dick & Jane cartoon in one corner, tools in another corner, WB logo, Alliance logo
  • Daniel can take care of ordering and printing, but needs someone to choose the design

Phenotype ontology patternization

  • Chris working on patternizing phenotype terms to standardize logical definitions for classes of terms
  • This is part of the ongoing effort to align phenotype ontologies across the organisms
  • Paul S: It's important for community submitted phenotypes (and the use of the form) to make sure the ontology makes sense and is readily browsable
  • Does "dumpy" mean the same thing to everyone? Is there a way to assess discrepancies in term definitions among members of the community?
  • Does someone annotate to Egl or vulvaless?
  • How do we help community curators decide the correct term?
  • Could we develop a smart annotation aid/tool/helper? Use images, examples, etc.

May 9, 2019

SObA for all ontologies

  • Revised version http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
  • Changed legend labelling, added linkouts
  • To implement on Gene pages. One vs. Five widgets?
  • Would be good to provide documentation on what the inferences mean; can we provide an indication of what relations a particular SObA edge could be comprised of?
    • Or click on an edge to get the, e.g., GO subgraph that connects the two nodes?
  • Let's release to the website, but gather feedback from (naive) users to see what documentation we need

Citace upload next Tuesday

  • Tuesday May 14, 2019, 10am Pacific

SPELL is now indexed by Google

  • Cool!

May 16, 2019

SObA graphs

  • Edges in graph can be clicked to generate pop ups with link to the (lower) term page showing the graph of inference to upper level nodes
  • May provide more information than the user needs/wants
  • Juancarlos working on implementing SObA widgets on gene pages (maybe for WS271 or WS272?)
  • IWM will have WS271 on staging during meeting; probably on production shortly after the meeting
    • Hope to show users demos at IWM

IWM swag: screen cloths

  • Paul is working on the graphic
  • Need to order soon

Testing on staging site

  • Adam and Sibyl request people to test Sequences widgets on Pseudogene, CDS, and Transcript pages on staging
  • Sibyl has asked for testing of new search on staging

May 23, 2019

WormBase Google folder

?Genotype class

  • Chris and Ranjana will work on early next week
  • Will need to accommodate disease model annotations
  • Will bring up again for discussion with larger group next week
  • Conclusion: ?Genotype objects will represent the entire genotype of any organism it inheres in, but we will specifically point out the causative agent (or agents) responsible for the disease or phenotype in the individual annotation

May 30, 2019

Phenotype Request Emails

  • New round for May 2019
  • 1139 emails total; 825 emails gone out so far today
  • Chris will report back next week with numbers

?Genotype class

  • Google doc: https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing
  • Are or aren't we moving to serial identifiers for strains, e.g. WBStrain0000001? Need to ask Kevin et al.
  • We would want to indicate in a ?Genotype object which are the "relevant" genes, proposed to be captured in a "Involves_gene" or some such labeled tag
    • For transgenes, which genes would be considered "relevant"? Only expressed genes? Or also genes for which the promoter and/or 3'UTR are used? We could start with expressed genes only, for now
    • We would like to infer which genes are involved/relevant based on the components, like variations, rearrangements, transgenes, but we may also want to indicate which genes the authors assert to be part-of/relevant-to the genotype such that if new mappings point to a different gene, users can still trace back to which genotype the authors referred to in the paper originally
    • Maybe we would want subtags of "Involves_gene" like "Author_asserted" and "WormBase_inferred"? We can try it; what would the XREF tag names be? Distinct?
    • Do we really want to list all genes that are affected by a rearrangement?
    • What about RNAi treatments? Should these be considered part of the genotype? Authors often report it that way
      • GENO ontology has made terms "intrinsic genotype" and "extrinsic genotype" to distinguish, for example, the nuclear genome genotype from "imposed" genotype effects like RNAi, morpholinos, etc.
  • We may want to have a tag "Has_background_strain" to refer to the original wild type strain/isolate from which the genotype was derived; this would largely be N2 and an XREF would (over?)populate the N2 strain object with 1000s of "Is_background_for" associations.
    • It may be best to include this tag, but make it a convention to only annotate it when it ISN'T N2