WormBase-Caltech Weekly Calls December 2019

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Revision as of 21:33, 19 December 2019 by Wchen (talk | contribs) (Created page with " == December 5, 2019 == === New interaction Venn diagram tool === * [https://staging.wormbase.org/species/c_elegans/gene/WBGene00000912#08--10 daf-16 interactions] * Venn dia...")
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December 5, 2019

New interaction Venn diagram tool

  • daf-16 interactions
  • Venn diagram shows how various interactors have multiple interaction types with a common focus gene
  • For a given selected gene set, you can copy to clipboard, download CSV, TSV, and link to enrichment analysis or WormMine
  • Very nice! It would be great to have the gene list options here available wherever lists are provided in WormBase (Sibyl working on it)
  • Request: add SimpleMine as another link out (go to SimpleMine with the gene list prepopulated)
  • Request: could there be a toggle to include/exclude high-throughput interactions?
  • Request: The Venn circle labels sometimes get in the way of seeing the diagram; can they be moved to the side or possibly replace simply with single letters like "P", "G" and "R" for "physical", "genetic" and "regulatory" respectively? Might still need a legend?
  • Request: Change the wording "Browse selection" to something like "View/analyze gene list"
  • Where else could we implement a similar type of Venn diagram tool? Disease or phenotype annotations?

New round of phenotype requests

  • GMail really throttling email sending
  • Chris will reach out to Google/GMail to see if we can:
    • A) get a clear explanation about what their restrictions are and how they work and
    • B) see if we can get a paid plan to help expedite the email process (see how much cost)

Aligning interaction data with GO and GO-CAM

  • The Alliance interactions working group is considering proposing a greater alignment between GO interaction annotations (like "binding" annotations with IPI evidence codes, for example) and Alliance molecular interaction annotations
  • Also, would like to propose a pipeline for possibly automatically generating GO-CAM annotations/networks based on inferences made from phenotype annotations, genetic interactions, regulatory interactions, and molecular interactions
  • Much of this depends on genetic perturbation (e.g. allele/variant) annotation to effects, like loss-of-function or gain-of-function annotations
    • Would be good to get a sense from other Alliance members the extent to which we could rely on the presence of such annotations
  • Chris and Kimberly will meet to discuss further

Short SObA talk at Alliance meeting

  • Raymond prepared to give short talk on SObA to the Alliance group

Single cell data visualization tool

  • Eduardo will present to Paul's lab meeting tomorrow
  • Will discuss at Alliance expression working group pre-meeting

December 19, 2019

AGR Face to Face meeting debrief

  • AGR data need to synchronize with MODs. AGR will have more frequent releases (monthly or every two months) so that it reflects the same data as MODs.
  • MODs have different curation policies. For example, BioGrid has predicted protein-protein interactions. AGR import them but WormBase does not have them. AGR needs to do its own prediction based on the current data, although BioGrid does a good job.
  • The gene description curation tool developed by Juancarlos got good feedback. Juancarlos will add more function to visualize and compare annotations.
  • The gene description working group will enter maintenance mode.
  • Allele phenotype WG will start to the AGR allele page.
  • SimpleMine vs intermine: Wen argues that there is no conflict. It is like 7-Eleven vs. Walmart (and Biomart is like Target ...)
  • High-throughput expression: Most of MODs have zero curation manpower thus they prefer to outsource to Express Atlas or GEO unless future grants prioritize curation on high-throughput. Expression Atlas regard worm as a low priority so they may not do much for the worm.
  • Software development: focus on AGR instead of MODs. SAB hopes all MODs to retire their features to turn more users to AGR.
  • WormBase should direct all links of orthologs to AGR. Currently, orthologs are pointed to a WormBase page with no content. Wen will create a github ticket for the web team to make the changes.
  • Paper triage working group: It will be good if MODs can share their paper sources. Karen, Michael Mueller, and Kimberly will be involved in this WG.
  • Working Groups need more cross-talks, for example, GO and gene description are related.
  • SoBA got positive feedback. Some groups want to use it to compare two-gene curations, as well as the enrichment analysis.
  • Non-coding RNA: Paul Sternberg will contact Frank Slack to see what they need for curation.