Difference between revisions of "WormBase-Caltech Weekly Calls"

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=== SPELL is now indexed by Google ===
 
=== SPELL is now indexed by Google ===
 
* Cool!
 
* Cool!
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 +
 +
 +
== May 16, 2019 ==
 +
 +
=== SObA graphs: edge info ===
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* 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
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* Juancarlos working on implementing SObA widgets on gene pages

Revision as of 15:45, 16 May 2019

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

March

April


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: edge info

  • 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