WormBase-Caltech Weekly Calls
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Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2019 Meetings
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