Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
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= 2020 Meetings =
  
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= 2019 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
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[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
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[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
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[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
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[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
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== May 2, 2019 ==
 
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=== SObA for all ontologies ===
 
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* http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
 
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* SObA graph search for all ontologies
 
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* Juancarlos and Raymond looking for feedback; let them know
 
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* 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?
 
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** Raymond: thinking of putting blurb on a separate documentation page
 
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* 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.)
 
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=== IWM swag - screen cloth ===
 
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* Need to finalize design
 
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* Put Dick & Jane cartoon in one corner, tools in another corner, WB logo, Alliance logo
 
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* Daniel can take care of ordering and printing, but needs someone to choose the design
 
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=== Phenotype ontology patternization ===
 
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* Chris working on patternizing phenotype terms to standardize logical definitions for classes of terms
 
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* This is part of the ongoing effort to align phenotype ontologies across the organisms
 
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* 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
 
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* Does "dumpy" mean the same thing to everyone? Is there a way to assess discrepancies in term definitions among members of the community?
 
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* Does someone annotate to Egl or vulvaless?
 
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* How do we help community curators decide the correct term?
 
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* Could we develop a smart annotation aid/tool/helper? Use images, examples, etc.
 
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== May 9, 2019 ==
 
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=== SObA for all ontologies ===
 
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* Revised version http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
 
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* Changed legend labelling, added linkouts
 
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* To implement on Gene pages. One vs. Five widgets?
 
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* 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?
 
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** Or click on an edge to get the, e.g., GO subgraph that connects the two nodes?
 
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* Let's release to the website, but gather feedback from (naive) users to see what documentation we need
 
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=== Citace upload next Tuesday ===
 
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* Tuesday May 14, 2019, 10am Pacific
 
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=== SPELL is now indexed by Google ===
 
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* Cool!
 
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== May 16, 2019 ==
 
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=== SObA graphs ===
 
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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
 
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* May provide more information than the user needs/wants
 
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* Juancarlos working on implementing SObA widgets on gene pages (maybe for WS271 or WS272?)
 
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* IWM will have WS271 on staging during meeting; probably on production shortly after the meeting
 
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** Hope to show users demos at IWM
 
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=== IWM swag: screen cloths ===
 
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* Paul is working on the graphic
 
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* Need to order soon
 
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=== Testing on staging site ===
 
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* Adam and Sibyl request people to test Sequences widgets on Pseudogene, CDS, and Transcript pages on staging
 
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* Sibyl has asked for testing of new search on staging
 
  
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
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== May 23, 2019 ==
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
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=== WormBase Google folder ===
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
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* https://drive.google.com/drive/folders/1VYJbGYTa-7PncQcZW7VAy73DZ2jL0p4u?usp=sharing
 
  
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=== ?Genotype class ===
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
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* Chris and Ranjana will work on early next week
 
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* Will need to accommodate disease model annotations
 
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* Will bring up again for discussion with larger group next week
 
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* 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
 
  
  
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== May 30, 2019 ==
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== June 4, 2020 ==
  
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=== Phenotype Request Emails ===
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=== Citace (tentative) upload ===
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* New round for May 2019
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* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
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* 1139 emails total; 825 emails gone out so far today
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* Citace upload to Hinxton on Friday, July 10th
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* Chris will report back next week with numbers
 
  
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=== ?Genotype class ===
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=== Caltech reopening ===
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* Google doc: https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing
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* Paul looking to get plan approved
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* Are or aren't we moving to serial identifiers for strains, e.g. WBStrain0000001? Need to ask Kevin et al.
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* People that want to come to campus need to watch training video
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* 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
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* Masks available in Paul's lab
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** 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
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* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
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** 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
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** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
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** 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?
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* Need to coordinate, maybe make a Google calendar to do so (also Slack)
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** Do we really want to list all genes that are affected by a rearrangement?
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* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
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** What about RNAi treatments? Should these be considered part of the genotype? Authors often report it that way
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* Also, need to submit who you were in contact with for contact tracing
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*** 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.
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* Form is used all week, and hold on to it until asked to be submitted
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* 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.
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* If someone goes in to the office, they could print several forms for people to pick up in WB offices
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** It may be best to include this tag, but make it a convention to only annotate it when it ISN'T N2
 
  
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=== Nameserver ===
 +
* Nameserver was down
 +
* CIT curators would still like to have a single form to interact with
 +
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 +
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 +
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 +
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
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== June 6, 2019 ==
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=== Alliance SimpleMine ===
 +
* Any updates? 3.1 feature freeze is tomorrow
 +
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call

Revision as of 00:09, 5 June 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
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