Difference between revisions of "WBConfCall 2020.03.05-Agenda and Minutes"

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= Agenda =  
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= Agenda & Minutes =  
 +
 
 +
== Project meeting ==
 +
* Hinxton attendance in doubt
 +
** EMBL Coronavirus guidelines: do not plan any unavoidable travel
 +
* Could important subsets of the agenda be done virually
 +
* Paul S: Travel looks like it's going to slow down due to restrictions
 +
** We should consider how to do the meeting remotely/virtually
 +
** Maybe we can do a conference call late March or early April
 +
** Could try one topic per day 2-3 hours each time (early for California, late for UK)
 +
** Will take some discipline and focus, but we can get it done
 +
** Taxis can be arranged for travel after public transport hours (still a lot cheaper than trans-Atlantic flights)
  
 
== WS277 data freeze ==
 
== WS277 data freeze ==
Line 7: Line 18:
 
** Can be flexible and push back by a week if required.
 
** Can be flexible and push back by a week if required.
 
* Several Caltech curators may take March 30 - April 3 off due to school break
 
* Several Caltech curators may take March 30 - April 3 off due to school break
 +
* Will WS276 go to FTP site this weekend?
 +
** There have been some delays, so probably won't be up until next week sometime (definitely up by March 13)
  
 
== Help Desk ==
 
== Help Desk ==
Line 15: Line 28:
 
** Unsure on this:
 
** Unsure on this:
 
*** Could this be added as a GO MF (GO:0050207)?
 
*** Could this be added as a GO MF (GO:0050207)?
 +
**** GO annotations added to Y53C10A.5 using WBPaper00059383 as evidence (2020-03-09 kmva)
 
* [https://github.com/WormBase/website/issues/7581 CGC bad WB link URL]; can this be closed?
 
* [https://github.com/WormBase/website/issues/7581 CGC bad WB link URL]; can this be closed?
 +
** Kimberly will follow up and then close
 +
*** Link fixed and issue now closed (2020-03-09 kmva)
 
* [https://github.com/WormBase/website/issues/7579 Maureen Barr's question about protein coding genes with known function]; can this be closed?
 
* [https://github.com/WormBase/website/issues/7579 Maureen Barr's question about protein coding genes with known function]; can this be closed?
 +
** Kimberly will follow up and then close
 
* [https://github.com/WormBase/website/issues/7578 Setting up local instance of JBrowse]; can this be closed?
 
* [https://github.com/WormBase/website/issues/7578 Setting up local instance of JBrowse]; can this be closed?
 +
** Scott hasn't heard back, will close for now
  
 
== Rearrangement IDs ==
 
== Rearrangement IDs ==
Line 24: Line 42:
 
* Todd suggested rolling them into the WBVariation class
 
* Todd suggested rolling them into the WBVariation class
 
* Rearrangement class model doc https://docs.google.com/document/d/1Zntv3UA30dYxyf0MLKgZnThlFMPdTJ_wOokD06vdxss/edit?usp=sharing
 
* Rearrangement class model doc https://docs.google.com/document/d/1Zntv3UA30dYxyf0MLKgZnThlFMPdTJ_wOokD06vdxss/edit?usp=sharing
 +
* We want to make sure that users can still find the Rearrangement objects as they have in the past; e.g. web pages, tracks in the genome browser for balancers, etc.
 +
* Rearrangements have been historically difficult to map; will mapping become a problem
 +
* Karen, Paul, et al. will setup a call
  
 
== Nameserver-to-Caltech info transmission ==
 
== Nameserver-to-Caltech info transmission ==
Line 30: Line 51:
 
* Caltech can create a local CGI to immediately update Postgres/OA with new terms before nightly dump occurs
 
* Caltech can create a local CGI to immediately update Postgres/OA with new terms before nightly dump occurs
 
* Is there an effective mechanism to make updates to Caltech Postgres/OA as immediately as possible?
 
* Is there an effective mechanism to make updates to Caltech Postgres/OA as immediately as possible?
−
 
 
** The Nameservice is available for curators to request IDs so they can immediately continue with curation.
 
** The Nameservice is available for curators to request IDs so they can immediately continue with curation.
 
** Extend the TempVariationObo system to all classes
 
** Extend the TempVariationObo system to all classes
 
** Potential for a queue system so that they get automatically added (Prototype system was added for different purpose but pulled a long time ago).
 
** Potential for a queue system so that they get automatically added (Prototype system was added for different purpose but pulled a long time ago).
 
** The rest API could be used to request IDs direct from the OA meaning that they would be available immediately without relying on additional services.
 
** The rest API could be used to request IDs direct from the OA meaning that they would be available immediately without relying on additional services.
 +
* Easiest current solution is to make the new Strain addition CGI, but still not ideal
 +
* Could possibly implement the OA to make requests to the Name service but would require login using wormbase.org Google accounts, but would likely take a considerable amount of code writing
 +
* Karen use case:
 +
** Phenotype curation; try to enter into the OA, doesn't come up; may look in WormBase, if not there, go to Name service; try to generate an ID, if exists will get a notice, if not, an ID will be generated an used in CGI to immediately import into Postgres/OA, need to refresh OA to see the variation
 +
** Genetics and G3 papers and microPublications need linking for objects; if not already in DB, create in Name service and create link
  
 
== Disease info changes in 6 classes ==
 
== Disease info changes in 6 classes ==
 
*I propose making these changes for WS278, gives us more time to revisit/change dumpers, and test the data here at Caltech (Ranjana)
 
*I propose making these changes for WS278, gives us more time to revisit/change dumpers, and test the data here at Caltech (Ranjana)
 
*If we want to go ahead with the new ?Genotype class, that's separate and I'm fine with that (Ranjana)
 
*If we want to go ahead with the new ?Genotype class, that's separate and I'm fine with that (Ranjana)
−
+
* https://wiki.wormbase.org/index.php/Model_changes_to_capture_and_consolidate_human_disease_data
 +
 
 
== Single cell expression tool ==
 
== Single cell expression tool ==
 
* Eduardo is looking for feedback on his tool to query C. elegans single cell expression
 
* Eduardo is looking for feedback on his tool to query C. elegans single cell expression
 
* Tool is here: http://de.wormcells.com/
 
* Tool is here: http://de.wormcells.com/
 +
* Can produce volcano plots
 +
** x axis log2 expression
 +
** y axis base factor (generalization of a p-value)
 +
*** Anything above 2 or 3 is a robust hit
 +
* Should send around to users who have asked about single cell data (e.g. Peter Roy)

Latest revision as of 14:36, 9 March 2020

Agenda & Minutes

Project meeting

  • Hinxton attendance in doubt
    • EMBL Coronavirus guidelines: do not plan any unavoidable travel
  • Could important subsets of the agenda be done virually
  • Paul S: Travel looks like it's going to slow down due to restrictions
    • We should consider how to do the meeting remotely/virtually
    • Maybe we can do a conference call late March or early April
    • Could try one topic per day 2-3 hours each time (early for California, late for UK)
    • Will take some discipline and focus, but we can get it done
    • Taxis can be arranged for travel after public transport hours (still a lot cheaper than trans-Atlantic flights)

WS277 data freeze

  • When will the schema be released?
    • Scheduled for 13th March
    • Upload 3rd April
    • Can be flexible and push back by a week if required.
  • Several Caltech curators may take March 30 - April 3 off due to school break
  • Will WS276 go to FTP site this weekend?
    • There have been some delays, so probably won't be up until next week sometime (definitely up by March 13)

Help Desk

  • The following 3 items are linked and the Gene has been named and a new lab created:
    • Has anyone replied to Padhu Padmanabhan (email Feb 4)? - Yes Paul D. replied on the 4th directing them to the genenames list
    • Asked about indicating Y53C10A.5 as having plasmanylethanolamine delta-1-desaturase (EC 1.14.99.19) activity - Can be closed
    • Has anyone replied to Montserrat Elías regarding naming of same gene, Y53C10A.5? - This name has been agreed by Tim S. and the issue can be closed.
    • Unsure on this:
      • Could this be added as a GO MF (GO:0050207)?
        • GO annotations added to Y53C10A.5 using WBPaper00059383 as evidence (2020-03-09 kmva)
  • CGC bad WB link URL; can this be closed?
    • Kimberly will follow up and then close
      • Link fixed and issue now closed (2020-03-09 kmva)
  • Maureen Barr's question about protein coding genes with known function; can this be closed?
    • Kimberly will follow up and then close
  • Setting up local instance of JBrowse; can this be closed?
    • Scott hasn't heard back, will close for now

Rearrangement IDs

  • From thread on Slack, "general" channel
  • Karen asked about getting WB IDs for rearrangements (they currently do not get serial IDs)
  • Todd suggested rolling them into the WBVariation class
  • Rearrangement class model doc https://docs.google.com/document/d/1Zntv3UA30dYxyf0MLKgZnThlFMPdTJ_wOokD06vdxss/edit?usp=sharing
  • We want to make sure that users can still find the Rearrangement objects as they have in the past; e.g. web pages, tracks in the genome browser for balancers, etc.
  • Rearrangements have been historically difficult to map; will mapping become a problem
  • Karen, Paul, et al. will setup a call

Nameserver-to-Caltech info transmission

  • Caltech curators would like quick turn around when requesting names/IDs
  • Currently relies on a nightly cronjob to dump GeneACE to Caltech Postgres database
  • Caltech can create a local CGI to immediately update Postgres/OA with new terms before nightly dump occurs
  • Is there an effective mechanism to make updates to Caltech Postgres/OA as immediately as possible?
    • The Nameservice is available for curators to request IDs so they can immediately continue with curation.
    • Extend the TempVariationObo system to all classes
    • Potential for a queue system so that they get automatically added (Prototype system was added for different purpose but pulled a long time ago).
    • The rest API could be used to request IDs direct from the OA meaning that they would be available immediately without relying on additional services.
  • Easiest current solution is to make the new Strain addition CGI, but still not ideal
  • Could possibly implement the OA to make requests to the Name service but would require login using wormbase.org Google accounts, but would likely take a considerable amount of code writing
  • Karen use case:
    • Phenotype curation; try to enter into the OA, doesn't come up; may look in WormBase, if not there, go to Name service; try to generate an ID, if exists will get a notice, if not, an ID will be generated an used in CGI to immediately import into Postgres/OA, need to refresh OA to see the variation
    • Genetics and G3 papers and microPublications need linking for objects; if not already in DB, create in Name service and create link

Disease info changes in 6 classes

Single cell expression tool

  • Eduardo is looking for feedback on his tool to query C. elegans single cell expression
  • Tool is here: http://de.wormcells.com/
  • Can produce volcano plots
    • x axis log2 expression
    • y axis base factor (generalization of a p-value)
      • Anything above 2 or 3 is a robust hit
  • Should send around to users who have asked about single cell data (e.g. Peter Roy)
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