Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
= 2021 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== March 5, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
=== WormBase curation ===
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Tim Schedl: WB needs to do more curation for phenotype and variation
 
* Doing community curation, but not fast enough
 
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 
  
=== Alaksa ===
 
* Joesph may be able to meet with Raymond
 
* How can the tool be maintained? If it can't it needs to be pulled
 
  
=== Single cell expression tool ===
+
== July 1, 2021 ==
* Tool is here: http://de.wormcells.com/
 
* What do we need to consider for pulling into WormBase?
 
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
 
** Would want it to be in sync with WormBase releases
 
** May not need to reprocess with every release with current (small-ish) data set
 
* Fully integrated tool versus an embedded tool?
 
  
=== Name service updates ===
+
=== Importing genes for tm alleles from GeneACE ===
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
+
* https://github.com/WormBase/website/issues/8262
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
+
* Nightly dump currently excludes tm allele genes
 +
* Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
 +
* Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
 +
* ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
 +
* Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?
  
 +
=== Citace upload ===
 +
* Curators upload files to Spica for citace upload on Tuesday (July 6)
  
== March 12, 2020 ==
+
=== Chen B1 kitchen Usage Considerations ===
 +
* Clean up after oneself.
 +
* Mark food storage with name and date.
 +
* Mark storage drawers
 +
* Consumables
  
=== Cancelled meetings ===
 
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
 
* We should start doing online advertisement for micropublications with webinars
 
  
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
+
== July 8, 2021 ==
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
 
* Valerio would like to add these to Postgres to keep a more central repository of them
 
* Chris would still like to be able to readily update/edit the content of those lists
 
  
* Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
+
=== Alliance work ===
 +
* Orange team presenting initial plans at Alliance PI meeting tomorrow
 +
* What working groups are still meeting? What are their responsibilities?
 +
** Expression
 +
** Variants
 +
** Disease & Phenotype
 +
** Technical working groups
 +
*** Technical call
 +
*** Data quartermasters
 +
*** DevOps
 +
* Expression working group working on LinkML model with Gil (FB)
 +
** Includes work on antibody class, image class, movie class
 +
** Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
 +
* Creating a curation interface/tool:
 +
** Will require loading auxiliary data types in addition to primary data types (e.g. if we are focused on disease annotation curation, we will need to load genes, alleles, strains, etc. in addition to the disease annotations themselves) to be available to make connections to
 +
** One requirement already expressed by curators is the need to generate new entities, like alleles, and have them quickly (immediately?) available for use in curation
 +
** Maybe this could be handled by an Alliance central name server that mints new IDs (Alliance IDs and maybe also MOD IDs?) for the objects to make them available (also with a mechanism for these new objects/IDs to make their way back to the MODs as well)
 +
** Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs
  
=== Updates on Alaska ===
+
== July 15, 2021 ==
  
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
+
=== hlh-34 expression ===
The future plan is to move the platform to Google colab to reduce maintainance work.
+
* Rebecca Mcwhirter (Miller lab) contacted WB saying that the annotations to AVJ for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.org/10.1016/j.cmet.2012.05.014) had to pick one neuron per reviewer's request. The neuron should instead be AVH.
 +
* Oliver is putting together a micropub to clarify the issue
 +
* How to deal with existing  annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
 +
* Should we also add public comments to the relevant papers?
  
==Nameservice discussion==
+
== July 22, 2021 ==
*Getting a token has worked for Chris and Ranjana
 
*Karen and Daniela need to get tokens
 
  
==Noctua GO-CAM updates==
+
=== Copying data from textpresso-dev to tazendra ===
*Noctua is a production tool available for annotations right now
+
* Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
*Create as many interconnected models and make available for curators is the ongoing goal
+
* Can we copy files to tazendra?
*Reactome models are in the process of being imported
+
* If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
*Real time validation messages as curation is being done, is being worked on
+
* Are there any size considerations for what we copy over?  There are 1.1T free in /home2 which is not backed up
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
 
  
 +
== July 29, 2021 ==
  
== March 19, 2020 ==
+
=== Textpresso Dev machine retiring ===
 +
* Need to work out when and how to move things off the machine before retiring for good
  
=== Citace Upload ===
+
=== Proxies for Caltech-hosted tools broken ===
* Tuesday, March 31st
+
* Several Caltech CGI tools using a proxy on WormBase site are broken (throwing 504 Gateway Time-out or Server Error)
 +
* Affected tools:
 +
** https://wormbase.org/tools/soba/soba.cgi?action=Gene+Pair+to+SObA+Graph
 +
** https://wormbase.org/tools/soba/soba.cgi?action=Terms+to+SObA+Graph
 +
** https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi
 +
** https://wormbase.org/tools/rnaseq/fpkmmine.cgi
 +
** https://wormbase.org/tools/ontology_browser
  
=== Latest ACEDB ===
+
=== 2021 Genetics paper ===
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
+
* Paul D has asked for contributions (~200 words each)
 
+
* Paul's preliminary suggested sections:
=== Storing email addresses/persons to omit from requests ===
+
** CeNGen (CalTech)
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
+
** Expression & Transcription (Wen)
 
+
*** Spell (Wen)
=== Mailing lists ===
+
** SimpleMine (CalTech Wen)
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
+
** WormiCloud - (Jae/Valerio Caltech)
 
+
** Vennter (Jae/Caltech)
 
+
** Gene Name Sanitizer (Wen/Raymond/Caltech?)
==March 26th==
+
** VFP (Valerio)
===Community curation===
+
** Author first pass (Daniela)
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
+
** Human disease (Ranjana)
* Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
+
** Molecular and genetic interactions (You/Chris)
* Blog about phenotype form to make people generally aware
+
** Pathways and Processes (Karen)
* Could the phenotype form be adapted for other species? Possibly but depends on:
+
** Anatomy and Cell (Raymond)
** Whether genotypes could be loaded and recognized
+
* Now have 'Community Curation' for AFP and other community curation
 
+
* Also, gene descriptions section
=== AFP for older papers ===
 
* Discussed recently
 
* Many (all?) Old papers have already gone through the old AFP pipeline
 
* Need to check what has already been curated
 
 
 
=== Omit form ===
 
* http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi
 
* Can view, add, or edit persons, email addresses, and IP addresses to omit from email requests (and IP addresses to block)
 
 
 
=== Problems accessing Textpresso Central ===
 
* Ranjana had noticed that the server was acting slow
 
* Unknown problem; hard to pin down
 
* Definitely a Caltech network system
 
* Issue for past couple of weeks
 
* May be able to ask Caltech IMSS for a diagnostic analysis
 
* Bad switch? Maybe; there is an unused switch that could be used to test
 

Latest revision as of 18:30, 29 July 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May

June


July 1, 2021

Importing genes for tm alleles from GeneACE

  • https://github.com/WormBase/website/issues/8262
  • Nightly dump currently excludes tm allele genes
  • Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
  • Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
  • ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
  • Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?

Citace upload

  • Curators upload files to Spica for citace upload on Tuesday (July 6)

Chen B1 kitchen Usage Considerations

  • Clean up after oneself.
  • Mark food storage with name and date.
  • Mark storage drawers
  • Consumables


July 8, 2021

Alliance work

  • Orange team presenting initial plans at Alliance PI meeting tomorrow
  • What working groups are still meeting? What are their responsibilities?
    • Expression
    • Variants
    • Disease & Phenotype
    • Technical working groups
      • Technical call
      • Data quartermasters
      • DevOps
  • Expression working group working on LinkML model with Gil (FB)
    • Includes work on antibody class, image class, movie class
    • Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
  • Creating a curation interface/tool:
    • Will require loading auxiliary data types in addition to primary data types (e.g. if we are focused on disease annotation curation, we will need to load genes, alleles, strains, etc. in addition to the disease annotations themselves) to be available to make connections to
    • One requirement already expressed by curators is the need to generate new entities, like alleles, and have them quickly (immediately?) available for use in curation
    • Maybe this could be handled by an Alliance central name server that mints new IDs (Alliance IDs and maybe also MOD IDs?) for the objects to make them available (also with a mechanism for these new objects/IDs to make their way back to the MODs as well)
    • Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs

July 15, 2021

hlh-34 expression

  • Rebecca Mcwhirter (Miller lab) contacted WB saying that the annotations to AVJ for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.org/10.1016/j.cmet.2012.05.014) had to pick one neuron per reviewer's request. The neuron should instead be AVH.
  • Oliver is putting together a micropub to clarify the issue
  • How to deal with existing annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
  • Should we also add public comments to the relevant papers?

July 22, 2021

Copying data from textpresso-dev to tazendra

  • Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
  • Can we copy files to tazendra?
  • If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
  • Are there any size considerations for what we copy over? There are 1.1T free in /home2 which is not backed up

July 29, 2021

Textpresso Dev machine retiring

  • Need to work out when and how to move things off the machine before retiring for good

Proxies for Caltech-hosted tools broken

2021 Genetics paper

  • Paul D has asked for contributions (~200 words each)
  • Paul's preliminary suggested sections:
    • CeNGen (CalTech)
    • Expression & Transcription (Wen)
      • Spell (Wen)
    • SimpleMine (CalTech Wen)
    • WormiCloud - (Jae/Valerio Caltech)
    • Vennter (Jae/Caltech)
    • Gene Name Sanitizer (Wen/Raymond/Caltech?)
    • VFP (Valerio)
    • Author first pass (Daniela)
    • Human disease (Ranjana)
    • Molecular and genetic interactions (You/Chris)
    • Pathways and Processes (Karen)
    • Anatomy and Cell (Raymond)
  • Now have 'Community Curation' for AFP and other community curation
  • Also, gene descriptions section