Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2017|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_March_2017|March]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
== April 6, 2017 ==
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
=== AGR time spent ===
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
* Paul S asking about %time spent on AGR project
 
* Time spent on working groups, conference calls, AGR development
 
* Send estimates to Paul
 
  
=== SimpleMine ===
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
* Two tables added to SimpleMine for human orthology
 
* Now SimpleMine output has many columns (30+)
 
* We may want to give users the option to specify which output they want
 
* Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc.
 
* All checkboxes can be checked by default
 
  
=== Enrichment tools ===
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
* Raymond working on display for paper
 
  
=== Gene Ontology SObA graph ===
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
* Raymond, Juancarlos working on
 
* Working on paper
 
  
=== WormMine updates ===
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* WS258 adding gene class
 
* WS259 adding more info (almost all meta data) on variations, laboratory and strains, RNAi phenotypes (hopefully)
 
* Expression data in WormMine is problematic
 
* Many genes being annotated to the same ~6 tissues or so
 
* Resulting in erroneous data for some genes
 
* Chris will send GitHub ticket to Todd
 
* Todd will discuss with Paulo today
 
  
=== Gene Ontology ===
 
* Some very complex terms becoming immediate children of root terms (e.g. "biological process")
 
* May be result of attempt to create logical definitions/equivalence axioms
 
* Raymond will discuss with Kimberly
 
  
 +
== July 1, 2021 ==
  
== April 13, 2017 ==
+
=== 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?
  
=== Methods in Molecular Biology chapter ===
+
=== Citace upload ===
* Chapter draft sent out Monday night
+
* Curators upload files to Spica for citace upload on Tuesday (July 6)
* Will send to Martin at MiMB by late next week
 
* Please take a look and send comments
 
* Authors check their sections and send figure legends to Chris
 
  
=== Progress report ===
+
=== Chen B1 kitchen Usage Considerations ===
* If someone finds the 2016 report, send around to group
+
* Clean up after oneself.
* May 1st deadline (need to verify)
+
* Mark food storage with name and date.
 +
* Mark storage drawers
 +
* Consumables
  
=== 2017 IWM ===
 
* Early registration Deadline May 18th
 
  
=== Models for citace ===
+
== July 8, 2021 ==
* Wen will fit models to local citace, should be ready by tomorrow
 
  
=== Citace Upload ===
+
=== Alliance work ===
* Tuesday, April 25th, 10am
+
* 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
  
=== Enrichment tool ===
+
== July 15, 2021 ==
* Now available for gene ontology and phenotype on live site
 
* Paper being submitted soon
 
* Need to change "Tissue Enrichment Analysis" link title under WormBase Tools menu
 
  
=== SObA for Gene Ontology ===
+
=== hlh-34 expression ===
* Data source was server on Berkeley BOP; thought it was public but were discouraged to use
+
* 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.
* Seth Carbon said we could use it but might not always be working; now it seems to be down or dysfunctional
+
* Oliver is putting together a micropub to clarify the issue
* SObA for GO will be broken until we install our own local server (Raymond working on)
+
* 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?
  
=== Dumping data for upload, taking over for Karen ===
+
== July 22, 2021 ==
* Karen will take care of dumping and uploading the data for this upload
 
* Karen will review the molecule curation with other curators at the IWM
 
  
=== Datomic meeting ===
+
=== Copying data from textpresso-dev to tazendra ===
* Matt, Sibyl, Adam, Todd, Juancarlos, Raymond sat in
+
* Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
* Raymond: thought Datomic would take over from ACEDB completely, but it seems we will still use ACEDB for some time for e.g. FMap
+
* Can we copy files to tazendra?
* Seems there should be an executive meeting about Datomic to make clear what it will be used for and what it won't be used for
+
* If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
* Several web pages and widgets are now being served by Datomic
+
* Are there any size considerations for what we copy over? There are 1.1T free in /home2 which is not backed up
* There's a question about how we now handle model changes going forward
 
* Juancarlos will send around link for newest Datomic querying tool; may require access for specific IP addresses
 
 
 
 
 
== April 20, 2017 ==
 
 
 
=== Gene Ontology data for SObA ===
 
* Use of GO server; hasn't been reliable
 
* Raymond working on establishing our own server to host all GO data
 
* Raymond and Juancarlos will keep working on SObA representation of GO annotations
 
 
 
=== Progress Report ===
 
* WS259 can be used as the current reference
 
* Paul will send around last year's progress report
 
* What was the last release that we referenced in last year's progress report? We'll say WS254
 
* Wen will generate numbers for WS254 (resurrect WS254 ACEDB)
 
* Opportunity to specify/narrow scope of project
 
* Want to push community/automated curation, with curators laying foundation of data models, forms
 
* Promote LEGO curation; need to learn what needs to be said about plan going forward/what we want to accomplish
 
 
 
=== LEGO curation ===
 
* Phenotype curation in LEGO? Need to review phenotype-to-GO pipeline
 
* Want/need a mapping of phenotype terms to GO process terms; may require context-dependent mapping (e.g. "dumpy" phenotype)
 
* We don't make direct associations of phenotypes to LEGO models, although we do have "inferred from mutant phenotype" evidence code
 
* Want a mechanism to automate conversion of WB annotations into LEGO models
 
* Want a display mechanism that is user friendly, convert hairball into pathway
 
* We could focus on a particular topic/disease and collectively contribute
 
* Do we want to write a proposal to take existing, granular annotations (e.g. at level of mutation details) and map to LEGO model?
 
* Can we integrate the micropublication pipeline into LEGO model generation?
 
* How to assess the confidence of assertions?
 
 
 
=== Follow up on transgene question from user ===
 
* Karen will contact authors of paper
 
 
 
=== Citace upload ===
 
* Tuesday, Apr 25th, 10am
 
  
 +
== July 29, 2021 ==
  
 +
=== Textpresso Dev machine retiring ===
 +
* Need to work out when and how to move things off the machine before retiring for good
  
== April 27, 2017 ==
+
=== Proxies for Caltech-hosted tools broken ===
 +
* 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
  
=== Gene Ontology data for SObA ===
+
=== 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

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