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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
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[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
  
== June 6, 2019 ==
+
== July 1, 2021 ==
  
=== New SObA graphs ===
+
=== Importing genes for tm alleles from GeneACE ===
* May put graphs within existing widgets, but don't need to rush to get that ready for IWM
+
* 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?
  
=== Phenotype association file format ===
+
=== Citace upload ===
* May be best to leave the format as is
+
* Curators upload files to Spica for citace upload on Tuesday (July 6)
* There are problems; paper IDs keep switching columns
 
* Would need to revisit the reasoning for why we do it that way
 
* When will the Alliance produce a similar/replacement file? Not sure
 
  
=== Phenotype requests ===
+
=== Chen B1 kitchen Usage Considerations ===
* Sent out 1140 emails on May 30
+
* Clean up after oneself.
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
+
* Mark food storage with name and date.
* 21 papers flagged as not having phenotypes
+
* Mark storage drawers
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
+
* Consumables
  
  
== June 13, 2019 ==
+
== July 8, 2021 ==
  
=== IWM ===
+
=== Alliance work ===
* Coordinating transportation of swag boxes to Pauley Pavilion
+
* Orange team presenting initial plans at Alliance PI meeting tomorrow
* Workshop on Saturday June 22, from 1pm to 2:30pm
+
* What working groups are still meeting? What are their responsibilities?
* Saturday morning micropublication breakfast 7:30 - 8:30am
+
** Expression
* Workshop
+
** Variants
** Presenters: it may be best to present as use cases rather than a research project
+
** Disease & Phenotype
** Chris will cover SimpleMine for Wen
+
** Technical working groups
** Chris: won't do live demo; only screenshots, maybe some video
+
*** Technical call
* Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
+
*** Data quartermasters
* Paul's talk
+
*** DevOps
** Cover Alliance
+
* Expression working group working on LinkML model with Gil (FB)
** New features
+
** Includes work on antibody class, image class, movie class
*** SObA (for new data)
+
** Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
*** Complete for protein-protein interactions
+
* Creating a curation interface/tool:
*** RNASeq tools
+
** 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
*** Updated automated gene concise descriptions?
+
** 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
** Phenotype community 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)
*** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
+
** Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs
** Author First Pass
 
** Micropublication
 
  
=== SGD SAB ===
+
== July 15, 2021 ==
* Paul attended
 
* Alliance publicity was discussed
 
* SAB likes the Alliance orthology features
 
* Working on topics: displaying papers and data
 
* Pathways: discussion about best approach
 
* Metabolic engineering
 
* Meta data about RNASeq data
 
** SPELL tool, basically only tool of its kind available; need new tools
 
* Species-specific proteins: how best to find them? HMMs (Jackhammer)?
 
  
=== Concise descriptions ===
+
=== hlh-34 expression ===
* Progress being made within the Alliance to update the automated concise gene descriptions
+
* 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.
* We will still accept manually written descriptions and display them in parallel with automated descriptions
+
* 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?
  
=== Micropublications ===
+
== July 22, 2021 ==
* If people are requesting manually written gene descriptions, they could submit a microreview
 
* Concern was expressed about how to handle a really high throughput of submissions:
 
** Daniela: Working towards automating as much of the processing pipeline as possible
 
** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
 
** Not getting lots of submissions yet, probably won't be inundated in the near future
 
** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
 
* Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
 
  
=== Undiagnosed Disease Network data ===
+
=== Copying data from textpresso-dev to tazendra ===
* Andy Golden will meet with Ranjana and Chris at IWM to discuss
+
* Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
* Andy asked about protocol pages at WormBase?
+
* Can we copy files to tazendra?
* Paul: Bioprotocols and Protocols IO
+
* If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
* Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
+
* 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 ==
  
==June 27th, 2019==
+
=== Textpresso Dev machine retiring ===
===IWM 2019===
+
* Need to work out when and how to move things off the machine before retiring for good
* Impressions, analysis, feedback from Users etc etc
 
* Anatomy term synonym search
 
** User pointed out that "RnB" search returns 0 results; GitHub ticket made to index anatomy synonyms
 
* Ciliated neurons
 
** User pointed out that male ciliated neurons are missing as a subclass of term "ciliated neuron"; GitHub ticket made, easy fix
 
* Import of 22G and 26G RNAs
 
** Spoke to Julie Claycomb
 
** These are short RNAs transcribed by RNA-dependent RNA Polymerase (RdRP) off of mRNA molecules
 
** Should these be instantiated as gene objects in WormBase? Julie argues that these are not genes
 
*** Should these just be transcript objects? Would they be linked to a gene? Or maybe also to any transcripts from which they could be derived?
 
** Many map uniquely to the genome, but some map in multiple locations
 
** Associated data for now would likely just be protein-RNA interactions (Argonaute-RNA interactions)
 
* Ranjana & Chris spoke with Andy Golden
 
** Andy and his lab will submit phenotype and disease data as they become available (likely pre-publication); we will likely point to a consortium as source until paper is published
 
** There is still a strong need for cross-species variant mapping/visualization
 
* miRNA binding sites
 
** User asked at workshop and at booth; can we show miRNA binding sites in JBrowse? We would need to collect the data
 
** There are many sources of miRNA-target interactions, some experimental, most predicted
 
*** Chris compiled [https://docs.google.com/spreadsheets/d/19-txXrGi-ROFuByyLnQYvWbKl3o12KZON56qto3MN6g/edit?usp=sharing list of interaction databases] for Alliance interactions working group
 
  
===Giving disease model annotations a stable identifier===
+
=== Proxies for Caltech-hosted tools broken ===
*Currently disease model annotations get a temporary ID at the time of dump,
+
* Several Caltech CGI tools using a proxy on WormBase site are broken (throwing 504 Gateway Time-out or Server Error)
<pre style="white-space: pre-wrap;
+
* Affected tools:
white-space: -moz-pre-wrap;
+
** https://wormbase.org/tools/soba/soba.cgi?action=Gene+Pair+to+SObA+Graph
white-space: -pre-wrap;
+
** https://wormbase.org/tools/soba/soba.cgi?action=Terms+to+SObA+Graph
white-space: -o-pre-wrap;
+
** https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi
word-wrap: break-word">
+
** https://wormbase.org/tools/rnaseq/fpkmmine.cgi
Disease_model_annotation : "00000004"
+
** https://wormbase.org/tools/ontology_browser
Disease_term "DOID:0050833"
+
 
Disease_of_species "Homo sapiens"
+
=== 2021 Genetics paper ===
Variation "WBVar00275555"
+
* Paul D has asked for contributions (~200 words each)
Disease_relevant_gene "WBGene00011559"
+
* Paul's preliminary suggested sections:
Inferred_gene "WBGene00011559"
+
** CeNGen (CalTech)
Association_type "is_implicated_in"
+
** Expression & Transcription (Wen)
Evidence_code "IMP"
+
*** Spell (Wen)
Genetic_sex "hermaphrodite"
+
** SimpleMine (CalTech Wen)
Paper_evidence "WBPaper00035924"
+
** WormiCloud - (Jae/Valerio Caltech)
Database "OMIM" "gene" "613891 "
+
** Vennter (Jae/Caltech)
Database "OMIM" "disease" "258900"
+
** Gene Name Sanitizer (Wen/Raymond/Caltech?)
Curator_confirmed "WBPerson324"
+
** VFP (Valerio)
Date_last_updated "2017-04-24"
+
** Author first pass (Daniela)
</pre>
+
** Human disease (Ranjana)
*Would like to institute stable identifiers across releases, so the plan is to call these objects, 'WBDisease_annotation:<number>', so then the above identifier would become 'WBDisease_annotation:00000004', or 'WBDiseaseannot:00000004' or 'WBDiseaseAnnot:00000004'
+
** Molecular and genetic interactions (You/Chris)
*ID convention--is underscore allowed?
+
** Pathways and Processes (Karen)
*Is 'WBDisease_annotation:00000004' too long for acedb?
+
** 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