Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== April 1, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
=== Antibodies ===
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Alignment of the antibody class to Alliance:
 
** Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
 
*** Other animal is sometimes used for older annotations, e.g. authors say that the antibodies were raised both  in rats and rabbits. Standard practice would create 2 records, one for the rat antibody and one for the rabbit.
 
*** Possible pseudonym was used when  a curator was not able to unambiguously assign a previous antibody to a record. (we have a Other name -synonym- tag to capture unambiguous ones). When moving to remarks we can keep a controlled vocabulary for easy future parsing, e.g. “possible_pseudonym:”
 
** Antigen field: currently separated into Protein, peptide, and other_antigen (e.g.: homogenate of early C.elegans embryos, sperm). Propose to use just one antigen field to capture antigen info.
 
  
All changes proposed above were approved by the group
 
  
=== textpress-dev clean up ===
+
== July 1, 2021 ==
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
 
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
 
* Direct access may be possible via Caltech VPN
 
* Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines
 
  
=== Braun servers ===
+
=== Importing genes for tm alleles from GeneACE ===
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
+
* https://github.com/WormBase/website/issues/8262
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
+
* 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 ===
 
=== Citace upload ===
* Next Friday, April 9th, by end of the day
+
* Curators upload files to Spica for citace upload on Tuesday (July 6)
* Wen will contact Paul Davis for the frozen WS280 models file
 
  
 +
=== Chen B1 kitchen Usage Considerations ===
 +
* Clean up after oneself.
 +
* Mark food storage with name and date.
 +
* Mark storage drawers
 +
* Consumables
  
== April 8, 2021 ==
 
  
=== Braun server outage ===
+
== July 8, 2021 ==
* Raymond fixed; now Spica, wobr and wobr2 are back up
 
  
=== Textpresso API ===
+
=== Alliance work ===
* Was down yesterday affecting WormiCloud; Michael has fixed
+
* Orange team presenting initial plans at Alliance PI meeting tomorrow
* Valerio will learn how to manage the API for the future
+
* 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
  
=== Grant opportunities ===
+
== July 15, 2021 ==
* Possibilities to apply for supplements
 
* May 15th deadline
 
* Druggable genome project
 
** Pharos: https://pharos.nih.gov/
 
** could we contribute?
 
* Visualization, tools, etc.
 
* Automated person descriptions?
 
* Automated descriptions for proteins, ion channels, druggable targets, etc.?
 
  
=== New WS280 ONTOLOGY FTP directory ===
+
=== hlh-34 expression ===
* Changes requested here: https://github.com/WormBase/website/issues/7900
+
* 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.  
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
+
* Oliver is putting together a micropub to clarify the issue
* Known issues (Chris will report):
+
* How to deal with existing  annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
** Ontology files are provided as ".gaf" in addition to ".obo"; we need to remove the ".gaf" OBO files
+
* Should we also add public comments to the relevant papers?
** Some files are duplicated and/or have inappropriate file extensions
 
  
=== Odd characters in Postgres ===
+
== July 22, 2021 ==
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
 
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
 
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
 
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
 
  
 +
=== 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
  
== April 15, 2021 ==
+
== July 29, 2021 ==
  
=== Special characters in Postgres/OA ===
+
=== Textpresso Dev machine retiring ===
* Juancarlos working on/proposing a plan to store UTF-8 characters in Postgres and the OA which would then get converted, at dumping, to HTML entities (e.g. α) for the ACE files
+
* Need to work out when and how to move things off the machine before retiring for good
* There is still a bit of cleanup needed to fix or remove special characters (not necessarily UTF-8) that apparently got munged upon copy/pasting into the OA in the past
 
* Note: copy/paste from a PDF often works fine, but sometimes does not work as expected so manual intervention would be needed (e.g. entering Greek characters by hand in UTF-8 format)
 
* Would copy/pasting from HTML be better than PDF?
 
* For Person curation it would be good to be able to faithfully store and display appropriate foreign characters (e.g. Chinese characters, Danish characters, etc.)
 
* Mangolassi script called "get_summary_characters.pl" located here: /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters
 
** Juancarlos will modify script to take a data type code as an argument on the command line and return all Postgres tables (and their respective PGIDs) that have special characters, e.g.
 
*** $ ./get_summary_characters.pl exp
 
*** $ ./get_summary_characters.pl int
 
*** $ ./get_summary_characters.pl grg
 
** or could pass just the datatype + field (postgres table). e.g.
 
*** $ ./get_summary_characters.pl pic_description
 
** Juancarlos will email everyone once it's ready.  It's ready, email sent.  Script is at /home/postgres/work/pgpopulation/oa_general/20210411_unicode_html/get_summary_characters.pl  Symlink this to your directory and run it from there, it will create files in the directory you are at when running it.
 
* Action items:
 
** Juancarlos will update the "get_summary_characters.pl" script as described above
 
** Curators should use the "get_summary_characters.pl" to look for (potentially) bad characters in their OAs/Postgres tables
 
** Need to perform bulk (automated) replacement of existing HTML entities into corresponding UTF-8 characters
 
** Curators will need to work with Juancarlos for each OA to modify the dumper
 
** Juancarlos will write (or append to existing) Postgres/OA dumping scripts to:
 
*** 1) Convert UTF-8 characters to HTML entities in ACE files
 
*** 2) Convert special quote and hyphen characters into simple versions that don't need special handling
 
  
=== CeNGEN pictures ===
+
=== Proxies for Caltech-hosted tools broken ===
* Model change went in to accommodate images from the CeNGEN project
+
* Several Caltech CGI tools using a proxy on WormBase site are broken (throwing 504 Gateway Time-out or Server Error)
* Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
+
* Affected tools:
* Raymond and Daniela will work with data producers to acquire images when ready
+
** 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
  
=== Supplement opportunities ===
+
=== 2021 Genetics paper ===
* Money available for software development to "harden" existing software
+
* Paul D has asked for contributions (~200 words each)
* Might be possible to make Eduardo's single cell analysis tools more sustainable
+
* Paul's preliminary suggested sections:
* Could make WormiCloud adapted to Alliance?
+
** CeNGen (CalTech)
* Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)
+
** Expression & Transcription (Wen)
 
+
*** Spell (Wen)
=== Student project for Textpresso ===
+
** SimpleMine (CalTech Wen)
* Create tool to allow user to submit text and return a list of similar papers
+
** WormiCloud - (Jae/Valerio Caltech)
* Use cases:
+
** Vennter (Jae/Caltech)
** curator wants an alert to find papers similar to what they've curated
+
** Gene Name Sanitizer (Wen/Raymond/Caltech?)
** look for potential reviewers of a paper based on similar text content
+
** VFP (Valerio)
 
+
** Author first pass (Daniela)
 
+
** Human disease (Ranjana)
== April 22, 2021 ==
+
** Molecular and genetic interactions (You/Chris)
 
+
** Pathways and Processes (Karen)
=== LinkML hackathon ===
+
** Anatomy and Cell (Raymond)
* Need to consider who works on what and how to coordinate
+
* Now have 'Community Curation' for AFP and other community curation
* Need to practice good Git practice
+
* Also, gene descriptions section
** Merge main branch into local branch before merging back into main branch to make sure everything works
 
* How will we best handle AceDB hash structures? likely use something like Mark QT demonstrated
 
** Do we have any/many hash-within-hash structures? #Molecular_change is used as a hash and tags within that model all reference the #Evidence hash
 
* GO annotation extensions offer an interesting challenge
 
 
 
=== IWM workshop ===
 
* Need to submit a workshop schedule (who speaks about what and when) by next Thursday April 29th
 
* An initial idea was to promote data in ACEDB that may be underutilized or many users may be unaware of
 
** An example might be transcription factor data: the ?Transcription_factor class and the modENCODE TF data
 
** Single cell data and tools? CeNGEN, Eduardo's single cell tools
 
** RNA-Seq FPKM values for genes and related data; Wen will write script to pull out FPKM values from SRA data and send to Magdalena
 
* In addition to WB data types, we will cover Alliance, AFP, and community curation
 
* Google doc for workshop here: https://docs.google.com/document/d/1H9ARhBRMKBNuOhjyxVQ_1o6cysvpppI7uA-TJrO_UZ4/edit?usp=sharing
 
 
 
=== WB Progress Report ===
 
* Due April 30th
 
* There will be two documents: progress and plans
 
* Place text in the appropriate places (don't write as a single integrated unit)
 
* Paul S will put together a Google doc
 
* We CAN include Alliance harmonization efforts
 
* 2020 Progress report: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
 
* Last year milestone was WS276; we will compare to WS280
 
* Google "WormBase Grants" folder: https://drive.google.com/drive/folders/1p8x9tEOfZ4DQvTcPSdNR5-JoPJu--ZAu?usp=sharing
 
* 2021 Progress Report document here: https://docs.google.com/document/d/13E9k5JvDpUN4kWnrTm4M2iphnAJSTpk02ZiGl8O6bM4/edit?usp=sharing
 
 
 
 
 
== April 29, 2021 ==
 
 
 
=== IWM Workshop Schedule ===
 
* Schedule format due today (April 29th)
 
* [https://docs.google.com/document/d/1H9ARhBRMKBNuOhjyxVQ_1o6cysvpppI7uA-TJrO_UZ4/edit#bookmark=id.jrjo4xhfnh7b Tentative schedule here]
 
* Format proposal is 4, 15-minute talks followed by 30 minutes of open discussion / Q&A
 
* Still need someone to speak (~15 minutes) about the Alliance
 
 
 
=== WB Progress Report ===
 
* 2021 documents in [https://drive.google.com/drive/folders/1p8x9tEOfZ4DQvTcPSdNR5-JoPJu--ZAu?usp=sharing this Google Drive folder]
 
* Note: there is one [https://docs.google.com/document/d/13E9k5JvDpUN4kWnrTm4M2iphnAJSTpk02ZiGl8O6bM4/edit?usp=sharing 2021 "Progress" document] and a second (separate) [https://docs.google.com/document/d/1j0HkCwuimK6DD-ui1tAkYMNpLRhxR9xb1FdSDZXFXCI/edit?usp=sharing "Future Plans" document]
 
* Existing future plans text has been moved to the "Future Plans" document
 
 
 
=== OpenBiosystems RNAi clone IDs ===
 
* User looking to map Open Biosystems RNAi clone names to WB clone names
 
* We may need to get a mapping file from Open Biosystems
 
 
 
=== FPKM data ===
 
* Wen has produced a csv file of FPKM values; can generate as part of the SPELL pipeline
 
* May be better to generate at Hinxton
 
 
 
=== OA Dumpers ===
 
* Daniela and Juancarlos have been working on the Picture OA and Expr OA dumpers
 
* Inconsistencies have accumulated for all OA dumpers as each has been made separately
 
* Juancarlos is working on a generalized, modular way to handle dumping
 
* Should we handle historical genes in the same way across OAs? Sure, but we need the "Historical_gene" tag in the respective ACEDB model
 
* Could we retroactively deal with paper-gene connections? We could possibly look in Postgres history tables to see which genes had been replaced previously (by Kimberly)
 
 
 
=== Gene name ambiguities ===
 
* Jae noticed that some gene names associated with multiple WBGene IDs (e.g. one public name is the same as another gene's other name) have the same references attached
 
* May require updating the paper-gene connections for some of these
 
* One example is cep-1 gene. It associates with 3 diff WBgeneID and sharing papers in the reference widget.
 
 
 
=== NIH Supplement for AI readiness ===
 
* Could we set up curation for neural circuits using a knowledge graph (e.g. GO-CAM)?
 

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

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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