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_March_2020|March]]
 
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
== April 1, 2021 ==
  
 +
=== Antibodies ===
 +
* 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
  
== May 7, 2020 ==
+
=== textpress-dev clean up ===
 +
* 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
  
=== Alliance COVID Page ===
+
=== Braun servers ===
* Available on stage
+
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
* Textpresso for Coronavirus up for testing
+
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
  
=== SimpleMine at Alliance ===
+
=== Citace upload ===
* Still some confusion about what it is
+
* Next Friday, April 9th, by end of the day
* Will try to help clarify on PI meeting on Friday
+
* Wen will contact Paul Davis for the frozen WS280 models file
  
=== Development environment for Alliance work ===
 
* Raymond and Juancarlos have been working on
 
* Existing hardware is strained; set up virtual machine
 
* Still some technical issues
 
  
=== Open Publishing Festival ===
+
== April 8, 2021 ==
* Later this month
 
* Micropublications involved
 
* Organized by the Collaborative Knowledge Foundation
 
* Will involve publishers of books, journals, etc.
 
* Will have a MOD-focused event, would be good to have WB curators participate/attend
 
* Open to all
 
  
=== Genotype class ===
+
=== Braun server outage ===
* Ranjana finished populating the Genotype OA with genotypes needed for disease curation
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
* Will need to keep in mind that we will have a mapping pipeline to determine which genes are involved for a variation
 
* There could end up being a discrepancy between an original or published name of a genotype and the components that are inferred by WormBase
 
* Would be good to be clear/transparent about which components were automatically inferred
 
  
=== WS277/278 ===
+
=== Textpresso API ===
* Pipelines are pushed back by about 14 days/2 weeks
+
* Was down yesterday affecting WormiCloud; Michael has fixed
 +
* Valerio will learn how to manage the API for the future
  
 +
=== Grant opportunities ===
 +
* 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.?
  
==May 13, 2020==
+
=== New WS280 ONTOLOGY FTP directory ===
 +
* Changes requested here: https://github.com/WormBase/website/issues/7900
 +
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
 +
* Known issues (Chris will report):
 +
** Ontology files are provided as ".gaf" in addition to ".obo"; we need to remove the ".gaf" OBO files
 +
** Some files are duplicated and/or have inappropriate file extensions
  
=== SURF students ===
+
=== Odd characters in Postgres ===
* Welcome Fernando!
+
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
* Will work on neuron function with respect to dauer formation
+
* 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
  
=== Progress Report ===
 
* Review Google Doc from Paul to make sure you're latest updates are there
 
* Doc here: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
 
  
===Genotype class===
+
== April 15, 2021 ==
*Have 27 genotypes in the genotype OA, dumper and test .ace file ready
 
*Will test ace file in citace as soon as we get the new models file, can also send to Paul D., in advance to test
 
*Disease OA annotations now converted to the newly created genotypes where needed
 
*Need to work on disease dumper changes next
 
  
=== What genes should be linked to genotypes? ===
+
=== Special characters in Postgres/OA ===
* We have a "Gene" tag in the ?Genotype model for capturing relevant genes
+
* 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
* What should we consider a "relevant gene"?
+
* 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
* We plan to populate the "Gene" tag with genes identified by the variation-to-gene mapping pipeline
+
* 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)
* For transgenes, what genes should be extracted as "relevant"? Genes whose promoters are cloned? Genes that are expressed? Genes whose 3'UTR's are cloned? Wild type rescue genes used as a marker/selection tool, e.g. "unc-119(+)"?
+
* Would copy/pasting from HTML be better than PDF?
* For rearrangements, consider relevant any genes "inside" the rearrangement?
+
* 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
  
=== Volunteer Community Curators ===
+
=== CeNGEN pictures ===
* Have had an additional 13 people volunteer
+
* Model change went in to accommodate images from the CeNGEN project
* Single one-on-one tutorial for someone in Hong Kong this past Monday
+
* Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
* Chris will hold a tutorial today and tomorrow for everyone else
+
* Raymond and Daniela will work with data producers to acquire images when ready
* Have received many new community annotations from volunteers (and authors), validation still pending
+
 
 +
=== Supplement opportunities ===
 +
* Money available for software development to "harden" existing software
 +
* Might be possible to make Eduardo's single cell analysis tools more sustainable
 +
* Could make WormiCloud adapted to Alliance?
 +
* Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)
 +
 
 +
=== Student project for Textpresso ===
 +
* Create tool to allow user to submit text and return a list of similar papers
 +
* Use cases:
 +
** curator wants an alert to find papers similar to what they've curated
 +
** look for potential reviewers of a paper based on similar text content
 +
 
 +
 
 +
== April 22, 2021 ==
 +
 
 +
=== LinkML hackathon ===
 +
* Need to consider who works on what and how to coordinate
 +
* Need to practice good Git practice
 +
** 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
 +
** Decision: we will continue to only dump historical genes for specific OAs, with a plan to maybe make consistent across OAs in the future
 +
* 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)?
 +
** Maybe we could convert the anatomy function model to LinkML -> OWL statements?
 +
** Maybe setup a graphical curation interface?
 +
* Transcriptional regulation
 +
** Would be good to establish a common model (for the Alliance?)
 +
** CeNGEN project produced lots of predictions of TF binding sites based on single-cell expression data; Eduardo: these models should be able to be regenerated each time new data sets are published, but this requires greater integration in a central, sustainable resource
 +
* Paul S can send a link for the supplement
 +
 
 +
=== Variant First Pass Pipeline ===
 +
* Valerio: Are there any existing pipelines to make allele-paper and/or strain-paper associations?
 +
* Not sure, should ask Karen

Latest revision as of 19:13, 29 April 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 1, 2021

Antibodies

  • 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

  • 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

  • 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
  • Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know

Citace upload

  • Next Friday, April 9th, by end of the day
  • Wen will contact Paul Davis for the frozen WS280 models file


April 8, 2021

Braun server outage

  • Raymond fixed; now Spica, wobr and wobr2 are back up

Textpresso API

  • Was down yesterday affecting WormiCloud; Michael has fixed
  • Valerio will learn how to manage the API for the future

Grant opportunities

  • Possibilities to apply for supplements
  • May 15th deadline
  • Druggable genome project
  • Visualization, tools, etc.
  • Automated person descriptions?
  • Automated descriptions for proteins, ion channels, druggable targets, etc.?

New WS280 ONTOLOGY FTP directory

Odd characters in Postgres

  • 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


April 15, 2021

Special characters in Postgres/OA

  • 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
  • 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

  • Model change went in to accommodate images from the CeNGEN project
  • Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
  • Raymond and Daniela will work with data producers to acquire images when ready

Supplement opportunities

  • Money available for software development to "harden" existing software
  • Might be possible to make Eduardo's single cell analysis tools more sustainable
  • Could make WormiCloud adapted to Alliance?
  • Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)

Student project for Textpresso

  • Create tool to allow user to submit text and return a list of similar papers
  • Use cases:
    • curator wants an alert to find papers similar to what they've curated
    • look for potential reviewers of a paper based on similar text content


April 22, 2021

LinkML hackathon

  • Need to consider who works on what and how to coordinate
  • Need to practice good Git practice
    • 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


April 29, 2021

IWM Workshop Schedule

  • Schedule format due today (April 29th)
  • 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

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
    • Decision: we will continue to only dump historical genes for specific OAs, with a plan to maybe make consistent across OAs in the future
  • 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)?
    • Maybe we could convert the anatomy function model to LinkML -> OWL statements?
    • Maybe setup a graphical curation interface?
  • Transcriptional regulation
    • Would be good to establish a common model (for the Alliance?)
    • CeNGEN project produced lots of predictions of TF binding sites based on single-cell expression data; Eduardo: these models should be able to be regenerated each time new data sets are published, but this requires greater integration in a central, sustainable resource
  • Paul S can send a link for the supplement

Variant First Pass Pipeline

  • Valerio: Are there any existing pipelines to make allele-paper and/or strain-paper associations?
  • Not sure, should ask Karen