Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
 
  
 
= 2021 Meetings =
 
= 2021 Meetings =
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[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
−
== March 4, 2021 ==
 
−
 
−
=== Webinar Monday ===
 
−
* Juancarlos can send a reminder email; he just needs the text for the body of the email message
 
−
* Can we send the webinar reminder to WB staff? Cannot use staff@wormbase.org to register
 
−
* Raymond will try to remember to forward to staff
 
  
−
=== Neural Network (NN) evaluation ===
+
== April 1, 2021 ==
−
* Kimberly (and other curators) looking through NN results
 
−
* Had previously prevented LOW scoring SVMs(?) from being sent to authors
 
−
* We need an agreed upon protocol for evaluation
 
−
* To avoid bias, we should randomly sample papers; usually will find negatives; how do we represent high, medium and low-scoring papers in the set without making curators review >> 100 papers?
 
−
* Michael will come up with protocol and send around list of papers for each data type (in Google Doc)
 
−
* Perhaps evaluation should happen on non-curated, newer papers
 
  
 +
=== 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.
  
−
== March 11, 2021 ==
+
All changes proposed above were approved by the group
  
−
=== Spreadsheet for Data not in ACEDB ===
+
=== textpress-dev clean up ===
−
* Magdalena/Hinxton would like to know how much data at Caltech doesn't get into ACEDB
+
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
−
* Sheet here: https://docs.google.com/spreadsheets/d/1VcFykdyBcoMBvYliem8tnch5Q2VDMImL6EqlcEBCU-s/edit?usp=sharing
+
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
−
* We want to pull everything into the Alliance eventually, but maybe not everything needs to be harmonized
+
* Direct access may be possible via Caltech VPN
−
* We should evaluate existing forms and fields/tables for whether they need to be harmonized or can stay as is
+
* Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines
  
−
=== CeNGEN To Dos ===
+
=== Braun servers ===
−
* Daniela, Wen, Valerio, Eduardo, Raymond met with CeNGEN
+
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
−
* Want to add JBrowse track for promoters(?)
+
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
−
* Three things:
 
−
** CeNGEN will provide histograms that we can put on each gene page, similar to modENCODE plots (do they provide static images or data that we process and display as histograms?) Both are possible (Raymond)
 
−
** Their tool can assess "enriched" genes by cell type (enriched vs. neurons or vs. all cell types; not just housekeeping genes); these can be sent to WB -> SObA and enrichment analysis
 
−
** We will link to the CeNGEN homepage wherever appropriate
 
−
* All else will depend on Eduardo's tools for single cell expression data
 
−
* Raymond will be WB point person to communicate with CeNGEN
 
−
* Display solutions can be used for Alliance single-cell data in general
 
−
* May want to consider future use cases, e.g. mutant-vs-WT expression, chemical/drug-induced expression, etc.
 
  
−
=== Chen building access ===
+
=== Citace upload ===
−
* You'll need an ID with RFID? (Yes, 20 year old IDs don't work)
+
* Next Friday, April 9th, by end of the day
−
* help.caltech.edu -> request type Card Office
+
* Wen will contact Paul Davis for the frozen WS280 models file
−
* It will be ready and wait for you at the Reddoor cafe.
 
  
  
−
== March 18, 2021 ==
+
== April 8, 2021 ==
  
−
=== Caltech Alliance source? ===
+
=== Braun server outage ===
−
* Could some data (like paper class/data) go to the Alliance directly from Caltech? Could be quicker and more efficient (and allow special characters that are lost at the acedb layer)
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
−
* Data would no longer be coming from the "Single Source of Truth" for WB data (i.e. ACEDB/Datomic)
 
−
* WB paper data would be ahead of the ACEDB paper data
 
−
* Kimberly will reach out to Magdalena et al. to propose
 
  
−
=== CITAce upload ===
+
=== Textpresso API ===
−
* Upload to Hinxton on April 19 (? Friday April 16th ?)
+
* Was down yesterday affecting WormiCloud; Michael has fixed
−
* Upload to CITace for Wen on Friday before (April 9th) by end of the day
+
* Valerio will learn how to manage the API for the future
  
−
=== Alliance biological working groups priority ===
+
=== Grant opportunities ===
−
* Keep working on harmonization and LinkML models for data types
+
* 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.?
  
−
=== LinkML data visualization ===
+
=== New WS280 ONTOLOGY FTP directory ===
−
* Is there a way to visualize data coming from LinkML models? Like in .ACE files?
+
* Changes requested here: https://github.com/WormBase/website/issues/7900
−
* There may be some software that can render that kind of visualization, but we need to see
+
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
−
* Curators want a way to make sure the model and the data are correct before officially submitting
+
* Known issues (Chris will report):
−
* Adam plans to demonstrate a visualization of literature data next Tuesday at literature acquisition working group
+
** 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
  
−
=== QC analysis for steps in Alliance ingest pipeline ===
+
=== Odd characters in Postgres ===
−
* Curators can get access to the FMS to look at uploaded files, processed files; need to know how to process JSON files
+
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
−
* Curators can also access Neo, but need to know how to query
+
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
−
* Would be good to have readable reports to provide numbers for overall data sets
+
* 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

Revision as of 19:05, 8 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
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