Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
m
(24 intermediate revisions by 5 users not shown)
Line 22: Line 22:
  
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
−
 
  
 
= 2021 Meetings =
 
= 2021 Meetings =
Line 30: Line 29:
 
[[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 ===
 
−
* 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
 
−
 
−
 
−
== March 11, 2021 ==
 
  
−
=== Spreadsheet for Data not in ACEDB ===
+
== April 1, 2021 ==
−
* Magdalena/Hinxton would like to know how much data at Caltech doesn't get into ACEDB
 
−
* Sheet here: https://docs.google.com/spreadsheets/d/1VcFykdyBcoMBvYliem8tnch5Q2VDMImL6EqlcEBCU-s/edit?usp=sharing
 
−
* We want to pull everything into the Alliance eventually, but maybe not everything needs to be harmonized
 
−
* We should evaluate existing forms and fields/tables for whether they need to be harmonized or can stay as is
 
  
−
=== CeNGEN To Dos ===
+
=== Antibodies ===
−
* Daniela, Wen, Valerio, Eduardo, Raymond met with CeNGEN
+
* Alignment of the antibody class to Alliance:
−
* Want to add JBrowse track for promoters(?)
+
** Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
−
* Three things:
+
*** 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.
−
** 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)
+
*** 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:”
−
** 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
+
** 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.
−
** 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 ===
+
All changes proposed above were approved by the group
−
* You'll need an ID with RFID? (Yes, 20 year old IDs don't work)
 
−
* help.caltech.edu -> request type Card Office
 
−
* It will be ready and wait for you at the Reddoor cafe.
 
  
 +
=== 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
  
−
== March 18, 2021 ==
+
=== 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
  
−
=== Caltech Alliance source? ===
+
=== Citace upload ===
−
* 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)
+
* Next Friday, April 9th, by end of the day
−
* Data would no longer be coming from the "Single Source of Truth" for WB data (i.e. ACEDB/Datomic)
+
* Wen will contact Paul Davis for the frozen WS280 models file
−
* WB paper data would be ahead of the ACEDB paper data
 
−
* Kimberly will reach out to Magdalena et al. to propose
 
  
−
=== CITAce upload ===
 
−
* Upload to Hinxton on April 19 (? Friday April 16th ?)
 
−
* Upload to CITace for Wen on Friday before (April 9th) by end of the day
 
  
−
=== Alliance biological working groups priority ===
+
== April 8, 2021 ==
−
* Keep working on harmonization and LinkML models for data types
 
  
−
=== LinkML data visualization ===
+
=== Braun server outage ===
−
* Is there a way to visualize data coming from LinkML models? Like in .ACE files?
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
−
* There may be some software that can render that kind of visualization, but we need to see
 
−
* Curators want a way to make sure the model and the data are correct before officially submitting
 
−
* Adam plans to demonstrate a visualization of literature data next Tuesday at literature acquisition working group (this was in the context of having a UI for seeing what's stored in the persistent database without waiting for elastic search processing to pass it to the regular UI, currently Literature is not modeled off of the LinkML yet)
 
  
−
=== QC analysis for steps in Alliance ingest pipeline ===
+
=== Textpresso API ===
−
* Curators can get access to the FMS to look at uploaded files, processed files; need to know how to process JSON files
+
* Was down yesterday affecting WormiCloud; Michael has fixed
−
* Curators can also access Neo, but need to know how to query
+
* Valerio will learn how to manage the API for the future
−
* Would be good to have readable reports to provide numbers for overall data sets
 
  
 +
=== 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.?
  
−
== March 25, 2021 ==
+
=== 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
  
−
=== How to access data at the Alliance ===
+
=== Odd characters in Postgres ===
−
* Google doc summary here: https://docs.google.com/document/d/1FvrsFHZ5ga5KzPtQCFJixSdulkOXJfAEjW-qJ4N34Gc/edit?usp=sharing
+
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
−
* Alliance data pipeline (simple): DQMs and Ferret pipelines --> FMS API & FMS --> Loader --> Neo4J --> Java API --> Web Interface & Download Files
+
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
−
* FMS Swagger UI: https://fms.alliancegenome.org/swagger-ui/index.html
+
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
−
* Peruse all data types: https://fms.alliancegenome.org/api/datatype/all
+
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
−
* Neo4J web browser:
 
−
** Stage: http://stage.alliancegenome.org:7474/browser/
 
−
** Production: http://www.alliancegenome.org:7474/browser/
 
−
* Alliance (Java) API Swagger UI: https://www.alliancegenome.org/api/swagger-ui/
 
−
* AGR Schemas repo: https://github.com/alliance-genome/agr_schemas
 

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
Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls&oldid=36623"