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]]
  
 +
= 2021 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
== April 1, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
=== 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.
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
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
  
== June 4, 2020 ==
+
=== 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 (tentative) upload ===
+
=== Citace upload ===
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
+
* Next Friday, April 9th, by end of the day
* Citace upload to Hinxton on Friday, July 10th
+
* Wen will contact Paul Davis for the frozen WS280 models file
  
=== Caltech reopening ===
 
* Paul looking to get plan approved
 
* People that want to come to campus need to watch training video
 
* Masks available in Paul's lab
 
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 
* Also, need to submit who you were in contact with for contact tracing
 
* Form is used all week, and hold on to it until asked to be submitted
 
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
 
  
=== Nameserver ===
+
== April 8, 2021 ==
* Nameserver was down
 
* CIT curators would still like to have a single form to interact with
 
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 
* Hinxton is pulling in CGC strains, how often?
 
* Caltech could possibly get a block of IDs
 
  
=== Alliance SimpleMine ===
+
=== Braun server outage ===
* Any updates? 3.1 feature freeze is tomorrow
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
 
  
 +
=== Textpresso API ===
 +
* Was down yesterday affecting WormiCloud; Michael has fixed
 +
* Valerio will learn how to manage the API for the future
  
== June 11, 2020 ==
+
=== 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.?
  
=== Name Service ===
+
=== New WS280 ONTOLOGY FTP directory ===
* Testing site now up; linked to Mangolassi
+
* Changes requested here: https://github.com/WormBase/website/issues/7900
* CGI from Juancarlos not accepting all characters, including double quotes like "
+
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
* Example submission that fails via CGI
+
* Known issues (Chris will report):
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
+
** Ontology files are provided as ".gaf" in addition to ".obo"; we need to remove the ".gaf" OBO files
* Juancarlos will look into and try to fix
+
** Some files are duplicated and/or have inappropriate file extensions
  
=== Alliance Literature group ===
+
=== Odd characters in Postgres ===
* Textpresso vs. OntoMate vs. PubMed
+
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
* Still some confusion about what the different tasks can be performed in each tool
+
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
* Working on collecting different use cases on spreadsheet
+
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
* Sentence-based search is big strength of Textpresso
+
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
* At latest meeting performed some large searches for OntoMate and Textpresso
 
* Literature acquisition: still needs work
 
** Using SVM vs. Textpresso search to find relevant papers
 
** Species based SVM? Currently use string matching to derive different corpora
 
** Finding genes and determining which species those genes belong to?
 
 
 
=== Alliance priorities? ===
 
* Transcription regulatory networks
 
* Interactions can focus on network viewer eventually
 
** May want different versions/flavors of interaction viewers
 
** May also want to work closely with GO and GO-CAMs
 
* Gene descriptions can focus on information poor genes, protein domains, etc.
 
 
 
=== Sandbox visual cues ===
 
* Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
 

Latest 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