Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2018 Meetings =
+
= 2021 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
== 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.
  
== June 7, 2018 ==
+
All changes proposed above were approved by the group
  
=== Alliance literature pipeline working group ===
+
=== textpress-dev clean up ===
* Has anyone gotten back to Carol Bult about WB/Textpresso membership in the group? Not yet
+
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
* Paul & Kimberly can join; Kimberly will sit in on group meetings
+
* 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
  
=== SPELL migration ===
+
=== Braun servers ===
* SGD put SPELL into the cloud; will give us code to set up WB SPELL in cloud
+
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
* Want to have common interface but two instances (yeast & worm)
+
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
* Worm data in SPELL may be more complicated than the yeast data (different species, platforms, meta data, etc.)
 
* Mike Cherry proposed to use GTEx to replace SPELL. (www.gtexportal.org)
 
* Trying to get GTEX to have same functionality as SPELL
 
  
=== Progress report ===
+
=== Citace upload ===
* Wen can generate numbers of changes since last year
+
* Next Friday, April 9th, by end of the day
* 5-year progress report coming up (for funding agencies)
+
* Wen will contact Paul Davis for the frozen WS280 models file
* Want a progress report-like document to give to SAB in July
 
* WS259 - WS265
 
  
=== Paper author name ===
 
* Jonathan Ewbank wrote in about an incorrect author name
 
* Issue for WBPaper00048704: https://wormbase.org/resources/paper/WBPaper00048704#0--10
 
* First author is "Li, C" as in PubMed (correct name) in WormBase as "Chun, L"
 
* Will make a GitHub ticket; web team may need to look at
 
  
=== Lab class ===
+
== April 8, 2021 ==
* Lab data is not clean/consistent; has gotten messy
 
* Cecilia trying to clean it up
 
* There is conflicting data from lab class, author class, and person class
 
* Currently there is a ~redundant curation pipeline; considering pulling person info into lab class
 
* When looking at lab page, if there is a problem with a person's info, changes would be made (requested) in the person class, not the lab class
 
* Cecilia will contact labs to ask about correctness of information
 
* Can have a discussion with Ann and Aric at CGC
 
  
=== How many C. elegans genes have "good" knockouts? ===
+
=== Braun server outage ===
* Paul giving talk next week, wants to report
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
* Chris will look into
 
* Mitani did 1,000 deletions in last year
 
  
=== Server logs ===
+
=== Textpresso API ===
* SimpleMine logs are all coming from Amazon; will need to ask Todd about SimpleMine usage (from AWS stats?)
+
* Was down yesterday affecting WormiCloud; Michael has fixed
 +
* Valerio will learn how to manage the API for the future
  
=== Migration of lab data ===
+
=== Grant opportunities ===
* Data for labs was coming from Name Server (in Hinxton) - <font color= red>Comment:</font>[PD] Not coming from the Name Server, geneace was the only source of Lab data prior to handover.  
+
* Possibilities to apply for supplements
* Now Paul D has stopped curating lab info - <font color= red>Comment:</font>[PD] Build config has been updated to take the majority of lab data from citace rather than geneace
+
* 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.?
  
* Now that Cecilia is curating, will pull lab info from Postgres
+
=== 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
 +
 
 +
=== 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

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