Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
= 2015 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2015|January]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2015|February]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_March_2015|March]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
= April 2015 =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
== April 2, 2015 ==
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
=== Adding Species information to nightly geneace dumps ===
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
** Michael Paulini is adding Species information for the WBGene IDs in the genes.ace file
 
** Does anyone want Species information for any of the other files
 
** For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/
 
** Data in postgres in table gin_species
 
  
=== WormBase Ontology Browser WS248 online on Dev ===
 
* Caveat: the rest of the WormBase data on the Dev site is WS247 (one release behind)
 
** Would explain some discrepancies
 
  
=== Micropublication form ===
+
== April 1, 2021 ==
* Daniela waiting for feedback from Paul's lab
 
* Will send to Alison Frand and Elissa Hallem at UCLA to get input
 
  
=== Mary Ann's IWM abstract for community annotation ===
+
=== Antibodies ===
* People can send comment over next day or two
+
* Alignment of the antibody class to Alliance:
* Will make revisions and send around next week
+
** 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
  
== April 9, 2015 ==
+
=== 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
  
=== Tazendra ===
+
=== Braun servers ===
* Had some glitches with secondary hard drive this week, not sure what the problem is
+
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
* /home2 directory is not intended as a primary storage; curators need to back data up
+
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
* Paper PDFs stored on /home2 as the primary storage location
 
* Papers are backed up on Athena (Wen's computer)
 
* TIF files are stored on CDs
 
* Main Tazendra hard drive backed up (RAIDed/mirrored), backed up nightly up to ~1 month (or 0.5 month), monthly for a year, but no older versions
 
  
=== Citace data upload ===
+
=== Citace upload ===
* April 28th, 10am
+
* Next Friday, April 9th, by end of the day
 +
* Wen will contact Paul Davis for the frozen WS280 models file
  
=== Community Annotation Forms ===
 
* Mary Ann's IWM (poster) abstract includes community annotation forms
 
* Community annotation form list:
 
** Micropublication
 
** Gene Expression form (made 15 years ago); mostly not used; micropublication form could be co-opted
 
** Gene description form (primarily for the community to edit the automated concise descriptions)
 
** "Submit Data" list on WormBase (http://www.wormbase.org/about/userguide/submit_data#0--10)
 
* Would be good to have a community annotation portal/landing page
 
* Mary Ann will send around a summary of discussions about community annotation, along with prioritization of forms for curators and Juancarlos
 
* Relevant curators should consider reviewing existing forms for updates
 
  
=== modSeek ===
+
== April 8, 2021 ==
* http://seek.princeton.edu/modSeek/
+
 
* Princeton 6th year grad student developed it (leaving within 6 months)
+
=== Braun server outage ===
* "Seek" developed for human on microarray and RNAseq data
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
* 5 model organisms in "modSeek": yeast, worm, fly, mouse, zebrafish
+
 
* Pulls in data from Gene Expression Omnibus (GEO)
+
=== Textpresso API ===
* Analysis computed from raw data
+
* Was down yesterday affecting WormiCloud; Michael has fixed
* Data from SPELL should be reasonably transferred to modSeek
+
* Valerio will learn how to manage the API for the future
* We need to determine if WormBase data can be updated per release
+
 
* Has text mining
+
=== Grant opportunities ===
* Cross-species comparisons available
+
* 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.?
 +
 
 +
=== 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