Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(947 intermediate revisions by 12 users not shown)
Line 19: Line 19:
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
== January 3, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
=== WS270 Citace upload ===
 
* Next Tuesday, Jan 8th, 10am Pacific
 
  
=== Gene descriptions ===
+
== April 1, 2021 ==
* Valerio generated new files to ignore/filter-out problematic genes
 
* Still need to validate new pipeline
 
* Barring any major issues, will submit new files for WS270 (can load old files if needed)
 
* Maybe should define a test set (random sample) to test each release? Already have a test set
 
  
=== Protege Tutorial ===
+
=== Antibodies ===
* Doodle poll open: https://doodle.com/poll/kn49rd3rggymn68g
+
* Alignment of the antibody class to Alliance:
* Please fill out poll if you are interested in attending; have responses from Kimberly and Gary S.
+
** 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
  
==January 11th, 2019==
+
=== 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
  
===WB workshop at IWM 2019===
+
=== Braun servers ===
Here's a draft, need to finalize as Jan 15th is the deadline
+
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
<pre style="white-space: pre-wrap;
+
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
white-space: -moz-pre-wrap;
 
white-space: -pre-wrap;
 
white-space: -o-pre-wrap;
 
word-wrap: break-word">
 
  
Title: WormBase 2019 - Data, Tools and Community Curation
+
=== Citace upload ===
This workshop will be an interactive session with users in order to discuss the types of data in WormBase and how to query them using specific tools.  We will discuss recent changes to WormBase community annotation forms and how to use them to contribute data to WormBase.  We will also present updates to ParaSite, a portal for parasitic worm genomic data, and guide participants on how to find data across model organisms at the Alliance of Genome Research.
+
* Next Friday, April 9th, by end of the day
 +
* Wen will contact Paul Davis for the frozen WS280 models file
  
Format: 90 minutes: 1 section of 40 minutes, followed by a second section of 20 mins and a third section which will be a 30 minute open discussion/Q&A session.  Talks in each section will also be tailored to allow time for questions from the audience.
 
  
Section 1: Introduction to the WormBase gene page and tools such as SimpleMine, Tools for RNA seq data and enrichment analysis, gene-related data using WormBase Ontology Browser and Annotation Visualization tools.
+
== April 8, 2021 ==
  
Section 2: WormBase Parasite database, Model Organism data at the Alliance of Genome Research and Community Curation forms
+
=== Braun server outage ===
 +
* Raymond fixed; now Spica, wobr and wobr2 are back up
  
Section 3: Open forum for discussion and Q&A.
+
=== Textpresso API ===
</pre>
+
* Was down yesterday affecting WormiCloud; Michael has fixed
 +
* Valerio will learn how to manage the API for the future
  
=== Finalize Protege tutorial time ===
+
=== Grant opportunities ===
* Best final options:
+
* Possibilities to apply for supplements
** Wed, Jan 16th, 1pm Pacific/4pm Eastern
+
* May 15th deadline
** Thurs, Jan 17th, 11am Pacific/2pm Eastern
+
* Druggable genome project
** Thurs, Jan 17th, 1pm Pacific/4pm Eastern
+
** Pharos: https://pharos.nih.gov/
* Propose we go with Wed, Jan 16th, 1pm Pacific/4pm Eastern
+
** could we contribute?
 +
* Visualization, tools, etc.
 +
* Automated person descriptions?
 +
* Automated descriptions for proteins, ion channels, druggable targets, etc.?
  
=== Automated descriptions ===
+
=== New WS280 ONTOLOGY FTP directory ===
* Distinguishing information rich vs. poor genes
+
* Changes requested here: https://github.com/WormBase/website/issues/7900
* Information poor genes can take advantage of information across MODs/species
+
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
* Need more robust QC pipeline; can work on for WormBase, and later apply to Alliance once worked out
+
* Known issues (Chris will report):
* Working on expression statements for Alliance genes
+
** Ontology files are provided as ".gaf" in addition to ".obo"; we need to remove the ".gaf" OBO files
* Considering rearrangement of description so disease features more prominently
+
** Some files are duplicated and/or have inappropriate file extensions
  
=== Disease curation ===
+
=== Odd characters in Postgres ===
* Disease model curation progressing; Lots of discussions about data standards and entities in Alliance Disease Working Group
+
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
* Considering SVM for disease; current paper flagging pipeline is rather broad
+
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
*200+ papers as positive training set available
+
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
* Results section are not being extracted in latest Textpresso (paper sectioning in general not happening)
+
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
 
 
=== Noctua / GO-CAM ===
 
* Making progress on best practices
 
* Can use Noctua to generate GO annotations
 
* Starting to incorporate proteins
 
* Working with an ever changing Noctua platform; bugs emerge as it is developed; may benefit from frozen release of the software
 
* Next month or two, will import entire set of C. elegans GO annotations into Noctua
 
** Many decisions to make: how to model?
 
** Each gene will become a single Noctua model; not linked to each other initially
 
** Working on batch updates/uploads to Noctua
 
 
 
=== Expression cluster curation ===
 
* Wen working on 40 paper backlog; hoping to finish by WS271
 
* Wen wants to work on RNA-Seq tools next
 
** FPKM tools
 
** Filtering by datasets
 
** Would like tools ready before International C. elegans Meeting (June 2019)
 
 
 
=== Neural function curation ===
 
* Raymond: want to use design pattern strategy to curate
 
 
 
=== WOBr ===
 
* Now incororating non-IEA disease annotations into WOBr
 
* Using disease-association file
 
 
 
=== Phenotype curation ===
 
* Will run a new round of phenotype requests on ~3,000 papers in next few weeks (last one ran in October)
 
* Processing community curation submissions
 
* Will recurate some community curation papers to check:
 
** 1. completeness of community curation
 
** 2. the time-savings of the phenotype form pipeline
 
* Have made recent improvements to phenotype request emails, allowing authors more feedback options which are now being readily used
 
* Working with new phenotype ontology GitHub repository
 
** OBO Foundry now pointing phenotype ontology at the GitHub repository (both OBO and OWL files)
 
** Need to update the citace upload procedure to generate phenotype .ACE file; currently the script is still running on the old OBO Tazendra location; need to update to work off new OBO file at GitHub
 
 
 
=== Metabolomics ===
 
* Karen working with Michael Witting to pull in metabolomics data
 
* Integrating information about endogenous concentrations of metabolites
 
 
 
=== Automated descriptions React tool ===
 
* Juancarlos developed tool to request versions of the automated descriptions
 
* Will update pipeline to pull data from Alliance; currently coming from Tazendra
 
* Tracking how the descriptions are changing, by data module for example
 
* React tool currently on mangolassi but will move to Alliance at a location of Olin's choosing (AWS resource)
 
 
 
=== Transgenes in the Alliance ===
 
* Are transgenes being discussed at the Alliance?
 
* Yes, the phenotype and disease working group has been discussing
 
* Hasn't come up in recent weeks, but was discussed at face-to-face meeting
 
* One significant issue is that WormBase uniquely has extra-chromosomal arrays, whereas other MODS (always?) have integrated transgenes and consider them types of alleles
 
* Chris will give Karen a heads up next time the issue is intended to be discussed within the Alliance
 

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