Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== April 1, 2021 ==
 
  
=== Antibodies ===
+
== May 13, 2021 ==
* 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
+
=== Textpresso supplement ===
 +
* Due Monday
 +
* Michael working with Paul S
  
=== textpress-dev clean up ===
+
=== AWS credits ===
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
+
* Michael and Valerio were awarded AWS credits, more than they can use
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
+
* Maybe they can be repurposed
* Direct access may be possible via Caltech VPN
+
* Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance
* 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 ===
+
=== Automated gene descriptions ===
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
+
* Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
+
* Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
 +
* May be the focus of an Alliance supplement
 +
* We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)
  
=== Citace upload ===
+
=== IWM 2021 WB Workshop ===
* Next Friday, April 9th, by end of the day
+
* Scheduled for June 22, 2021
* Wen will contact Paul Davis for the frozen WS280 models file
+
* Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
 
+
* Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
 
+
* Here is the submitted workshop schedule:
== April 8, 2021 ==
+
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
 
+
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
=== Braun server outage ===
+
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
* Raymond fixed; now Spica, wobr and wobr2 are back up
+
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
 
+
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
=== 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
 
** 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
 
 
 
 
 
== April 15, 2021 ==
 
 
 
=== Special characters in Postgres/OA ===
 
* Juancarlos working on/proposing a plan to store UTF-8 characters in Postgres and the OA which would then get converted, at dumping, to HTML entities (e.g. α) for the ACE files
 
* There is still a bit of cleanup needed to fix or remove special characters (not necessarily UTF-8) that apparently got munged upon copy/pasting into the OA in the past
 
* Note: copy/paste from a PDF often works fine, but sometimes does not work as expected so manual intervention would be needed (e.g. entering Greek characters by hand in UTF-8 format)
 
* Would copy/pasting from HTML be better than PDF?
 
* For Person curation it would be good to be able to faithfully store and display appropriate foreign characters (e.g. Chinese characters, Danish characters, etc.)
 
* Mangolassi script called "get_summary_characters.pl" located here: /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters
 
** Juancarlos will modify script to take a data type code as an argument on the command line and return all Postgres tables (and their respective PGIDs) that have special characters, e.g.
 
*** $ ./get_summary_characters.pl exp
 
*** $ ./get_summary_characters.pl int
 
*** $ ./get_summary_characters.pl grg
 
** or could pass just the datatype + field (postgres table). e.g.
 
*** $ ./get_summary_characters.pl pic_description
 
** Juancarlos will email everyone once it's ready.  It's ready, email sent.  Script is at /home/postgres/work/pgpopulation/oa_general/20210411_unicode_html/get_summary_characters.pl  Symlink this to your directory and run it from there, it will create files in the directory you are at when running it.
 
* Action items:
 
** Juancarlos will update the "get_summary_characters.pl" script as described above
 
** Curators should use the "get_summary_characters.pl" to look for (potentially) bad characters in their OAs/Postgres tables
 
** Need to perform bulk (automated) replacement of existing HTML entities into corresponding UTF-8 characters
 
** Curators will need to work with Juancarlos for each OA to modify the dumper
 
** Juancarlos will write (or append to existing) Postgres/OA dumping scripts to:
 
*** 1) Convert UTF-8 characters to HTML entities in ACE files
 
*** 2) Convert special quote and hyphen characters into simple versions that don't need special handling
 
 
 
=== CeNGEN pictures ===
 
* Model change went in to accommodate images from the CeNGEN project
 
* Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
 
* Raymond and Daniela will work with data producers to acquire images when ready
 
 
 
=== Supplement opportunities ===
 
* Money available for software development to "harden" existing software
 
* Might be possible to make Eduardo's single cell analysis tools more sustainable
 
* Could make WormiCloud adapted to Alliance?
 
* Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)
 
 
 
=== Student project for Textpresso ===
 
* Create tool to allow user to submit text and return a list of similar papers
 
* Use cases:
 
** curator wants an alert to find papers similar to what they've curated
 
** look for potential reviewers of a paper based on similar text content
 
 
 
 
 
== April 22, 2021 ==
 
 
 
=== LinkML hackathon ===
 
* Need to consider who works on what and how to coordinate
 
* Need to practice good Git practice
 
** Merge main branch into local branch before merging back into main branch to make sure everything works
 
* How will we best handle AceDB hash structures? likely use something like Mark QT demonstrated
 
** Do we have any/many hash-within-hash structures? #Molecular_change is used as a hash and tags within that model all reference the #Evidence hash
 
* GO annotation extensions offer an interesting challenge
 
 
 
=== IWM workshop ===
 
* Need to submit a workshop schedule (who speaks about what and when) by next Thursday April 29th
 
* An initial idea was to promote data in ACEDB that may be underutilized or many users may be unaware of
 
** An example might be transcription factor data: the ?Transcription_factor class and the modENCODE TF data
 
** Single cell data and tools: CeNGEN, Eduardo's single cell tools
 
* In addition to WB data types, we will cover Alliance, AFP, and community curation
 

Revision as of 18:31, 13 May 2021

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May 13, 2021

Textpresso supplement

  • Due Monday
  • Michael working with Paul S

AWS credits

  • Michael and Valerio were awarded AWS credits, more than they can use
  • Maybe they can be repurposed
  • Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance

Automated gene descriptions

  • Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
  • Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
  • May be the focus of an Alliance supplement
  • We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)

IWM 2021 WB Workshop

  • Scheduled for June 22, 2021
  • Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
  • Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
  • Here is the submitted workshop schedule:
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A