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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== April 1, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
=== 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
+
== June 3, 2021 ==
  
=== textpress-dev clean up ===
+
=== Reserving meeting rooms ===
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
+
* Raymond encountering challenges with setting up regular meeting room reservations in Chen building
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
+
* We've been asked to make reservations one week in advance
* Direct access may be possible via Caltech VPN
+
* Need to use a room if we reserve it
* 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 ===
+
=== Summer student(s) ===
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
+
* Anatomy function project with Raymond
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
+
* Many types of anatomy function data submitted via AFP
  
=== Citace upload ===
+
== June 10, 2021 ==
* Next Friday, April 9th, by end of the day
 
* Wen will contact Paul Davis for the frozen WS280 models file
 
  
 +
=== Variation-Gene Associations ===
 +
*Some QC on AFP-extracted data led to the realization that at least some of the 'tm' variations aren't associated with genes on tazendra
 +
*https://github.com/WormBase/author-first-pass/issues/204
 +
*https://github.com/WormBase/website/issues/8262
 +
*It looks like non-manually asserted variation-gene associations will be generated via the VEP pipeline during the build, so Caltech would need to get this information from each WB release
  
== April 8, 2021 ==
+
===Variation in name service but not in OA===
 +
*Ranjana: I could not find gk315316 in the OA though it exists in the name server. I agree that we probably don’t want to let all the million mutations into the OA since that would slow the drop-downs, but when we need one for curation, what needs to be done?
 +
*Juancarlos: That might be right.  It seems to try to create the variation in the name service, and if it gets a 409 Conflict error, it adds it to the temp variation file, and the obo_ tables in postgres. Since it fails to create in the name service, that's probably okay with Hinxton, and since it gets added to postgres, you should be able to use it in the OA, and since it gets added to the temp variation file, on future updates of the ontology it gets added again. Probably best if someone confirms that's the process (and maybe points us to a wiki ?)
  
=== Braun server outage ===
+
*Solution from Karen and Chris: If the Hinxton name server already has the variation but it isn't in the OA (as expected for Million Mutation Project variants like gk315316), we just need to add it through the old temp variations CGI:
* Raymond fixed; now Spica, wobr and wobr2 are back up
 
  
=== Textpresso API ===
+
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
* Was down yesterday affecting WormiCloud; Michael has fixed
 
* Valerio will learn how to manage the API for the future
 
  
=== Grant opportunities ===
+
making sure to enter the variation with name-space-WBVarID like:
* 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 ===
+
gk315316 WBVar01148785
* 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 ===
+
and then, after refresh, it should be available to the OA. Hinxton never has to get involved in this scenario.
* 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
 
  
 +
=== Confirm WS282 Upload Dates ===
 +
*July 6th?
 +
*Data freeze/upload date on the release schedule is July 12th
  
== April 15, 2021 ==
+
=== CenGen bar plots ===
 +
*Initially discussed to have the bar plot images going in as image data
 +
*CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.
 +
*They can provide the underlying data and have the WB team generate interactive plots for each gene
 +
*Sibyl said that this is feasible and we could: 1. bring the data files in OR 2. call the CenGen API on the fly
 +
*The first approach may be more work but better in the long run as we store the data
 +
*Will ping Hinxton and see how they can integrate the data
  
=== Special characters in Postgres/OA ===
+
* Bring in data  both as pictures and interactive bar plots
* 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
+
* Ping Hinxon on GitHub to move this forward
* 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
 
** RNA-Seq FPKM values for genes and related data; Wen will write script to pull out FPKM values from SRA data and send to Magdalena
 
* In addition to WB data types, we will cover Alliance, AFP, and community curation
 
* Google doc for workshop here: https://docs.google.com/document/d/1H9ARhBRMKBNuOhjyxVQ_1o6cysvpppI7uA-TJrO_UZ4/edit?usp=sharing
 
 
 
=== WB Progress Report ===
 
* Due April 30th
 
* There will be two documents: progress and plans
 
* Place text in the appropriate places (don't write as a single integrated unit)
 
* Paul S will put together a Google doc
 
* We CAN include Alliance harmonization efforts
 
* 2020 Progress report: https://docs.google.com/document/d/1f3ettnkvwoKKiaAA4TSrpSQPEF7FmVVn6u2UdflA_So/edit?usp=sharing
 
* Last year milestone was WS276; we will compare to WS280
 
* Google "WormBase Grants" folder: https://drive.google.com/drive/folders/1p8x9tEOfZ4DQvTcPSdNR5-JoPJu--ZAu?usp=sharing
 
* 2021 Progress Report document here: https://docs.google.com/document/d/13E9k5JvDpUN4kWnrTm4M2iphnAJSTpk02ZiGl8O6bM4/edit?usp=sharing
 
 
 
 
 
== April 29, 2021 ==
 
 
 
=== IWM Workshop Schedule ===
 
* Schedule format due today (April 29th)
 
* [https://docs.google.com/document/d/1H9ARhBRMKBNuOhjyxVQ_1o6cysvpppI7uA-TJrO_UZ4/edit#bookmark=id.jrjo4xhfnh7b Tentative schedule here]
 
* Format proposal is 4, 15-minute talks followed by 30 minutes of open discussion / Q&A
 
* Still need someone to speak (~15 minutes) about the Alliance
 
 
 
=== WB Progress Report ===
 
* 2021 documents in [https://drive.google.com/drive/folders/1p8x9tEOfZ4DQvTcPSdNR5-JoPJu--ZAu?usp=sharing this Google Drive folder]
 
* Note: there is one [https://docs.google.com/document/d/13E9k5JvDpUN4kWnrTm4M2iphnAJSTpk02ZiGl8O6bM4/edit?usp=sharing 2021 "Progress" document] and a second (separate) [https://docs.google.com/document/d/1j0HkCwuimK6DD-ui1tAkYMNpLRhxR9xb1FdSDZXFXCI/edit?usp=sharing "Future Plans" document]
 
* Existing future plans text has been moved to the "Future Plans" document
 
 
 
=== OpenBiosystems RNAi clone IDs ===
 
* User looking to map Open Biosystems RNAi clone names to WB clone names
 
* We may need to get a mapping file from Open Biosystems
 
 
 
=== FPKM data ===
 
* Wen has produced a csv file of FPKM values; can generate as part of the SPELL pipeline
 
* May be better to generate at Hinxton
 
 
 
=== OA Dumpers ===
 
* Daniela and Juancarlos have been working on the Picture OA and Expr OA dumpers
 
* Inconsistencies have accumulated for all OA dumpers as each has been made separately
 
* Juancarlos is working on a generalized, modular way to handle dumping
 
* Should we handle historical genes in the same way across OAs? Sure, but we need the "Historical_gene" tag in the respective ACEDB model
 
* Could we retroactively deal with paper-gene connections? We could possibly look in Postgres history tables to see which genes had been replaced previously (by Kimberly)
 
 
 
=== Gene name ambiguities ===
 
* Jae noticed that some gene names associated with multiple WBGene IDs (e.g. one public name is the same as another gene's other name) have the same references attached
 
* May require updating the paper-gene connections for some of these
 

Latest revision as of 18:59, 10 June 2021

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January

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March

April

May


June 3, 2021

Reserving meeting rooms

  • Raymond encountering challenges with setting up regular meeting room reservations in Chen building
  • We've been asked to make reservations one week in advance
  • Need to use a room if we reserve it

Summer student(s)

  • Anatomy function project with Raymond
  • Many types of anatomy function data submitted via AFP

June 10, 2021

Variation-Gene Associations

Variation in name service but not in OA

  • Ranjana: I could not find gk315316 in the OA though it exists in the name server. I agree that we probably don’t want to let all the million mutations into the OA since that would slow the drop-downs, but when we need one for curation, what needs to be done?
  • Juancarlos: That might be right. It seems to try to create the variation in the name service, and if it gets a 409 Conflict error, it adds it to the temp variation file, and the obo_ tables in postgres. Since it fails to create in the name service, that's probably okay with Hinxton, and since it gets added to postgres, you should be able to use it in the OA, and since it gets added to the temp variation file, on future updates of the ontology it gets added again. Probably best if someone confirms that's the process (and maybe points us to a wiki ?)
  • Solution from Karen and Chris: If the Hinxton name server already has the variation but it isn't in the OA (as expected for Million Mutation Project variants like gk315316), we just need to add it through the old temp variations CGI:

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo

making sure to enter the variation with name-space-WBVarID like:

gk315316 WBVar01148785

and then, after refresh, it should be available to the OA. Hinxton never has to get involved in this scenario.

Confirm WS282 Upload Dates

  • July 6th?
  • Data freeze/upload date on the release schedule is July 12th

CenGen bar plots

  • Initially discussed to have the bar plot images going in as image data
  • CenGen group wants interactive bar plots similar to the modENCODE bar plots currently displayed in the FPKM expression data section on the expression widget. That way users could hover over a bar plot and see the cell type, the expression value (TPM, in our case) and the proportion of cells of each neuron type expressing the gene.
  • They can provide the underlying data and have the WB team generate interactive plots for each gene
  • Sibyl said that this is feasible and we could: 1. bring the data files in OR 2. call the CenGen API on the fly
  • The first approach may be more work but better in the long run as we store the data
  • Will ping Hinxton and see how they can integrate the data
  • Bring in data both as pictures and interactive bar plots
  • Ping Hinxon on GitHub to move this forward