Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
== April 1, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
=== 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.
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
All changes proposed above were approved by the group
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
=== 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
  
==July 9th, 2020==
 
===Gene names issue in SimpleMine and other mining tools===
 
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
 
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
 
*Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
 
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
 
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
 
**single public name is assigned to multiple WBgene ID, Wen has a list of these genes
 
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 
**overlapped or dicistronic, but has a single sequence name, examples:
 
    exos-4.1 and tin-9.2 (B0564.1)
 
    eat-18 and lev-10 (Y105E8A.7)
 
    cha-1 and unc-17 (ZC416.8)
 
  
**simple confusion from authors, ex. mdh-1 and mdh-2
+
== April 8, 2021 ==
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
 
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
 
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools.  They will also write a microPub explaining this issue to the community.
 
  
===Wormicloud===
+
=== Braun server outage ===
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
 
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
 
  
===Noctua 2.0 form ready to use===
+
=== Textpresso API ===
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
+
* Was down yesterday affecting WormiCloud; Michael has fixed
 +
* Valerio will learn how to manage the API for the future
  
===Nightly names service updates to postgres===
+
=== Grant opportunities ===
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
+
* 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
  
==July 16th, 2020==
+
=== Odd characters in Postgres ===
===Citing ontologies and their versions===
+
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
*Came up in the context of the Alliance: It would be best practice to provide users with the list of ontologies used and their versions/date.
+
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
*If WB ontology developers could make sure their ontology file headers (WB anatomy ontology, WB life stage, etc.) conformed to obo file header specifications, then it would be easy to pull in version and date information into the Alliance.
+
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
*Some useful links
+
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
**http://www.obofoundry.org/principles/fp-004-versioning.html
 
**http://obo-dashboard-test.ontodev.com/ (you can see that wbbt, wbls version metadata attribute is generating a warning).
 
**Note: OBO-foundry may not have been updated, but good practice to check your headers, anyway.
 
* Chris worked with Nico yesterday to update the ODK version for WBbt and WBls; versioning should be fine now (once the OBO dashboard runs again (hasn't run since February))
 
* Important point: the GitHub release version date tag (e.g. "v2020-06-30") needs to match the ODK release date (as stored in the OBO and OWL file headers)
 
** There are some existing mismatches, Chris is cataloging them now
 
 
 
=== Gene Name Sanitizer ===
 
* Would be good to always (when possible) make users aware of name ambiguities
 
* Wen will keep the "Multiple Output" section at the bottom of SimpleMine output
 
* The gene name sanitizer will be built as a stand alone tool
 
* Important to include history of gene names
 
 
 
=== Tools linking to SimpleMine ===
 
* Vennter and other tools link to SimpleMine with hard coded field/column names; we should have more dynamic/robust linking without relying on hard coded field names
 
 
 
 
 
== July 23rd, 2020 ==
 
 
 
=== Alliance pathway working group ===
 
* Integrating pathways from GO-CAM, Reactome, Meta-cyc
 
* Raymond, Chris interested
 
* Laurent-Philippe wants to work on user-friendly displays of GO-CAM models
 
 
 
=== Working on Alliance paralogs ===
 
* In the works
 
 
 
=== Summer project ===
 
* Neuronal regulation of dauer formation
 
* Fernando has been collecting literature
 
* Will work on GO-CAMs and build a relevant model(s)
 
 
 
=== Disk failures ===
 
* Brought down wobr1, wobr2, spica
 
* Raymond has upgraded OS from 8-year old OS, beefed up hardware
 
* wobr1 and wobr2 are back to full function
 
* Having trouble bringing back spica on the network
 
 
 
=== WormMine updates ===
 
* Paulo working on importing new classes: SO_term, disease_model_annotation, transgene, construct, molecule, wbprocess, interaction
 
* Chris is working with Paulo to move them in; talk to Paulo and/or Chris if interested in discussing
 
* Spreadsheet to map ACEDB/XML attributes to ACEDB attributes: https://docs.google.com/spreadsheets/d/1-fpzVU3rblN3Rp38wQjd3121z3rVkxmR9_i5T0EIPNo/edit?usp=sharing
 
* Still have some loader headaches
 
* Do we know the usage stats of WormMine?
 
* BlueGenes
 
** New interface coming; in the works, not sure when it will be fully functional
 
** Lacks some useful features in the current Intermine (Intermine devs are aware and working on it)
 
** Does BlueGenes have better loading? Don't know
 
 
 
=== WB move to Chen building ===
 
* Need to sort out what will get moved over; will be more limited space
 
* How late can move happen? If all is OK, move will happen 2nd week of January 2021
 
 
 
=== Caltech BBE retreat ===
 
* Will be online; may be more accessible
 
* Wen will submit a request to present on the Alliance
 
 
 
=== WormBase Webinars ===
 
* Could run a WormMine webinar in September
 
** 30-45 minute webinar with 15 minutes of questions and discussion
 
** Would be good have people register
 
* Chris has slot at Worcester Area Worm Meeting and Boston Area Worm Meeting coming up (late in 2020); these will likely be virtual
 
 
 
=== Gene Name Sanitizer ===
 
* Juancarlos and Wen are working on tool prototype
 
* Prototype recognizes ambiguous gene names/IDs and returns them to the user
 
* Will return HTML or single download file with a status/classification column
 
* Four types:
 
** good/valid (unambiguous match to a live gene)
 
** ambiguous (matches multiple genes)
 
** invalid (unambiguous match to dead or suppressed gene)
 
** not found (no match)
 
 
 
 
 
== July 30, 2020 ==
 
 
 
=== Gene Name Sanitizer ===
 
 
 
=== Help Desk ===
 
 
 
* https://github.com/WormBase/website/issues/7803
 
* Hi, I was wondering if there is a way to search for maternally versus zygotically enriched splice variants of a gene. I was looking through the RNAseq data and am not sure how to pull that out. I'm specifically looking at afd-1, but any help on that would be great!
 
* Ask Gary Williams
 
 
 
=== Summer project ===
 
* Fernando has made curation progress on neural control of dauer development (couple papers)
 
* Acquiring list of papers is important:
 
** Bargmann (1991) ablation paper; start at beginning
 
** WormBook chapter (old but good)
 
** WormAtlas, check references
 
** Look at Nikhil Bhatla's worm web tools and references (wormweb.org)
 
* Ablation, mosaic analysis
 
* Maybe add a Wiki page for methodology for addressing questions of cell function
 
** Address necessity/sufficiency issues
 
** Address cell autonomous/cell nonautonomous experiments
 
** What are basic approaches and their caveats?
 

Latest revision as of 19:05, 8 April 2021

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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