Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(48 intermediate revisions by 4 users not shown)
Line 36: Line 36:
 
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
 +
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
== June 4, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
=== Citace (tentative) upload ===
 
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 
* Citace upload to Hinxton on Friday, July 10th
 
  
=== Caltech reopening ===
+
==July 9th, 2020==
* Paul looking to get plan approved
+
===Gene names issue in SimpleMine and other mining tools===
* People that want to come to campus need to watch training video
+
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
* Masks available in Paul's lab
+
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
+
*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).
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
+
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
+
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
+
**single public name is assigned to multiple WBgene ID, Wen has a list of these genes
* Also, need to submit who you were in contact with for contact tracing
+
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
* Form is used all week, and hold on to it until asked to be submitted
+
**overlapped or dicistronic, but has a single sequence name, examples:
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
+
    exos-4.1 and tin-9.2 (B0564.1)
 +
    eat-18 and lev-10 (Y105E8A.7)
 +
    cha-1 and unc-17 (ZC416.8)
  
=== Nameserver ===
+
**simple confusion from authors, ex. mdh-1 and mdh-2
* Nameserver was down
+
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
* CIT curators would still like to have a single form to interact with
+
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
+
*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.
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 
* Hinxton is pulling in CGC strains, how often?
 
* Caltech could possibly get a block of IDs
 
  
=== Alliance SimpleMine ===
+
===Wormicloud===
* Any updates? 3.1 feature freeze is tomorrow
+
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
+
*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===
 +
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
  
== June 11, 2020 ==
+
===Nightly names service updates to postgres===
 +
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.
  
=== Name Service ===
 
* Testing site now up; linked to Mangolassi
 
* CGI from Juancarlos not accepting all characters, including double quotes like "
 
* Example submission that fails via CGI
 
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
 
* Juancarlos will look into and try to fix
 
  
=== Alliance Literature group ===
+
==July 16th, 2020==
* Textpresso vs. OntoMate vs. PubMed
+
===Citing ontologies and their versions===
* Still some confusion about what the different tasks can be performed in each tool
+
*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.
* Working on collecting different use cases on spreadsheet
+
*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.
* Sentence-based search is big strength of Textpresso
+
*Some useful links
* At latest meeting performed some large searches for OntoMate and Textpresso
+
**http://www.obofoundry.org/principles/fp-004-versioning.html
* Literature acquisition: still needs work
+
**http://obo-dashboard-test.ontodev.com/ (you can see that wbbt, wbls version metadata attribute is generating a warning).
** Using SVM vs. Textpresso search to find relevant papers
+
**Note: OBO-foundry may not have been updated, but good practice to check your headers, anyway.
** Species based SVM? Currently use string matching to derive different corpora
+
* 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))
** Finding genes and determining which species those genes belong to?
+
* 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
  
=== Alliance priorities? ===
+
=== Gene Name Sanitizer ===
* Transcription regulatory networks
+
* Would be good to always (when possible) make users aware of name ambiguities
* Interactions can focus on network viewer eventually
+
* Wen will keep the "Multiple Output" section at the bottom of SimpleMine output
** May want different versions/flavors of interaction viewers
+
* The gene name sanitizer will be built as a stand alone tool
** May also want to work closely with GO and GO-CAMs
+
* Important to include history of gene names
* Gene descriptions can focus on information poor genes, protein domains, etc.
 
  
=== Sandbox visual cues ===
+
=== Tools linking to SimpleMine ===
* Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
+
* 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
* AFP and Micropub dev sites have indicators
 
* Could play with changing the background color? Maybe too hard to look at?
 
* Change the color of the title of the form, e.g. the OA?
 
* Will add red text "Development Site" at top of the OA form
 
  
=== Evidence Code Ontology ===
 
* Kimberly and Juancarlos have worked on a parser
 
* Will load into ACEDB soon
 
  
 +
== July 23rd, 2020 ==
  
== June 18, 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
  
=== Undergrad phenotype submissions ===
+
=== Working on Alliance paralogs ===
* Chris gave presentation to Lina Dahlberg's class about community phenotype curation
+
* In the works
* Class took survey about experience with presentation and experience trying to curate worm phenotypes
 
** Survey results: https://www.dropbox.com/s/00cit5aitv8yu27/Dahlberg_class_survey_results.xlsx?dl=0
 
** Some students didn't benefit, but most did; nice feedback!
 
** Lina intends to publish/micropublish the survey results so please don't share
 
* Since April 24, the class has submitted 171 annotations from 23 papers (some redundant and some still under review)
 
  
=== Special characters in OA/Postgres ===
+
=== Summer project ===
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
+
* Neuronal regulation of dauer formation
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
+
* Fernando has been collecting literature
* It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
+
* Will work on GO-CAMs and build a relevant model(s)
* Juancarlos wrote Perl script on Mangolassi at:
 
** /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters/get_summary_characters.pl
 
** Will find bad characters and their pgids for a given Postgres table
 
** Will find bad data and their pgids for the same table
 
** People can query their data tables for these characters
 
* Chris & Wen will work on compiling a list of bad characters that tend to come up
 
  
=== Citace upload ===
+
=== Disk failures ===
* July 10th citace-to-Hinxton upload
+
* Brought down wobr1, wobr2, spica
* July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th
+
* 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
  
== June 25, 2020 ==
+
=== 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 Summer Student ===
+
=== Caltech BBE retreat ===
* Paul has new summer student
+
* Will be online; may be more accessible
** Molecular lesion curation, maybe
+
* Wen will submit a request to present on the Alliance
** Are early stops more or less likely to be null mutations?
 
** Alleles are flagged as null in WB in the context of phenotypes
 
* Fernando
 
** Anatomy function
 
** GO curation? Curating transcription factors?
 
*** Checking for consistent curation
 
  
=== Worm Community Diversity Meeting ===
+
=== WormBase Webinars ===
* Organized by Ahna Skop and Dana Miller
+
* Could run a WormMine webinar in September
* Invite posted on Facebook "C. elegans Researchers" group
+
** 30-45 minute webinar with 15 minutes of questions and discussion
* Two meetings held: one Thursday (June 18th), one Friday (June 19th)
+
** Would be good have people register
* Chris attended last Friday (June 19th)
+
* Chris has slot at Worcester Area Worm Meeting and Boston Area Worm Meeting coming up (late in 2020); these will likely be virtual
* Worm Board looking to take input and ideas from this meeting and incorporate into meetings and events
+
 
* One idea was to document and track outreach efforts and what people have learned from them and organize them in a central location, maybe WormBase or Worm Community Forum
+
=== Gene Name Sanitizer ===
* Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
+
* 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 ===
 +
* Currently there are many cases where even live C. elegans gene IDs result in an "Ambiguous - Split" status that doesn't return a matching gene ID
 +
* This happens with 647 live C. elegans (N2) gene IDs, all of which do not have any indication of ambiguity when uploading to SimpleMine or WormMine, or sample searching in the WormBase website interface
 +
* Many (all?) cases involve an existing, live, valid gene having been split at some point to create an adjacent gene model but the original gene retained its identity
 +
* It would be good to still make sure people are aware of this split, but still provide a "suggested" matching gene (i.e. the actual same input gene ID); also "Ambiguous" may not be the appropriate word
 +
* There are also cases where there really is an ambiguity (e.g. a name matches the "Public_name" of one gene but the "Other_name" of another gene) but we still might want to return a suggested mapping to the "most likely" gene match, e.g. the gene where the input matches the public name
 +
* Maybe we can have multiple columns in the output to provide the gene IDs of other matches
 +
* We could have a core "suggested" match/mapping gene ID column, plus a column to indicate "siblings of a split", "Matches to public name", "Matches to sequence name", "Matches to other name"
 +
* Chris will draw up some mockups with examples
 +
 
 +
=== 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:
 +
** [https://pubmed.ncbi.nlm.nih.gov/2006412/ 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 20:02, 30 July 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July


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
  • 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

  • Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
  • 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

  • Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways

Nightly names service updates to postgres

  • Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.


July 16th, 2020

Citing ontologies and their versions

  • 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.
  • 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.
  • Some useful links
  • 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

  • Currently there are many cases where even live C. elegans gene IDs result in an "Ambiguous - Split" status that doesn't return a matching gene ID
  • This happens with 647 live C. elegans (N2) gene IDs, all of which do not have any indication of ambiguity when uploading to SimpleMine or WormMine, or sample searching in the WormBase website interface
  • Many (all?) cases involve an existing, live, valid gene having been split at some point to create an adjacent gene model but the original gene retained its identity
  • It would be good to still make sure people are aware of this split, but still provide a "suggested" matching gene (i.e. the actual same input gene ID); also "Ambiguous" may not be the appropriate word
  • There are also cases where there really is an ambiguity (e.g. a name matches the "Public_name" of one gene but the "Other_name" of another gene) but we still might want to return a suggested mapping to the "most likely" gene match, e.g. the gene where the input matches the public name
  • Maybe we can have multiple columns in the output to provide the gene IDs of other matches
  • We could have a core "suggested" match/mapping gene ID column, plus a column to indicate "siblings of a split", "Matches to public name", "Matches to sequence name", "Matches to other name"
  • Chris will draw up some mockups with examples

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?