Difference between revisions of "WormBase-Caltech Weekly Calls"

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GoToMeeting link: https://www.gotomeet.me/wormbase1
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= 2020 Meetings =
 
= 2020 Meetings =
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 +
 +
 +
== June 4, 2020 ==
 +
 +
=== Citace (tentative) upload ===
 +
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 +
* Citace upload to Hinxton on Friday, July 10th
 +
 +
=== Caltech reopening ===
 +
* Paul looking to get plan approved
 +
* People that want to come to campus need to watch training video
 +
* Masks available in Paul's lab
 +
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 +
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 +
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
== March 5, 2020 ==
+
=== Nameserver ===
 +
* Nameserver was down
 +
* CIT curators would still like to have a single form to interact with
 +
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 +
* 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
  
=== WormBase curation ===
+
=== Alliance SimpleMine ===
* Tim Schedl: WB needs to do more curation for phenotype and variation
+
* Any updates? 3.1 feature freeze is tomorrow
* Doing community curation, but not fast enough
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 
  
=== Alaksa ===
 
* Joesph may be able to meet with Raymond
 
* How can the tool be maintained? If it can't it needs to be pulled
 
  
=== Single cell expression tool ===
+
== June 11, 2020 ==
* Tool is here: http://de.wormcells.com/
 
* What do we need to consider for pulling into WormBase?
 
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
 
** Would want it to be in sync with WormBase releases
 
** May not need to reprocess with every release with current (small-ish) data set
 
* Fully integrated tool versus an embedded tool?
 
  
=== Name service updates ===
+
=== Name Service ===
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
+
* Testing site now up; linked to Mangolassi
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
+
* 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 ===
 +
* Textpresso vs. OntoMate vs. PubMed
 +
* Still some confusion about what the different tasks can be performed in each tool
 +
* Working on collecting different use cases on spreadsheet
 +
* Sentence-based search is big strength of Textpresso
 +
* At latest meeting performed some large searches for OntoMate and Textpresso
 +
* Literature acquisition: still needs work
 +
** Using SVM vs. Textpresso search to find relevant papers
 +
** Species based SVM? Currently use string matching to derive different corpora
 +
** Finding genes and determining which species those genes belong to?
  
== March 12, 2020 ==
+
=== Alliance priorities? ===
 +
* Transcription regulatory networks
 +
* Interactions can focus on network viewer eventually
 +
** May want different versions/flavors of interaction viewers
 +
** May also want to work closely with GO and GO-CAMs
 +
* Gene descriptions can focus on information poor genes, protein domains, etc.
  
=== Cancelled meetings ===
+
=== Sandbox visual cues ===
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
+
* 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)
* We should start doing online advertisement for micropublications with webinars
+
* 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
  
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
+
=== Evidence Code Ontology ===
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
+
* Kimberly and Juancarlos have worked on a parser
* Valerio would like to add these to Postgres to keep a more central repository of them
+
* Will load into ACEDB soon
* Chris would still like to be able to readily update/edit the content of those lists
 
  
* Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
 
  
=== Updates on Alaska ===
+
== June 18, 2020 ==
  
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
+
=== Undergrad phenotype submissions ===
The future plan is to move the platform to Google colab to reduce maintainance work.
+
* Chris gave presentation to Lina Dahlberg's class about community phenotype curation
 +
* 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)
  
==Nameservice discussion==
+
=== Special characters in OA/Postgres ===
*Getting a token has worked for Chris and Ranjana
+
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
*Karen and Daniela need to get tokens
+
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
 +
* It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
 +
* 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
  
==Noctua GO-CAM updates==
+
=== Citace upload ===
*Noctua is a production tool available for annotations right now
+
* July 10th citace-to-Hinxton upload
*Create as many interconnected models and make available for curators is the ongoing goal
+
* July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th
*Reactome models are in the process of being imported
 
*Real time validation messages as curation is being done, is being worked on
 
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
 
  
  
== March 19, 2020 ==
+
== June 25, 2020 ==
  
=== Citace Upload ===
+
=== Caltech Summer Student ===
* Tuesday, March 31st
+
* Paul has new summer student
 +
** Molecular lesion curation, maybe
 +
** Are early stops more or less likely to be null mutations?
 +
** Alleles are flagged as null in WB in the context of phenotypes
 +
** Would be good to query Postgres for null alleles and work from there
 +
* Fernando
 +
** Anatomy function
 +
** GO curation? Curating transcription factors?
 +
*** Checking for consistent curation
  
=== Latest ACEDB ===
+
=== Worm Community Diversity Meeting ===
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
+
* Organized by Ahna Skop and Dana Miller
 +
* Invite posted on Facebook "C. elegans Researchers" group
 +
* Two meetings held: one Thursday (June 18th), one Friday (June 19th)
 +
* Chris attended last Friday (June 19th)
 +
* 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
 +
* Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
 +
** Ask Todd; he used to have a map of researchers; Todd had asked Cecilia to curate lab location and institution
 +
* Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
 +
* Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently
 +
** Most labs were real
  
=== Storing email addresses/persons to omit from requests ===
+
=== C_elegans Slack group ===
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
+
* Called "C_elegans"
 +
* Chris made a "WormBase" channel for people to post questions, comments
 +
* Chris will look into inviting everyone and possibly integrating with help@wormbase.org email list
  
=== Mailing lists ===
+
=== WormBase Outreach Webinars ===
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
+
* While travel is still restricted, we should consider WormBase webinars
 +
* Scott working on a JBrowse webinar
 +
* Could have a different topic each month
 +
* Should collect topics to cover and assign speakers (maybe multiple speakers per topic; keep it lively)
 +
* Should set up a schedule
 +
* How should we advertise? Can post on blog, twitter, etc.
  
 +
=== New transcripts expanding gene range ===
 +
* Will bring up at next week's site-wide call
 +
* Possibly due to incorporation of newer nanopore reads
 +
* Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
 +
** Example genes: pes-2.2, pck-2, herc-1, atic-1
 +
* Has several repercussions:
 +
** WormBase does not submit alleles affecting more than one gene; with these gene expansions suddenly alleles once only affecting a single gene are now affecting two genes, and so are now omitted from loading into the Alliance (including any phenotype and/or disease annotations)
 +
** Some expanded genes are now being attributed with thousands of alleles/variants
  
==March 26th==
+
=== Citace upload ===
====Community curation====
+
* Upload files to Spica/Wen by Tuesday (June 30th) 10am
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
+
* Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)

Latest revision as of 19:13, 25 June 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 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • 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

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call


June 11, 2020

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::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | α β Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “   ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
  • Juancarlos will look into and try to fix

Alliance Literature group

  • Textpresso vs. OntoMate vs. PubMed
  • Still some confusion about what the different tasks can be performed in each tool
  • Working on collecting different use cases on spreadsheet
  • Sentence-based search is big strength of Textpresso
  • At latest meeting performed some large searches for OntoMate and Textpresso
  • Literature acquisition: still needs work
    • Using SVM vs. Textpresso search to find relevant papers
    • Species based SVM? Currently use string matching to derive different corpora
    • Finding genes and determining which species those genes belong to?

Alliance priorities?

  • Transcription regulatory networks
  • Interactions can focus on network viewer eventually
    • May want different versions/flavors of interaction viewers
    • May also want to work closely with GO and GO-CAMs
  • Gene descriptions can focus on information poor genes, protein domains, etc.

Sandbox visual cues

  • 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)
  • 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


June 18, 2020

Undergrad phenotype submissions

  • Chris gave presentation to Lina Dahlberg's class about community phenotype curation
  • Class took survey about experience with presentation and experience trying to curate worm phenotypes
  • Since April 24, the class has submitted 171 annotations from 23 papers (some redundant and some still under review)

Special characters in OA/Postgres

  • There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
  • In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
  • It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
  • 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

  • July 10th citace-to-Hinxton upload
  • July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th


June 25, 2020

Caltech Summer Student

  • Paul has new summer student
    • Molecular lesion curation, maybe
    • Are early stops more or less likely to be null mutations?
    • Alleles are flagged as null in WB in the context of phenotypes
    • Would be good to query Postgres for null alleles and work from there
  • Fernando
    • Anatomy function
    • GO curation? Curating transcription factors?
      • Checking for consistent curation

Worm Community Diversity Meeting

  • Organized by Ahna Skop and Dana Miller
  • Invite posted on Facebook "C. elegans Researchers" group
  • Two meetings held: one Thursday (June 18th), one Friday (June 19th)
  • Chris attended last Friday (June 19th)
  • 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
  • Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
    • Ask Todd; he used to have a map of researchers; Todd had asked Cecilia to curate lab location and institution
  • Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
  • Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently
    • Most labs were real

C_elegans Slack group

  • Called "C_elegans"
  • Chris made a "WormBase" channel for people to post questions, comments
  • Chris will look into inviting everyone and possibly integrating with help@wormbase.org email list

WormBase Outreach Webinars

  • While travel is still restricted, we should consider WormBase webinars
  • Scott working on a JBrowse webinar
  • Could have a different topic each month
  • Should collect topics to cover and assign speakers (maybe multiple speakers per topic; keep it lively)
  • Should set up a schedule
  • How should we advertise? Can post on blog, twitter, etc.

New transcripts expanding gene range

  • Will bring up at next week's site-wide call
  • Possibly due to incorporation of newer nanopore reads
  • Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
    • Example genes: pes-2.2, pck-2, herc-1, atic-1
  • Has several repercussions:
    • WormBase does not submit alleles affecting more than one gene; with these gene expansions suddenly alleles once only affecting a single gene are now affecting two genes, and so are now omitted from loading into the Alliance (including any phenotype and/or disease annotations)
    • Some expanded genes are now being attributed with thousands of alleles/variants

Citace upload

  • Upload files to Spica/Wen by Tuesday (June 30th) 10am
  • Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)