Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(128 intermediate revisions by 6 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 ===
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
* 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 ===
+
== September 3, 2020 ==
* 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 ===
+
=== WS279 Citace upload ===
* Any updates? 3.1 feature freeze is tomorrow
+
* September 25
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
+
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
  
 +
=== New AFP datatype for curation status form (CSF)? ===
 +
* afp_othergenefunc (to capture gene function other than enzymatic activity)
 +
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
  
== June 11, 2020 ==
+
=== GO annotation for description ===
 +
* Kimberly will look into 'male tail tip developement' terms for description
  
=== Name Service ===
+
=== Migrate wobr1 server to AWS ===
* Testing site now up; linked to Mangolassi
+
* SOLR, WOBr, SObA, Enrichment analysis
* CGI from Juancarlos not accepting all characters, including double quotes like "
+
* Working with Sibyl on the process
* Example submission that fails via CGI
+
* Will try migrating wobr1 first, as a test case
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
+
* May eventually move, for example, Tazendra
* Juancarlos will look into and try to fix
+
** Will there be drawbacks to doing this?
 +
** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
 +
* Don't yet know the details of the costs, but we can try and keep track
 +
* We should move into WB or Alliance AWS instances (or Stanford)
  
=== Alliance Literature group ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Textpresso vs. OntoMate vs. PubMed
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Still some confusion about what the different tasks can be performed in each tool
+
* Meeting will be virtual on Zoom
* Working on collecting different use cases on spreadsheet
+
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
* Sentence-based search is big strength of Textpresso
+
* Send topic requests to Chris for the talk
* At latest meeting performed some large searches for OntoMate and Textpresso
+
* Current topics:
* Literature acquisition: still needs work
+
** Micropublications
** Using SVM vs. Textpresso search to find relevant papers
+
** Author First Pass
** Species based SVM? Currently use string matching to derive different corpora
+
** Automated Gene Descriptions
** Finding genes and determining which species those genes belong to?
+
** Community Curation
 +
** WB Query Tools
 +
* Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
 +
* If the organizers record the talk, we can post it on the blog and WB YouTube channel
  
=== 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 ===
+
== September 10, 2020 ==
* 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 ===
+
=== GO GAF Files ===
* Kimberly and Juancarlos have worked on a parser
+
* WS278 GO GAF is using the new 2.2 file format
* Will load into ACEDB soon
+
* [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md Specifications]
 +
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
 +
* Implications for gene descriptions, but what about other tools, applications at WB?
 +
* Some errors in the current WS278 GAF, but will get fixed soon
 +
** Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed
  
 +
===Disease files on FTP===
 +
*No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
 +
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
  
== June 18, 2020 ==
+
=== WormBase talk at Worcester Area Worm Meeting ===
 +
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
 +
* 30 minute slot; complementary to BAWM talk?
 +
* WormBase members can attend
  
=== Undergrad phenotype submissions ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Chris gave presentation to Lina Dahlberg's class about community phenotype curation
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Class took survey about experience with presentation and experience trying to curate worm phenotypes
+
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
** Survey results: https://www.dropbox.com/s/00cit5aitv8yu27/Dahlberg_class_survey_results.xlsx?dl=0
+
* WormBase members can attend; Zoom link will be sent next Monday
** 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 ===
+
=== Worm Anatomy Ontology Fixes ===
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
+
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
+
* Assessing the best way to address them
* It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
+
* Would be good to be able to automate some edits; options:
* Juancarlos wrote Perl script on Mangolassi at:
+
** Use OWL API (need someone proficient in coding with OWL API)
** /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters/badChar
+
** Convert to OBO, programmatically edit, convert back to OWL?
** Will find bad characters for a given Postgres table
+
** Use Cellfie plugin for Protege?
** People can query their data tables for these characters
+
** Should discuss with Nico once we have a sense as to what changes need to be made
* Chris & Wen will work on compiling a list of bad characters that tend to come up
 
  
=== Citace upload ===
+
=== Dead Variations in Postgres ===
* July 10th citace-to-Hinxton upload
+
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
* July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th
+
* Noticed that many transgene names were being included, which can result in false positives for the categories
 +
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
 +
* Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
 +
* May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
 +
* We could use pattern matching to filter out transgene names
 +
* Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories
 +
 
 +
=== WS279 Citace Upload ===
 +
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
 +
 
 +
 
 +
== September 17, 2020 ==
 +
 
 +
=== Species errors in CITace ===
 +
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
 +
 
 +
=== Webinars ===
 +
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
 +
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
 +
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
 +
* Chris and Wen can discuss how to setup
 +
* Should we have people register? Maybe
 +
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
 +
 
 +
=== Transcription factors and regulatory networks ===
 +
* Had another question about TFs, asking for common TFs for a list of genes
 +
* An issue is that the TF binding data we have is in disparate forms, trying to reconcile
 +
* We have a ?Transcription_factor class; it would be good to update and integrate with other related data types
 +
 
 +
=== Alzheimer's disease portal ===
 +
* Funding has been awarded for Alzheimer's research
 +
* Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
 +
* Paul S: Alliance SAB tomorrow; we'll see what the SAB says
 +
* Can look at other resources like RGD disease portals and Reactome disease-related pathway models
 +
* Ruth Lovering is doing some work in this regard
 +
 
 +
=== GO meeting ===
 +
* All are welcome to attend
 +
* Will discuss GAF format changes, etc.
 +
* Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
 +
** Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss
 +
 
 +
=== New GAF 2.2 file ===
 +
* Kimberly has reviewed and sent feedback to Michael P
 +
* Valerio would like to stay in the loop to test the new files
 +
 
 +
=== Data mining tool comparison sheet ===
 +
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
 +
* Needs an update
 +
* Could we make this available to users? A link in the Tools menu?
 +
* Is this useful to users? Would they understand it? Maybe be better as a curator resource
 +
* Could this be micropublished?
 +
** Possible; may want to consider a series of publications with videos of webinars, etc.

Latest revision as of 16:39, 17 September 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

August


September 3, 2020

WS279 Citace upload

  • September 25
  • Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific

New AFP datatype for curation status form (CSF)?

  • afp_othergenefunc (to capture gene function other than enzymatic activity)
  • Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later

GO annotation for description

  • Kimberly will look into 'male tail tip developement' terms for description

Migrate wobr1 server to AWS

  • SOLR, WOBr, SObA, Enrichment analysis
  • Working with Sibyl on the process
  • Will try migrating wobr1 first, as a test case
  • May eventually move, for example, Tazendra
    • Will there be drawbacks to doing this?
    • Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
  • Don't yet know the details of the costs, but we can try and keep track
  • We should move into WB or Alliance AWS instances (or Stanford)

WormBase talk at Boston Area Worm Meeting

  • https://www.umassmed.edu/ambroslab/meetings/bawm/
  • Meeting will be virtual on Zoom
  • Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
  • Send topic requests to Chris for the talk
  • Current topics:
    • Micropublications
    • Author First Pass
    • Automated Gene Descriptions
    • Community Curation
    • WB Query Tools
  • Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
  • If the organizers record the talk, we can post it on the blog and WB YouTube channel


September 10, 2020

GO GAF Files

  • WS278 GO GAF is using the new 2.2 file format
  • Specifications
  • GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
  • Implications for gene descriptions, but what about other tools, applications at WB?
  • Some errors in the current WS278 GAF, but will get fixed soon
    • Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed

Disease files on FTP

  • No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
  • Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??

WormBase talk at Worcester Area Worm Meeting

  • Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
  • 30 minute slot; complementary to BAWM talk?
  • WormBase members can attend

WormBase talk at Boston Area Worm Meeting

Worm Anatomy Ontology Fixes

  • Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
  • Assessing the best way to address them
  • Would be good to be able to automate some edits; options:
    • Use OWL API (need someone proficient in coding with OWL API)
    • Convert to OBO, programmatically edit, convert back to OWL?
    • Use Cellfie plugin for Protege?
    • Should discuss with Nico once we have a sense as to what changes need to be made

Dead Variations in Postgres

  • Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
  • Noticed that many transgene names were being included, which can result in false positives for the categories
  • Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
  • Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
  • May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
  • We could use pattern matching to filter out transgene names
  • Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories

WS279 Citace Upload

  • Local Caltech upload to Spica, Tuesday September 22, 10am Pacific


September 17, 2020

Species errors in CITace

  • Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction

Webinars

  • We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
  • Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
  • Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
  • Chris and Wen can discuss how to setup
  • Should we have people register? Maybe
  • AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?

Transcription factors and regulatory networks

  • Had another question about TFs, asking for common TFs for a list of genes
  • An issue is that the TF binding data we have is in disparate forms, trying to reconcile
  • We have a ?Transcription_factor class; it would be good to update and integrate with other related data types

Alzheimer's disease portal

  • Funding has been awarded for Alzheimer's research
  • Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
  • Paul S: Alliance SAB tomorrow; we'll see what the SAB says
  • Can look at other resources like RGD disease portals and Reactome disease-related pathway models
  • Ruth Lovering is doing some work in this regard

GO meeting

  • All are welcome to attend
  • Will discuss GAF format changes, etc.
  • Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
    • Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss

New GAF 2.2 file

  • Kimberly has reviewed and sent feedback to Michael P
  • Valerio would like to stay in the loop to test the new files

Data mining tool comparison sheet