Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
 
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
 +
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
== September 3, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
  
=== WS279 Citace upload ===
 
* September 25
 
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
 
  
=== New AFP datatype for curation status form (CSF)? ===
+
==Nov 5th, 2020==
* 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 ===
+
===WS279 GAF 2.0 and disease files===
* Kimberly will look into 'male tail tip developement' terms for description
+
*Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
 +
*Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
 +
*Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
 +
*Raymond needs the GAFs for WoBR
  
=== Migrate wobr1 server to AWS ===
+
===Experimenting with addeding new citace data to the current WS release ===
* SOLR, WOBr, SObA, Enrichment analysis
+
*Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.
* 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 ===
+
===MicroPub user webinar on Nov 9th===
* https://www.umassmed.edu/ambroslab/meetings/bawm/
+
*Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.
* 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
 
  
 +
===WS280 deadlines===
 +
*Caltech files due for citace: Dec 15th, 2020
  
== September 10, 2020 ==
 
  
=== GO GAF Files ===
+
==Nov 12th, 2020==
* WS278 GO GAF is using the new 2.2 file format
+
=== Cynthia Kenyon tool ===
* [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]
+
* developed a new tool for the worm, complete with tutorials, for analyzing gene expression data using Gene Module analysis.  
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
+
* tool at http://genemodules.org
* Implications for gene descriptions, but what about other tools, applications at WB?
+
* add link outs from the gene expression widget or add in general WB tools?
* Some errors in the current WS278 GAF, but will get fixed soon
+
* if we want to incorporate we need to have it updated.
** Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed
+
* are they maintaining it?
 +
* there's no RNAseq, can be outdated
 +
* maybe good to add a blog post
  
===Disease files on FTP===
+
=== Graphical curation tool update===
*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)
+
* We will show a live demo on the current state of the graphical curation tool
*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 ===
+
=== Curating to human genes in ACEDB ===
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
+
* Karen requested option to curate constructs with human genes
* 30 minute slot; complementary to BAWM talk?
+
* Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
* WormBase members can attend
+
* Will discuss on next site-wide call
  
=== WormBase talk at Boston Area Worm Meeting ===
+
=== GAF (and GAF-like) file headers ===
* https://www.umassmed.edu/ambroslab/meetings/bawm/
+
* GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
+
!gaf-version: 2.2
* WormBase members can attend; Zoom link will be sent next Monday
+
!generated-by: WormBase
 +
!date-generated: 2020-10-30
 +
! WB annotations 00015014
 +
* For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
 +
* For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
 +
!gaf-version: 2.0
 +
!generated-by: WormBase
 +
!date-generated: 2020-10-30
 +
* Current need is to include information about format specification, possibly in addition to other extra header content.
 +
* New proposed headers:
 +
!project-URL: https://wormbase.org
 +
!specification-URL: https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md
 +
OR
 +
!specification-URL: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
 +
!project-release: WS279
 +
* Could repurpose the Wiki page: https://wiki.wormbase.org/index.php/WormBase_gene_association_file from internal docs only to include user guide info, including how our GAF-like files deviate in format from standard GAF
  
=== 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 ===
+
== Nov 19, 2020 ==
* 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 ===
+
=== Webinars ===
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
+
* JBrowse webinar tomorrow (Friday)
 
+
** Ranjana will host; Wen will provide tech support; Daniela will collect user questions from chat in Google Doc; Chris will write staff answers to questions in Google Doc
 
+
* Background slides put together for when audience is waiting
== September 17, 2020 ==
+
* Wen will start the meeting at 9:30am Pacific; can run a test poll
 +
* Questions will be collected in Google Doc; answers can be written into the Google Doc in real time; we can use the Google Doc as a reference to assemble FAQs later
  
=== Species errors in CITace ===
+
=== Alaska ===
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
+
* Is Eduardo still working on it?
 +
* He replied to a user asking about Alaska
 +
* Is it still running? Maintained?
 +
* Can we tell what usage it gets?
 +
* Is it useful for the Alliance? Maybe can write it into grant?
 +
* Is it commercially viable? Maybe someone can write an SBIR grant proposal?
  
=== Webinars ===
+
=== Server space ===
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
+
* No new space in Chen building
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
+
* Many servers will stay in a server room where they are currently
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP
+
* Other servers we will need to see if they can be moved to Chen
* Chris and Wen can discuss how to setup
+
* Paul may have some space for servers in his lab designated space (or his own office)
* Should we have people register? Maybe
+
* It may be possible to move some machines over to the WB space in Chen as soon as we can get a key, but may have to wait until the official move in late January
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
 

Latest revision as of 17:52, 19 November 2020

Previous Years

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2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

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2020 Meetings

January

February

March

April

May

June

July

August

September

October


Nov 5th, 2020

WS279 GAF 2.0 and disease files

  • Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
  • Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
  • Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
  • Raymond needs the GAFs for WoBR

Experimenting with addeding new citace data to the current WS release

  • Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.

MicroPub user webinar on Nov 9th

  • Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.

WS280 deadlines

  • Caltech files due for citace: Dec 15th, 2020


Nov 12th, 2020

Cynthia Kenyon tool

  • developed a new tool for the worm, complete with tutorials, for analyzing gene expression data using Gene Module analysis.
  • tool at http://genemodules.org
  • add link outs from the gene expression widget or add in general WB tools?
  • if we want to incorporate we need to have it updated.
  • are they maintaining it?
  • there's no RNAseq, can be outdated
  • maybe good to add a blog post

Graphical curation tool update

  • We will show a live demo on the current state of the graphical curation tool

Curating to human genes in ACEDB

  • Karen requested option to curate constructs with human genes
  • Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
  • Will discuss on next site-wide call

GAF (and GAF-like) file headers

  • GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
!gaf-version: 2.2
!generated-by: WormBase
!date-generated: 2020-10-30
! WB annotations 00015014
  • For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
  • For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
!gaf-version: 2.0
!generated-by: WormBase
!date-generated: 2020-10-30
  • Current need is to include information about format specification, possibly in addition to other extra header content.
  • New proposed headers:
!project-URL: https://wormbase.org
!specification-URL: https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md

OR

!specification-URL: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
!project-release: WS279


Nov 19, 2020

Webinars

  • JBrowse webinar tomorrow (Friday)
    • Ranjana will host; Wen will provide tech support; Daniela will collect user questions from chat in Google Doc; Chris will write staff answers to questions in Google Doc
  • Background slides put together for when audience is waiting
  • Wen will start the meeting at 9:30am Pacific; can run a test poll
  • Questions will be collected in Google Doc; answers can be written into the Google Doc in real time; we can use the Google Doc as a reference to assemble FAQs later

Alaska

  • Is Eduardo still working on it?
  • He replied to a user asking about Alaska
  • Is it still running? Maintained?
  • Can we tell what usage it gets?
  • Is it useful for the Alliance? Maybe can write it into grant?
  • Is it commercially viable? Maybe someone can write an SBIR grant proposal?

Server space

  • No new space in Chen building
  • Many servers will stay in a server room where they are currently
  • Other servers we will need to see if they can be moved to Chen
  • Paul may have some space for servers in his lab designated space (or his own office)
  • It may be possible to move some machines over to the WB space in Chen as soon as we can get a key, but may have to wait until the official move in late January