Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
== October 4, 2018 ==
 
  
=== SimpleMine ===
+
== September 3, 2020 ==
* Automated descriptions will be removed from Postgres/OA
 
* SimpleMine needed to update where it pulls the automated descriptions from
 
* Will add expression cluster and automated description columns output (in addition to concise description)
 
* Added RNAseq FPKM download function for 9 species: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/fpkmmine.cgi
 
* Added SimpleMine-like topic search: http://tazendra.caltech.edu/%7Eazurebrd/cgi-bin/forms/spellmine.cgi
 
* Should put the new tools under the WormBase Tools menu
 
  
 +
=== WS279 Citace upload ===
 +
* September 25
 +
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
  
== October 11, 2018 ==
+
=== 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
  
=== Ready for new round of phenotype requests ===
+
=== GO annotation for description ===
* Some users are getting confused about the name & email prepopulation based on IP address
+
* Kimberly will look into 'male tail tip developement' terms for description
** May want to stop autopopulating name and email or autopopulate based on email recipient only (encode in URL sent in email)
 
** Could we use cookies? Possibly, but may only help if a computer is shared but the browser isn't
 
* Current autocomplete expects exact match to person primary name; e.g. "Scott Emmons" will not match the official name "Scott Wilson Emmons"
 
** Maybe we could improve search matching; algorithm from Cecilia/Juancarlos? Elastic search by Valerio?
 
** Can we capture incomplete sessions? We may be able to learn from them. May be flooded by robot visits? Is it worth going through all the logs/sessions? Info is there if we want to look at it.
 
* Will go ahead and send emails for only new set of papers (won't resend requests for papers that had emails sent in June/July)
 
* Maybe go back to papers that already had a request sent at the 6 month time point
 
* Include other papers in need of curation at bottom of email; possibly, would it turn off users?
 
  
=== Worm Phenotype Ontology ===
+
=== Migrate wobr1 server to AWS ===
* WPO has a new home on GitHub
+
* SOLR, WOBr, SObA, Enrichment analysis
** https://github.com/obophenotype/c-elegans-phenotype-ontology
+
* Working with Sibyl on the process
* Edits should only be made to the edit file
+
* Will try migrating wobr1 first, as a test case
** https://github.com/obophenotype/c-elegans-phenotype-ontology/blob/master/src/ontology/wbphenotype-edit.owl
+
* May eventually move, for example, Tazendra
* Anyone interested in contributing to the WPO should contact Chris for update pipeline info
+
** Will there be drawbacks to doing this?
* Need to make sure that all users of the WPO have the updated link information
+
** 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)
  
=== Provide provenance in query tools ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Prompted by user question/request
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Specifically in WOBr, Anatomy pages
+
* Meeting will be virtual on Zoom
* WOBr provides genes annotated to term; should provide provenance of each gene and its annotations
+
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
* Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
+
* Send topic requests to Chris for the talk
* Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page
+
* 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
  
=== WOBr disease associations ===
 
* Ranjana wondering if WOBr is using updated disease-gene associations
 
* Gene association file (for disease) being generated by script; likely need to update where the data is coming from
 
* Ranjana will discuss with Raymond and Kevin
 
  
=== New WormMine superuser ===
+
== September 10, 2020 ==
* Now all template queries are owned by a new superuser
 
* If people are interested in adding or editing templates talk to Chris or Paulo for superuser access
 
* We were running into login, template ownership, and consistency issues
 
  
=== Next upload Nov 16 ===
+
=== GO GAF Files ===
* WS269 citace upload Tuesday, November 13
+
* WS278 GO GAF is using the new 2.2 file format
* Can we add upload dates to Google calendar for WormBase?
+
* [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, ??
  
== October 18, 2018 ==
+
=== 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
  
=== Upload for WS269===
+
=== WormBase talk at Boston Area Worm Meeting ===
* To Hinxton Nov 16
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Citace upload to Wen Nov 13
+
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 +
* WormBase members can attend; Zoom link will be sent next Monday
  
=== Data provenance in WOBr tools ===
+
=== Worm Anatomy Ontology Fixes ===
* Juancarlos and Raymond have been working on
+
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
* Awaiting pull request
+
* Assessing the best way to address them
* Can test: juancarlos.wormbase.org
+
* Would be good to be able to automate some edits; options:
** Go to WOBr and test anatomy ontology
+
** Use OWL API (need someone proficient in coding with OWL API)
** Now WOBr gene count results show data objects from which the associations come (Expr_pattern and Expression_cluster objects)
+
** 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
  
=== New SPELL server ===
+
=== Dead Variations in Postgres ===
* New server on Amazon (modifying server SGD uses)
+
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
* Raymond, Wen, and Todd working on
+
* Noticed that many transgene names were being included, which can result in false positives for the categories
* Currently only have an SGD mirror running
+
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
* Wen will swap the data later today
+
* Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
* WormBase header link (to WormBase) or only link to Alliance site? We want a unified site for Alliance
+
* May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
* Each MOD would still support their own server for their data (MOD-specific grants support each server, for now)
+
* 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
  
=== Alliance expression data ===
+
=== WS279 Citace Upload ===
* Anatomy-LifeStage pair required for Alliance expression annotations
+
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
* Since many expression pattern annotations don't have both, the missing entity would default to ontology root term
 
* Need to link anatomy root term to Uberon for ribbon display; root term annotations fall under the "Other" category in the ribbon slim
 
* Create "Anatomical_part" term to serve as the default "Other"/root term?
 
* All life-stage-only annotations will fall into anatomy "Other" and flood the list; should these be filtered out?
 
  
  
== October 25, 2018 ==
+
== September 17, 2020 ==
  
=== WormBase SPELL on Amazon Web Service ===
+
=== Species errors in CITace ===
* http://34.224.93.60/ is running WormBase SPELL on WS267, based on the SPELL code supported by SGD. It is more stable and faster than the current Caltech server
+
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
* Waiting for Todd to respond if we can use this site as the official server for WormBase SPELL.
 
* Also need to get an instance (preferably also from WormBase AWS as a development site of WormBase SPELL.
 
* Caltech will focus on generating new data instead of SPELL code development.
 
  
=== Linking annotation evidence to Anatomy Ontology Browser ===
+
=== Webinars ===
Each gene expression annotation shown on WOBr is linked to the object so that users can more easily examine the evidence.
+
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
[https://juancarlos.wormbase.org/tools/ontology_browser/show_genes?focusTermName=neuron&focusTermId=WBbt:0003681 Example]
+
* 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