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]]
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 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
  
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= 2018 Meetings =
+
= 2019 Meetings =
 
 
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
 
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
  
== October 4, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
=== SimpleMine ===
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
* 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
 
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
== October 11, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
=== Ready for new round of phenotype requests ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Some users are getting confused about the name & email prepopulation based on IP address
 
** 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 ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* WPO has a new home on GitHub
 
** https://github.com/obophenotype/c-elegans-phenotype-ontology
 
* Edits should only be made to the edit file
 
** https://github.com/obophenotype/c-elegans-phenotype-ontology/blob/master/src/ontology/wbphenotype-edit.owl
 
* Anyone interested in contributing to the WPO should contact Chris for update pipeline info
 
* Need to make sure that all users of the WPO have the updated link information
 
  
=== Provide provenance in query tools ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* Prompted by user question/request
 
* Specifically in WOBr, Anatomy pages
 
* WOBr provides genes annotated to term; should provide provenance of each gene and its annotations
 
* Expression pattern and expression cluster gene lists (in context of Anatomy WOBr); want to provide provenance for this data
 
* Provenance = an object ID, like "Expr1234" or "WBPaper00032062:age_regulated_genes" with link to relevant page
 
  
=== WOBr disease associations ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* 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 ===
 
* 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 ===
+
== October 3, 2019 ==
* WS269 citace upload Tuesday, November 13
 
* Can we add upload dates to Google calendar for WormBase?
 
  
 +
=== SObA comparison graphs ===
 +
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
 +
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
 +
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
 +
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 +
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 +
* What information does a user most care about?
 +
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 +
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 +
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 +
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 +
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 +
* In either case users need a good legend and/or documentation
 +
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
  
== October 18, 2018 ==
+
=== Germ line discussion ===
 +
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
 +
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
 +
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
 +
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
  
=== Upload for WS269===
+
=== Script to remove blank entries from Postgres ===
* To Hinxton Nov 16
+
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
* Citace upload to Wen Nov 13
+
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
 +
* Does anyone object to removing these entries throughout Postgres?
 +
* Juancarlos will remove all the empty fields identified by his script
  
=== Data provenance in WOBr tools ===
 
* Juancarlos and Raymond have been working on
 
* Awaiting pull request
 
* Can test: juancarlos.wormbase.org
 
** Go to WOBr and test anatomy ontology
 
** Now WOBr gene count results show data objects from which the associations come (Expr_pattern and Expression_cluster objects)
 
  
=== New SPELL server ===
+
== October 10, 2019 ==
* New server on Amazon (modifying server SGD uses)
 
* Raymond, Wen, and Todd working on
 
* Currently only have an SGD mirror running
 
* Wen will swap the data later today
 
* WormBase header link (to WormBase) or only link to Alliance site? We want a unified site for Alliance
 
* Each MOD would still support their own server for their data (MOD-specific grants support each server, for now)
 
  
=== Alliance expression data ===
+
=== Biocuration 2020 ===
* Anatomy-LifeStage pair required for Alliance expression annotations
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
* Since many expression pattern annotations don't have both, the missing entity would default to ontology root term
+
* Dates: Sunday May 17th to Wednesday May 20th, 2020
* Need to link anatomy root term to Uberon for ribbon display; root term annotations fall under the "Other" category in the ribbon slim
+
* Will have 3rd POTATO workshop
* Create "Anatomical_part" term to serve as the default "Other"/root term?
+
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
* All life-stage-only annotations will fall into anatomy "Other" and flood the list; should these be filtered out?
+
* Key Dates
 +
** October 31, 2019 - Paper Submission Deadline
 +
** January 24, 2020 - Abstract  and Workshop Submission Deadline
 +
** March 6, 2020 - Notification of Acceptance
 +
** April 6, 2020 - Early Bird Registration Ends
 +
** May 8, 2020 - Registration Deadline
 +
* Academic ISB Member, early bird registration fee is $250
 +
* Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
  
 +
=== ICBO 2020 ===
 +
* International Conference on Biomedical Ontologies
 +
* [https://icbo2020.inf.unibz.it/ Meeting website]
 +
* Held in Bozen-Bolzano, Italy
 +
* 16 - 19 September 2020
  
== October 25, 2018 ==
+
=== SObA comparison tool ===
 +
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
  
=== WormBase SPELL on Amazon Web Service ===
+
=== Textpresso derived paper connections ===
* http://34.224.93.60/ is running WormBase SPELL on WS267, based on the SPELL code supported by SGD.
+
* For example for strains and constructs, maybe anatomy terms?
 +
* May want to flag Textpresso predictions (as opposed to manually connected)
 +
* Couple of options:
 +
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
 +
** 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
 +
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
 +
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
 +
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
 +
* Transgene pipeline:
 +
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
 +
** Another script, captures Ex transgenes as well, automatically connects to construct objects
 +
** WB only displays verified papers; unverified (predicted) associations are not dumped
 +
* Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
 +
* Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
 +
* Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
 +
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities

Revision as of 15:06, 11 October 2019

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1


2019 Meetings

January

February

March

April

May

June

July

August

September


October 3, 2019

SObA comparison graphs

  1. What terms (nodes) are annotated to gene 1 and what terms to gene 2
  2. For a given term, what is the relative number of annotations between gene 1 and gene 2.
  3. For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
  • # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
  • Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
  • In either case users need a good legend and/or documentation
  • Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes

Germ line discussion

  • Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
  • Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
  • Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)

Script to remove blank entries from Postgres

  • Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
  • Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
  • Does anyone object to removing these entries throughout Postgres?
  • Juancarlos will remove all the empty fields identified by his script


October 10, 2019

Biocuration 2020

  • Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
  • Dates: Sunday May 17th to Wednesday May 20th, 2020
  • Will have 3rd POTATO workshop
  • Meeting website
  • Key Dates
    • October 31, 2019 - Paper Submission Deadline
    • January 24, 2020 - Abstract and Workshop Submission Deadline
    • March 6, 2020 - Notification of Acceptance
    • April 6, 2020 - Early Bird Registration Ends
    • May 8, 2020 - Registration Deadline
  • Academic ISB Member, early bird registration fee is $250
  • Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference

ICBO 2020

  • International Conference on Biomedical Ontologies
  • Meeting website
  • Held in Bozen-Bolzano, Italy
  • 16 - 19 September 2020

SObA comparison tool

Textpresso derived paper connections

  • For example for strains and constructs, maybe anatomy terms?
  • May want to flag Textpresso predictions (as opposed to manually connected)
  • Couple of options:
    • 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
    • 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
      • A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
      • Do a diff so that Textpresso pulls up only additional papers (not already associated)?
    • 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
  • Transgene pipeline:
    • Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
    • Another script, captures Ex transgenes as well, automatically connects to construct objects
    • WB only displays verified papers; unverified (predicted) associations are not dumped
  • Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
  • Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
  • Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
  • Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities