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_January_2019|January]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
[[WormBase-Caltech_Weekly_Calls_September_2018|September]]
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
[[WormBase-Caltech_Weekly_Calls_October_2018|October]]
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
 +
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
== November 1, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
=== Community phenotype requests ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* Sent out 1,000 request emails for community submissions of phenotypes on October 18 and October 20
 
* As before, request focuses on a single paper, but we've now added extra papers at bottom of email message
 
* We've also added a link for users to click on to indicate that the paper in question (focus paper) has no nematode phenotypes
 
* 21 emails bounced
 
* 56 papers received annotations, 44 from direct requests, 12 not directly requested
 
* 9 of 12 not directly requested were appended requests to email message
 
* 277 annotations submitted (raw) via the form (some more submitted as Excel spreadsheets)
 
** 247 allele/transgene phenotype annotations
 
** 30 RNAi phenotype annotations
 
* 48 distinct community curators
 
  
=== SPELL ===
 
* Todd working on a spell.wormbase.org site for doing worm SPELL analyses
 
* Should be faster, more stable
 
  
=== Predicted protein-protein interactions ===
+
== October 3, 2019 ==
* Jae has requested data set
 
* Total data set 20GB (how much is C. elegans?)
 
* Haven't heard back from author recently
 
* How much do we want this data? Should reach out a couple more times (once every ~two weeks)
 
  
 +
=== 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
  
== November 8, 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)
  
=== Author First Pass ===
+
=== Script to remove blank entries from Postgres ===
* Do curators want to be notified by e-mail when authors flag their datatype in the AFP form?
+
* 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
** Raymond, Ranjana, Gary, Jae and Karen ok to have a monthly digest. Chris, Wen no email
+
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
** Will check in with Gary W and see if he wants to be notified for RNAseq data flagging
+
* Does anyone object to removing these entries throughout Postgres?
** Should ask April what she wants to do
+
* Juancarlos will remove all the empty fields identified by his script
* Shall we add  in the Curation status form Datatypes that are not currently in it (e.g. Time and site of action)
 
** Yes, Add site and time of action
 
* How would we like to handle Methods papers?  These may have reagents and some bona fide experimental results, but are not our 'typical' experimental papers.  Possibly add a new 'methods' flag?
 
** Worth flagging methods papers. Will send methods papers to authors for 6 months and then evaluate how useful it is
 
* Do we need to still maintain the cfp form? If we can keep the data tables and still see the flags in the curation status form, do we need the cfp form?
 
** The CFP form can be retired
 
* Add back in the AFP from ‘this is a review paper, I am not curating this’
 
  
  
=== Expression Pattern Model ===
+
== October 10, 2019 ==
  
* there would be value in having a separate ?Expr_annotation class, like we did for ?GO_annotation. It might look something like this (details not completely thought through):
+
=== Biocuration 2020 ===
     
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
<pre>     
+
* Dates: Sunday May 17th to Wednesday May 20th, 2020
Class ?Expr_annotation
+
* Will have 3rd POTATO workshop
  Life_stage ?Life_stage XREF Expr_pattern #Qualifier
+
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
  Not_in_Life_stage ?Life_stage #Qualifier
+
* Key Dates
  Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
+
** October 31, 2019 - Paper Submission Deadline
  Not_in_Anatomy_term ?Anatomy_term #Qualifier
+
** January 24, 2020 - Abstract  and Workshop Submission Deadline
  GO_CC ?GO_term XREF Expr_pattern
+
** March 6, 2020 - Notification of Acceptance
  GO_BP ?GO_term XREF Expr_pattern
+
** April 6, 2020 - Early Bird Registration Ends
  Cell ?Cell
+
** May 8, 2020 - Registration Deadline
  Cell_group ?Cell_group
+
* 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
  
#Qualifer Certain
+
=== ICBO 2020 ===
          Partial
+
* International Conference on Biomedical Ontologies
          Uncertain
+
* [https://icbo2020.inf.unibz.it/ Meeting website]
</pre>
+
* Held in Bozen-Bolzano, Italy
An Expr_pattern can then have a list of ?Expr_annotations, each grouping together all properties of a single observation.
+
* 16 - 19 September 2020
  
Daniela will work on a model for an ?Expression_annotation class.
+
=== SObA comparison tool ===
The change can be gradual. We can Add the ?Expression_annotation class and still dump anatomy, life stage and GO in the old tags. Down the line those tags will be deprecated and fully replaced by the ?Expression_annotation tags
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
  
?Cell and ?Cell group could go away
+
=== 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

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