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 =
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= 2019 Meetings =
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[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
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[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
 
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[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
 
  
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[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
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[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
  
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[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
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[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
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[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
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[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
−
== July 5, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
−
=== Community Curation Mass Email update ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
−
* Emails (1 per paper) sent (most batches 75 at a time): 3,227 total
 
−
** June 11: 5
 
−
** June 20: 15
 
−
** June 21: 82
 
−
** June 22: 6
 
−
** June 25: 75
 
−
** June 26: 80
 
−
** June 28: 363
 
−
** June 29: 600
 
−
** June 30: 300
 
−
** July 1: 450
 
−
** July 2: 1,251
 
−
** Email success rate:
 
−
*** 482 emails bounced (15%)
 
−
**** 74 bounced emails had a backup email (2%)
 
−
**** 292 bounced emails had no backup (12%)
 
−
**** 88% of emails were successfully sent
 
−
*** 52 out of office replies (2%)
 
−
* Total community annotations received since June 11: 718 (115 papers)
 
−
** June 13: 24 (3 papers)
 
−
** June 14: 8 (3 papers)
 
−
** June 17: 1 (1 paper)
 
−
** June 20: 13 (3 papers)
 
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** June 21: 13 (4 papers)
 
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** June 25: 13 (4 papers)
 
−
** June 26: 20 (7 papers)
 
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** June 28: 17 (8 papers)
 
−
** June 29: 131 (8 papers)
 
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** June 30: 4 (2 papers)
 
−
** July 1: 24 (5 papers)
 
−
** July 2: 184 (36 papers)
 
−
** July 3: 179 (20 papers)
 
−
** July 4: 27 (9 papers)
 
−
** July 5: 62 (pre-meeting) (4 papers)
 
−
* We may want to give people the option to "opt-out" either for a paper or for all emails or both
 
−
* May be good to ask SAB and users at meetings how they feel about these email requests
 
−
* Is it worthwhile to send requests about same paper to same people after a wait period?
 
  
−
=== SAB Literature Curation overview ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
−
* Outline: https://docs.google.com/document/d/1OUHoFYC3deEmZvgzmOtmxpt5iBrVio9sAZG66kRHwsE/edit?usp=sharing
 
−
* Want to ask about:
 
−
** Data type history, current types, priorities going forward?
 
−
** Community curation? Pilot results, should we expand?
 
−
** Data type vs. topic-based curation?
 
−
** Val Wood and PomBase have found topic-based curation to be more efficient
 
−
* Alliance working groups:
 
−
** data type focused
 
−
** Has affected our curation approach
 
  
−
=== WS267 Citace upload ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
−
* July 20th, upload to Hinxton
 
−
* July 17th, local CIT upload
 
  
−
=== Model changes ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
−
* Some minor tag name changes
 
−
* Changes to GO_annotation to accommodate RO terms
 
  
−
=== Curation Status Form: flagged vs. validated papers ===
 
−
* Papers validated by curators are not necessarily considered flagged
 
−
* Author first pass forms: prepopulated with SVM, string-matches
 
−
* Curation First Pass: are forms still used?
 
−
* TFP (Textpresso first pass) not currently used?
 
  
 +
== October 3, 2019 ==
  
−
== July 19, 2018 ==
+
=== 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
  
−
=== PomBase SObA ===
+
=== Germ line discussion ===
−
* Val Wood would be interested in using SObA for PomBase
+
* 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"
−
* Some immediate action items to deal with for expanding SObA to other ontologies and databases
+
* 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"
−
* Maybe highlight leaf nodes with more granular information? Already available in unweighted view
+
** [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)
  
−
=== Outreach ===
+
=== Script to remove blank entries from Postgres ===
−
* SAB suggested continuing site visits for WormBase tutorials
+
* 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
−
* SAB suggested host institution provide funds; we can at least ask
+
* 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
  
−
== July 26th, 2018 ==
 
  
−
=== Temporarily Withdrawn Paper (WBPaper00054672) ===
+
== October 10, 2019 ==
−
*A recently epublished Genetics paper (2018 Jun 26)  "...has been temporarily removed at the authors' request, to allow review of a companion article. The article 301078 will appear in a future issue of GENETICS."
 
−
*We already have the PDF in postgres (as of 2018-07-10), but I don't see the paper in TPC or the curation status form.
 
−
*Is there anything we should do here? Temporarily remove the PDF from postgres?
 
−
** Remove entirely and get new paper from scratch? OK
 
  
−
=== Expression display on the anatomy page ===
+
=== Biocuration 2020 ===
−
* Suggested last week to have a way to display genes and associated evidences on the anatomy page. Rank order by number of evidences.
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
−
* Mock here: https://docs.google.com/presentation/d/1HE_QhJrs5oScmORdiAAdTxfavAnF6NUQhtJGWvcC7EQ/edit#slide=id.p2
+
* Dates: Sunday May 17th to Wednesday May 20th, 2020
−
* Consider grouping evidence per gene (Expr_pattern objects)
+
* Will have 3rd POTATO workshop
−
* Should we apply a weight to each piece of evidence, type of evidence?
+
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
−
** Apply less weight to large scale, e.g. RNAseq data?
+
* Key Dates
−
* Users likely want to know confidence of presence/absence call as well as degree of specificity
+
** October 31, 2019 - Paper Submission Deadline
−
* Need to consider methods used: Single-cell RNAseq of pool of cell types IDed by sequencing may not be as reliable an annotation to a specific cell, cell type or tissue; but single-cell RNAseq from physically isolated cells based on marker/reporter expression may be more reliable
+
** January 24, 2020 - Abstract  and Workshop Submission Deadline
−
* We will first rank-order the list based on genes with a higher number of Expr_pattern objects
+
** 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
  
−
=== SAB Follow Up ===
+
=== ICBO 2020 ===
−
*SAB Report (Paul sent around a Word doc)
+
* International Conference on Biomedical Ontologies
 +
* [https://icbo2020.inf.unibz.it/ Meeting website]
 +
* Held in Bozen-Bolzano, Italy
 +
* 16 - 19 September 2020
  
−
=== Noctua ===
+
=== SObA comparison tool ===
−
* Can import annotations, but can't edit them and resubmit them; essentially read-only
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
−
* Possibility of micropublishing a Noctua model
 
  
−
=== Picture curation ===
+
=== Textpresso derived paper connections ===
−
* Marie-Claire started picture curation with Daniela
+
* For example for strains and constructs, maybe anatomy terms?
−
* Jae reported that Simon James at Florey Institute of Neuroscience and Mental Health, Australia wants to submit many images (some published, some not)
+
* 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
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