Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
m
(251 intermediate revisions by 8 users not shown)
Line 21: Line 21:
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
Line 28: Line 27:
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
== February 7, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
 
=== Automation of curation ===
 
* For paper-by-paper curators (vs. datatype-by-datatype) it's difficult to parse papers into data types
 
* MGI and WB curate by datatype, so may have an easier time
 
* All MODS still need paper triage
 
  
=== IWM workshop ===
+
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
* Ranjana replied to Julie about a consolidated WormBase workshop; hasn't heard back
 
  
=== Site-specific outreach ===
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
* Wen has been invited to small RNA meeting in Mexico in April; may go if they offer to pay (waiting to hear back)
 
  
=== SObA ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Raymond and Juancarlos have worked out a way to display top-slicing of the ontology (trimming to higher level nodes)
 
* Needs a bit more clean up; will send around a URL when ready
 
  
 +
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
== February 21, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
=== SObA ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
  
* SObA GO graph, with top slicing function. You can try it here <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi> by entering the name of your favorite gene.
 
  
* specific genes, from simple to complex
+
== October 3, 2019 ==
let-4 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=let-4%20(Caenorhabditis%20elegans,%20WB:WBGene00002282,%20-,%20C44H4.2,%20sym-5)>
 
  
let-60 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=let-60%20(Caenorhabditis%20elegans,%20WB:WBGene00002335,%20-,%20ZK792.6,%20lin-34)>
+
=== 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
  
daf-2 <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi?action=annotSummaryCytoscape&showControlsFlag=0&autocompleteValue=daf-2%20(Caenorhabditis%20elegans,%20WB:WBGene00000898,%20-,%20Y55D5A.5)>
+
=== 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)
  
* Looks good
+
=== Script to remove blank entries from Postgres ===
* Some confusion with filled circle legend (half red and half blue) for slim terms; maybe make two separate circles, one red, one blue and possibly indicate each as direct/indirect, respectively
+
* 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
* May be good to make graph depth options more obvious; we can move it up to the top of the legend, maybe also display all graph depths by default so a user can see them and select one
+
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
* Would it be possible to force display of any AGR/Alliance slim terms on the path from an annotation node to root (not all pertinent slim terms are currently displaying due to the trimming algorithms in place); might be possible but would probably significantly interfere with the current trimming and display algorithm
+
* Does anyone object to removing these entries throughout Postgres?
 +
* Juancarlos will remove all the empty fields identified by his script
  
=== Moving away from dependency on OBO format files ===
 
* Nico, an ontology developer with the Monarch group, has some suggestions for how we can move away from dependency on OBO files
 
* Planning to have a meeting on Monday (Feb 25) at 9am Pacific, 12pm Eastern, 5pm UK to discuss
 
* How are we handling OBO for GO? GO OBO is parsed into ACE format
 
* This should be a group-wide discussion as we have many OBO dependencies
 
* There are several OBO-to-ACE conversion scripts we use
 
* What is the trend in the ontology field? Seems to be that OBO will become deprecated and OWL will supersede it
 
* We will try to reschedule to Tuesday (same time) to include more people
 
  
=== Phenotype request mass emails ===
+
== October 10, 2019 ==
* 1,820 emails gone out this week (since Monday) for 1,820 papers (957 still in queue; need to wait for Google limit to expire)
 
* Have received 217 direct annotations for 49 papers (45 requested papers) from 47 distinct community curators
 
** 158 to Phenotype OA
 
** 59 to RNAi OA
 
* Have received 5 submissions via email (4 worksheets)
 
** 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
 
** 4 phenotype submissions, 4 curators, 93 phenotype annotations
 
* 57 papers flagged as not having phenotypes
 
* Total: 310 phenotype annotations from 51 community curators for 53 papers
 
  
 +
=== 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
 +
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference 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
  
== February 28, 2019 ==
+
=== ICBO 2020 ===
 +
* International Conference on Biomedical Ontologies
 +
* [https://icbo2020.inf.unibz.it/ Meeting website]
 +
* Held in Bozen-Bolzano, Italy
 +
* 16 - 19 September 2020
  
=== Phenotype request mass emails ===
+
=== SObA comparison tool ===
* 2,777 emails gone out (last week) for 2,777 papers
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
* Have received 421 direct annotations for 88 papers (81 requested papers; ~3% response rate) from 84 distinct community curators
 
** 313 to Phenotype OA
 
** 108 to RNAi OA
 
* Have received 5 submissions via email (4 worksheets)
 
** 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
 
** 4 phenotype submissions, 4 curators, 93 phenotype annotations
 
* 83 papers flagged as not having phenotypes
 
* Total: 514 phenotype annotations from 88 community curators for 92 papers
 
  
=== OBO axioms ===
+
=== Textpresso derived paper connections ===
* Nico is asking for a list of all OBO axioms needed by WormBase
+
* For example for strains and constructs, maybe anatomy terms?
* He will then make sure that any OWL-derived OBO files (from ODK pipeline) will include required axioms
+
* May want to flag Textpresso predictions (as opposed to manually connected)
* Collecting list of OBO relations in [https://docs.google.com/document/d/1V7KnAIcFsf2Kydm3NyHQT0wUBU3Z8zmfk8ByssTJeLA/edit?usp=sharing minutes doc from meeting on Tuesday]
+
* 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