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]]
  
[[WormBase-Caltech_Weekly_Calls_October_2018|October]]
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
[[WormBase-Caltech_Weekly_Calls_November_2018|November]]
+
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
== December 6, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
=== SObA for disease (& other ontology?) annotations ===
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
* Next Alliance all-hands call in February, present SObA for Skunkworks (innovation talks)?
 
* SObA top-slicing (summary view) gets tricky; Raymond looking into better solutions, if available
 
* SObA summary could be redundant with ribbon? SObA would provide dynamic, trimmed nodes
 
  
=== Worm phenotype ontology ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* Meeting today at 12pm Pacific, 3pm Eastern
 
* In process of adding back obsolete terms to the ontology
 
* Question about "has_obo_namespace" attribute; not required for ODK process; used by WB pipelines?
 
  
=== ISB Meeting, Cambridge, UK, April 2019 ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* Abstracts from WB?
 
** New Author First Pass - Daniela, Valerio, Kimberly, et al.
 
** Automated gene descriptions - Ranjana, gene description working group
 
  
=== GO expression data using Uberon anatomy terms ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* Some GO curators curating C. elegans expression annotations (from synapse annotation project) to Uberon anatomy terms, not WBbt terms
 
* Kimberly will look into enforcing Noctua editor to use C. elegans anatomy ontology when creating C. elegans annotations
 
* Can possibly perform automated mapping if appropriate cross-references exist
 
* Kimberly has already found annotations to inappropriate Uberon terms
 
  
  
== December 13, 2018 ==
+
== October 3, 2019 ==
  
=== Protege Tutorial ===
+
=== SObA comparison graphs ===
* Doodle poll open: https://doodle.com/poll/kn49rd3rggymn68g
+
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
* Please fill out poll if you are interested in attending
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
* Resources available
+
** [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]
** here (right-click and Save As): https://www.dropbox.com/s/6fygtby4x6d2t0r/ProtegeShortCourse.zip?dl=0
+
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
** and here: https://protege.stanford.edu/shortcourse/201810/resources.html
+
** [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
  
=== Updates to Gene Regulation OA ===
+
=== Germ line discussion ===
* Removed two unused fields/tables: Trans-regulator Seq and Trans-regulated Seq
+
* 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"
* (In progress) Now a single field for anatomy, life stage, and subcellular localization (SCL) (as opposed to a set of each for each type of regulation result)
+
* 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"
* May require ?Interaction model change if anatomy, lifestage, and/or SCL to be annotated without a result type
+
** [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)
  
=== Micropublication workshop IWM 2019 ===
+
=== Script to remove blank entries from Postgres ===
* Micropublication group will apply for a workshop
+
* 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
* If they get it they will need a tiny (~5 min) slot in the general WB
+
* 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
  
=== RNAi uniquely_mapped tags ===
 
* User pointed out that an RNAi object in WormMine was not flagged as "Uniquely mapped"
 
* Turns out that the current RNAi mapping pipeline does not add a "Uniquely_mapped" tag
 
* All existing tags are coming from older RNAi objects in CitaceMinus
 
* Chris working on .ACE file to delete all of these tags from CitaceMinus
 
* Chris will upload the .ACE file to citpub@spica in the Data_for_midbuild directory for Wen
 
  
=== Worm wiring & Worm Atlas ===
+
== October 10, 2019 ==
* Todd and Raymond meeting this afternoon
 
* Chris will join
 
* 2pm Pacific time
 
  
=== WS270 upload ===
+
=== Biocuration 2020 ===
* Jan 11th upload to Hinxton
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
* Tuesday, January 8th citace upload 10am
+
* 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
  
=== Alliance grant renewal ===
+
=== ICBO 2020 ===
* Send Paul drafts for working group updates before next Thursday Dec 20, just to give him a heads up on content
+
* International Conference on Biomedical Ontologies
* Paul currently working off All-Hands meeting presentations
+
* [https://icbo2020.inf.unibz.it/ Meeting website]
 +
* Held in Bozen-Bolzano, Italy
 +
* 16 - 19 September 2020
  
=== Alliance vs. MODs efficiencies ===
+
=== SObA comparison tool ===
* Compare user pipelines for getting info like:  
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
** for a human disease gene, what are the phenotypes in model organisms?
 
* What are the best work products of the Alliance so far?
 
** Expression ribbon
 
** Orthology
 
** Molecular interactions? Good to have nicer interface, consolidation of data; no automated comparative tools yet, but can get equivalent results with some clicking
 
** How to best measure impact?
 
  
=== Noctua imports ===
+
=== Textpresso derived paper connections ===
* Can we export/duplicate a Noctua model to apply to a different gene?
+
* For example for strains and constructs, maybe anatomy terms?
* Can export in GPAD or GAF
+
* May want to flag Textpresso predictions (as opposed to manually connected)
* Want to seed Noctua models with MOD data; efficient, large scale import
+
* 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