Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
== May 2, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
=== SObA for all ontologies ===
+
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
* http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
 
* SObA graph search for all ontologies
 
* Juancarlos and Raymond looking for feedback; let them know
 
* Would be good to make it clear to users what the edges/arrows mean; what relations are included for inference? Can we include blurb in the legend?
 
** Raymond: thinking of putting blurb on a separate documentation page
 
* Can we track who is using this tool (and others)? SObA is hosted by WormBase so we'd have to ask Todd (Google analytics); SimpleMine is Caltech hosted so we'd need to look at Tazendra logs to see who (and how many people) are using the tool (cannot rule out bots etc.)
 
  
=== IWM swag - screen cloth ===
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
* Need to finalize design
 
* Put Dick & Jane cartoon in one corner, tools in another corner, WB logo, Alliance logo
 
* Daniel can take care of ordering and printing, but needs someone to choose the design
 
  
=== Phenotype ontology patternization ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* Chris working on patternizing phenotype terms to standardize logical definitions for classes of terms
 
* This is part of the ongoing effort to align phenotype ontologies across the organisms
 
* Paul S: It's important for community submitted phenotypes (and the use of the form) to make sure the ontology makes sense and is readily browsable
 
* Does "dumpy" mean the same thing to everyone? Is there a way to assess discrepancies in term definitions among members of the community?
 
* Does someone annotate to Egl or vulvaless?
 
* How do we help community curators decide the correct term?
 
* Could we develop a smart annotation aid/tool/helper? Use images, examples, etc.
 
  
  
== May 9, 2019 ==
+
== October 3, 2019 ==
=== SObA for all ontologies ===
 
* Revised version http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi
 
* Changed legend labelling, added linkouts
 
* To implement on Gene pages. One vs. Five widgets?
 
* Would be good to provide documentation on what the inferences mean; can we provide an indication of what relations a particular SObA edge could be comprised of?
 
** Or click on an edge to get the, e.g., GO subgraph that connects the two nodes?
 
* Let's release to the website, but gather feedback from (naive) users to see what documentation we need
 
  
=== Citace upload next Tuesday ===
+
=== SObA comparison graphs ===
* Tuesday May 14, 2019, 10am Pacific
+
* 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
  
=== SPELL is now indexed by Google ===
+
=== Germ line discussion ===
* Cool!
+
* 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)
  
 +
=== 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
  
  
== May 16, 2019 ==
+
== October 10, 2019 ==
  
=== SObA graphs ===
+
=== Biocuration 2020 ===
* Edges in graph can be clicked to generate pop ups with link to the (lower) term page showing the graph of inference to upper level nodes
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
* May provide more information than the user needs/wants
+
* Dates: Sunday May 17th to Wednesday May 20th, 2020
* Juancarlos working on implementing SObA widgets on gene pages (maybe for WS271 or WS272?)
+
* Will have 3rd POTATO workshop
* IWM will have WS271 on staging during meeting; probably on production shortly after the meeting
+
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
** Hope to show users demos at IWM
+
* 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
 +
 
 +
=== SObA comparison tool ===
 +
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
 +
 
 +
=== 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
 +
 
 +
 
 +
== October 17, 2019 ==
 +
 
 +
=== Alliance All Hands Face-to-Face ===
 +
* Flights: has everyone already booked? No, not yet
 +
* Any coordination of flights from Pasadena/LA?
 +
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
 +
 
 +
=== SObA Comparison Tool ===
 +
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 +
* Prototype discussed last week, updated with feedback from prior discussions
 +
* Would this be a stand-alone tool discoverable under the Tools menu?
 +
** Possibly; could be a gene page widget, but may be out of place
 +
** Stand-alone tool probably makes more sense
 +
* Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
 +
 
 +
=== SObA ===
 +
* Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
 +
* For example, share GO SObA graph for other species
 +
* Will need to be dependent on a SOLR server with all species data
 +
** Raymond has run into problems trying to setup his own SOLR server
 +
** Raymond asked Seth Carbon if we could us GO server, but he prefers not
 +
** Appear to be software versioning issues, possible memory issues
 +
 
 +
=== GO meeting ===
 +
* Kimberly can give update on recent updates to GO from the recent GO meeting
 +
* Slides are shared online
 +
 
 +
=== "all stages Ce" life stage ===
 +
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
 +
* "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
 +
* Should we:
 +
** 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
 +
*** Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
 +
** 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
 +
* Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
 +
* Wen: not comfortable making a decision right now; want to discuss with Gary Williams and with other MOD members about how to handle large scale expression data
 +
* Daniela: will look through existing (old and new) expression pattern annotations made to "all stages Ce" to see if it would be reasonable to annotate each case individually to "embryo Ce", "larva Ce", and "adult Ce" individually
 +
 
 +
=== Gene class missing description ===
 +
* The gene class "aatf" has no description, so in the aatf-1 gene page Overview widget, the gene has empty parentheses next to the gene name where there should be a description of what "aatf" stands for (coming from the ?Gene_class description)
 +
* Jae or Ranjana will create a ticket and assign it to someone at Hinxton

Revision as of 17:12, 17 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


October 17, 2019

Alliance All Hands Face-to-Face

  • Flights: has everyone already booked? No, not yet
  • Any coordination of flights from Pasadena/LA?
    • Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings

SObA Comparison Tool

  • http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
  • Prototype discussed last week, updated with feedback from prior discussions
  • Would this be a stand-alone tool discoverable under the Tools menu?
    • Possibly; could be a gene page widget, but may be out of place
    • Stand-alone tool probably makes more sense
  • Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)

SObA

  • Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
  • For example, share GO SObA graph for other species
  • Will need to be dependent on a SOLR server with all species data
    • Raymond has run into problems trying to setup his own SOLR server
    • Raymond asked Seth Carbon if we could us GO server, but he prefers not
    • Appear to be software versioning issues, possible memory issues

GO meeting

  • Kimberly can give update on recent updates to GO from the recent GO meeting
  • Slides are shared online

"all stages Ce" life stage

  • Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
  • "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
  • Should we:
    • 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
      • Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
    • 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
  • Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
  • Wen: not comfortable making a decision right now; want to discuss with Gary Williams and with other MOD members about how to handle large scale expression data
  • Daniela: will look through existing (old and new) expression pattern annotations made to "all stages Ce" to see if it would be reasonable to annotate each case individually to "embryo Ce", "larva Ce", and "adult Ce" individually

Gene class missing description

  • The gene class "aatf" has no description, so in the aatf-1 gene page Overview widget, the gene has empty parentheses next to the gene name where there should be a description of what "aatf" stands for (coming from the ?Gene_class description)
  • Jae or Ranjana will create a ticket and assign it to someone at Hinxton