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_January_2019|January]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
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[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
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[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
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[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
  
[[WormBase-Caltech_Weekly_Calls_August_2018|August]]
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[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
  
 +
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
  
== September 6, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
  
=== Genotype class ===
+
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
* Chris started initial document to draw up ?Genotype class and make appropriate changes to ?Strain class
 
**  https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing
 
* Would be good for people to look at so we can discuss next time
 
* Would also be good to have Kevin H take a look and provide feedback
 
  
=== Citace Upload ===
 
* Send citace files to Wen by Sept 18, 10am Pacific
 
  
=== Automated gene descriptions ===
+
== October 3, 2019 ==
* Group making improvements
 
* Added disease, protein domains
 
** When direct experimental evidence for disease relevance, will say "gene has been used to study"
 
* When minimal data (information-poor genes), we can refer to human ortholog and data stored for that human gene in Alliance
 
* Continue to receive feedback from users; include enrichment information, etc.
 
* Now have good trimming algorithms to retain important info without flooding a description with too many granular terms
 
* Will not store automated descriptions in Postgres
 
* Wen will modify SimpleMine scripts to accommodate change
 
* Would be good to write a paper on automated concise descriptions
 
* Came up at GO meeting/hackathon: Translating GO-CAM models into concise descriptions?
 
** Should be doable; just need to develop code when we're ready to do that
 
  
=== Textpresso presentation at next Alliance all-hands call ===
+
=== SObA comparison graphs ===
* Who should present? Maybe have several people? Kimberly, Valerio, Michael for sections?
+
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
* We can discuss at next Textpresso meeting
+
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
* Should cover techniques and software, but keep it generally simple and comprehensible for a larger audience
+
** [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
  
 +
=== 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)
  
== September 13, 2018 ==
+
=== 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
  
=== Citace upload ===
 
* Send files to Wen by 10am Tuesday (18th)
 
  
=== Genotype class ===
+
== October 10, 2019 ==
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing ?Genotype class proposal]
 
* Genotype_name tag: free text summary of the genotype
 
** Can this be automatically generated from components? Ideally, yes, but may be difficult
 
** Otherwise, can be manually written, as we have been doing, but is a bit denormalized and may require maintenance
 
* Genotype_description tag: free-text description of the genotype
 
** No precedent and probably not going to start now, so will remove from model
 
* Genotype_components supertag: to collect genotype component objects and, where necessary, free text
 
** We want to be able to express zygosity for each referenced object, likely requires a #Zygosity hash (and hence a ?Zygosity model)
 
** ?Zygosity model can have three main tags: "Homozygous", "Heterozygous_with_wild_type", or "Heteroallelic_combination_with"
 
*** Heteroallelic_combination_with tag could further specify the type and identity of the object that is in heteroallelic combination with the original object
 
*** Since it is not ideal to store an arbitrary component in the #Zygosity hash, we should probably just state the zygosity as "Heteroallelic_combination" and for display purposes have an automated way to calculate which components affect the same locus/loci (if necessary)
 
  
 +
=== 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
  
 +
=== ICBO 2020 ===
 +
* International Conference on Biomedical Ontologies
 +
* [https://icbo2020.inf.unibz.it/ Meeting website]
 +
* Held in Bozen-Bolzano, Italy
 +
* 16 - 19 September 2020
  
== September 20, 2018 ==
+
=== SObA comparison tool ===
 +
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
  
=== Kimberly's talk at Rutgers ===
+
=== Textpresso derived paper connections ===
* Kimberly went to worm meeting at Rutgers (10 labs using C. elegans? 6-7 totally worm-centric)
+
* For example for strains and constructs, maybe anatomy terms?
* 30-40 attendees (PIs, postdocs, grad students)
+
* May want to flag Textpresso predictions (as opposed to manually connected)
* Discussed tools and features at WB
+
* Couple of options:
* Presented Alliance pages and Textpresso
+
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
* PIs are enthusiastic about WB
+
** 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
* Monica Driscoll made a good plug for Textpresso
+
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
* People requesting FAQs and user guides (text and videos)
+
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
* Monica suggested a WB tutorial for PIs ;p
+
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
* Some people surprised about what they can accomplish using the tools available, like SimpleMine
+
* Transgene pipeline:
* Covered gene set enrichment, WormMine, SPELL, SimpleMine, ParaSite BioMart, Textpresso
+
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
* Would be good to show people how to use Textpresso Central
+
** Another script, captures Ex transgenes as well, automatically connects to construct objects
* Can we make a within-page search available to find, for example, field names etc.
+
** WB only displays verified papers; unverified (predicted) associations are not dumped
* Some challenges in find genes/proteins of certain class
+
* 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
** Had question about histone genes recently
+
* 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?
** Repeatedly have had questions about finding "ion channels"
+
* 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
** Searching gene class with text pulls out lots of false positives
+
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
** Could perform an analysis on particular classes of genes (e.g. histones or ion channels) and generate a micropublication providing the curated list
 
** Can generate a WormMine template query to pull these out for each release
 
** What classes of genes would we want to identify: histones, transcription factors, ion channels, protein kinases
 
** Chris will look into WormMine templates using gene class info and look into pulling in protein motif information
 
** We will ask other MODs and UniProt about how they deal with this issue
 

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