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 ==
 
  
=== SObA graphs ===
+
== October 10, 2019 ==
* 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
 
* May provide more information than the user needs/wants
 
* Juancarlos working on implementing SObA widgets on gene pages (maybe for WS271 or WS272?)
 
* IWM will have WS271 on staging during meeting; probably on production shortly after the meeting
 
** Hope to show users demos at IWM
 
  
=== IWM swag: screen cloths ===
+
=== Biocuration 2020 ===
* Paul is working on the graphic
+
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
* Need to order soon
+
* 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
  
=== Testing on staging site ===
+
=== ICBO 2020 ===
* Adam and Sibyl request people to test Sequences widgets on Pseudogene, CDS, and Transcript pages on staging
+
* International Conference on Biomedical Ontologies
* Sibyl has asked for testing of new search on staging
+
* [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
  
== May 23, 2019 ==
+
=== Textpresso derived paper connections ===
 
+
* For example for strains and constructs, maybe anatomy terms?
=== WormBase Google folder ===
+
* May want to flag Textpresso predictions (as opposed to manually connected)
* https://drive.google.com/drive/folders/1VYJbGYTa-7PncQcZW7VAy73DZ2jL0p4u?usp=sharing
+
* 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
=== ?Genotype class ===
+
** 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
* Chris and Ranjana will work on early next week
+
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
* Will need to accommodate disease model annotations
+
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
* Will bring up again for discussion with larger group next week
+
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
* Conclusion: ?Genotype objects will represent the entire genotype of any organism it inheres in, but we will specifically point out the causative agent (or agents) responsible for the disease or phenotype in the individual annotation
+
* 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
== May 30, 2019 ==
+
** 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
=== Phenotype Request Emails ===
+
* 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?
* New round for May 2019
+
* 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
* 1139 emails total; 825 emails gone out so far today
+
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
* Chris will report back next week with numbers
 
 
 
=== ?Genotype class ===
 
* Google doc: https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing
 
* Are or aren't we moving to serial identifiers for strains, e.g. WBStrain0000001? Need to ask Kevin et al.
 
* We would want to indicate in a ?Genotype object which are the "relevant" genes, proposed to be captured in a "Involves_gene" or some such labeled tag
 
** For transgenes, which genes would be considered "relevant"? Only expressed genes? Or also genes for which the promoter and/or 3'UTR are used? We could start with expressed genes only, for now
 
** We would like to infer which genes are involved/relevant based on the components, like variations, rearrangements, transgenes, but we may also want to indicate which genes the authors assert to be part-of/relevant-to the genotype such that if new mappings point to a different gene, users can still trace back to which genotype the authors referred to in the paper originally
 
** Maybe we would want subtags of "Involves_gene" like "Author_asserted" and "WormBase_inferred"? We can try it; what would the XREF tag names be? Distinct?
 
** Do we really want to list all genes that are affected by a rearrangement?
 
** What about RNAi treatments? Should these be considered part of the genotype? Authors often report it that way
 
*** GENO ontology has made terms "intrinsic genotype" and "extrinsic genotype" to distinguish, for example, the nuclear genome genotype from "imposed" genotype effects like RNAi, morpholinos, etc.
 
* We may want to have a tag "Has_background_strain" to refer to the original wild type strain/isolate from which the genotype was derived; this would largely be N2 and an XREF would (over?)populate the N2 strain object with 1000s of "Is_background_for" associations.
 
** It may be best to include this tag, but make it a convention to only annotate it when it ISN'T N2
 
 
 
 
 
== June 6, 2019 ==
 
 
 
=== Phenotype requests ===
 
* Sent out 1140 emails on May 30
 
* Since have received 374 annotations from 54 papers (42 requested, 12 additional)
 
* 21 papers flagged as not having phenotypes
 
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
 

Revision as of 15:06, 11 October 2019

Previous Years

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2011 Meetings

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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