Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
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= 2020 Meetings =
  
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
 
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
 
 
 
 
== October 3, 2019 ==
 
 
 
=== 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
 
 
 
=== 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)
 
 
 
=== 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
 
* [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
 
  
=== SObA comparison tool ===
+
== February 6, 2020 ==
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
 
  
=== Textpresso derived paper connections ===
+
=== Worcester Area Worm Meeting talk ===
* For example for strains and constructs, maybe anatomy terms?
+
* Confirmed for December 2020 or February 2021
* 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
 
  
 +
=== Alaska software ===
 +
* Code developed and maintained by Joseph, but not long term solution
 +
* Raymond and Eduardo talked about taking it over
 +
* Why have a web application vs. a command-line application?
 +
** Wanted to make it easy, but also to capture meta data for WB
 +
* Should/will find out from Joseph about how hard it is to maintain the software
 +
* Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
 +
* Expression working group working with Brian Oliver to have GEO take in more structured meta data
 +
* Array Express tried requiring more structured meta data, but authors stopped submitting
 +
* May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
  
== October 17, 2019 ==
 
  
=== Alliance All Hands Face-to-Face ===
+
== February 13, 2020 ==
* 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 ===
+
=== Alliance Literature Group ===
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
* Held first meeting on Monday, February 10th
* Prototype discussed last week, updated with feedback from prior discussions
+
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
* Would this be a stand-alone tool discoverable under the Tools menu?
+
* Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
** Possibly; could be a gene page widget, but may be out of place
+
* Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
** 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 ===
+
=== ?Genotype class model ===
* Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
+
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
* For example, share GO SObA graph for other species
+
* Can aim to implement for WS277 but may have to wait until WS278
* 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 ===
+
=== Genotype OA ===
* Kimberly can give update on recent updates to GO from the recent GO meeting
+
* Will put documentation [[Genotype|here]]
* Slides are shared online
 
  
=== "all stages Ce" life stage ===
+
=== WB All-Hands Meeting ===
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
+
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
* "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
+
* Any thoughts at this point? Still need to discuss with Hinxton, Toronto.
* 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
 

Latest revision as of 19:30, 13 February 2020

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January


February 6, 2020

Worcester Area Worm Meeting talk

  • Confirmed for December 2020 or February 2021

Alaska software

  • Code developed and maintained by Joseph, but not long term solution
  • Raymond and Eduardo talked about taking it over
  • Why have a web application vs. a command-line application?
    • Wanted to make it easy, but also to capture meta data for WB
  • Should/will find out from Joseph about how hard it is to maintain the software
  • Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
  • Expression working group working with Brian Oliver to have GEO take in more structured meta data
  • Array Express tried requiring more structured meta data, but authors stopped submitting
  • May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel


February 13, 2020

Alliance Literature Group

  • Held first meeting on Monday, February 10th
  • Regular meetings will be on Tuesdays at 10am/1pm/6pm
  • Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
  • Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed

?Genotype class model

  • Proposal
  • Can aim to implement for WS277 but may have to wait until WS278

Genotype OA

  • Will put documentation here

WB All-Hands Meeting

  • Doodle poll
  • Any thoughts at this point? Still need to discuss with Hinxton, Toronto.