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]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
 +
= 2020 Meetings =
 +
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
== February 6, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
=== Worcester Area Worm Meeting talk ===
 +
* Confirmed for December 2020 or February 2021
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
== February 13, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
+
=== 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
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
=== ?Genotype class model ===
 +
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
 +
* Can aim to implement for WS277 but may have to wait until WS278
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
=== Genotype OA ===
 +
* Will put documentation [[Genotype|here]]
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
=== WB All-Hands Meeting ===
 +
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
 +
* Any thoughts at this point?  Still need to discuss with Hinxton, Toronto.
  
  
== October 3, 2019 ==
+
== February 20, 2020 ==
  
=== SObA comparison graphs ===
+
=== Genotype ===
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
+
* We will equate superficially similar/identical genotypes for now
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
+
* What if labs sequence strains later and find out more?  
** [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]
+
* Labs will have to report strains and their sequence and we back-curate accordingly
* [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 ===
+
=== VC2010 assembly genes ===
* 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"
+
* WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
* 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"
+
* How to best handle these "extra" genes?
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
+
* We could make different species entries that specify the assembly version
* 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
 
  
 +
== February 27, 2020 ==
  
== October 10, 2019 ==
+
=== WB Project meeting ===
 +
* Early May (~May 7th, 8th)
 +
* Discussion topics:
 +
** Creating more transparency/communication in the Alliance DQM data submission process for QC
 +
*** Can there be a landing page for all uploaded files to check?
 +
*** JSON or TSV, etc.?
  
=== Biocuration 2020 ===
+
=== Genotype ===
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
+
* [[Genotype|Genotype Wiki page]] updated
* Dates: Sunday May 17th to Wednesday May 20th, 2020
+
* Will start building Genotype OA
* 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 ===
+
=== Outreach inbox ===
* International Conference on Biomedical Ontologies
+
* 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
* [https://icbo2020.inf.unibz.it/ Meeting website]
+
* Many are bounced emails messages
* Held in Bozen-Bolzano, Italy
+
* Do we want a common place to track bad/bouncing email addresses? We need to distinguish addresses that bounce for policy/SPAM reasons versus those that are likely outdated or no longer in use.
* 16 - 19 September 2020
 
  
=== SObA comparison tool ===
+
=== New nameserver issues ===
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
+
* Many variations and strains getting submitted to new nameserver are not making it into the OA/Postgres
 +
* Should be getting dumped nightly to Postgres, but something seems to be wrong
 +
* Ranjana added a list of strains last week, but still doesn't see them in the OA
 +
* Daniela has been using the old CGI to add in new variation objects to Postgres
 +
* These objects are coming up when querying the nameserver, but not showing up in OA
  
=== Textpresso derived paper connections ===
+
=== GO CAM/Noctua modeling ===
* For example for strains and constructs, maybe anatomy terms?
+
* Should be major improvements in Noctua in place after recent hackathon
* May want to flag Textpresso predictions (as opposed to manually connected)
+
* Would be good to make a big push on curating models; e.g. signalling pathways that act somewhat differently in different cell types (in same organism) and in different organisms (e.g. Wnt signaling)
* 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
 
  
 +
=== SObA ===
 +
* Raymond working on writing paper
 +
* While reviewing pipeline, Raymond encountered some issues
 +
* Seth suggested using Docker
 +
* Raymond wants to go through and explain the development pipeline from the beginning
  
== October 17, 2019 ==
+
=== Alaska ===
 +
* Stalled; no word from Joseph

Latest revision as of 20:01, 27 February 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


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.


February 20, 2020

Genotype

  • We will equate superficially similar/identical genotypes for now
  • What if labs sequence strains later and find out more?
  • Labs will have to report strains and their sequence and we back-curate accordingly

VC2010 assembly genes

  • WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
  • How to best handle these "extra" genes?
  • We could make different species entries that specify the assembly version


February 27, 2020

WB Project meeting

  • Early May (~May 7th, 8th)
  • Discussion topics:
    • Creating more transparency/communication in the Alliance DQM data submission process for QC
      • Can there be a landing page for all uploaded files to check?
      • JSON or TSV, etc.?

Genotype

Outreach inbox

  • 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
  • Many are bounced emails messages
  • Do we want a common place to track bad/bouncing email addresses? We need to distinguish addresses that bounce for policy/SPAM reasons versus those that are likely outdated or no longer in use.

New nameserver issues

  • Many variations and strains getting submitted to new nameserver are not making it into the OA/Postgres
  • Should be getting dumped nightly to Postgres, but something seems to be wrong
  • Ranjana added a list of strains last week, but still doesn't see them in the OA
  • Daniela has been using the old CGI to add in new variation objects to Postgres
  • These objects are coming up when querying the nameserver, but not showing up in OA

GO CAM/Noctua modeling

  • Should be major improvements in Noctua in place after recent hackathon
  • Would be good to make a big push on curating models; e.g. signalling pathways that act somewhat differently in different cell types (in same organism) and in different organisms (e.g. Wnt signaling)

SObA

  • Raymond working on writing paper
  • While reviewing pipeline, Raymond encountered some issues
  • Seth suggested using Docker
  • Raymond wants to go through and explain the development pipeline from the beginning

Alaska

  • Stalled; no word from Joseph