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
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
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= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
== August 1, 2019 ==
 
  
=== Life stage public names missing in WS271 ===
+
==August 6th, 2020==
* Did we ever get a patch in for this?
+
===Experimental conditions data flow into Alliance===
* WormMine only has WBls IDs (no public name) for almost all life stages
+
*Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
* Wen will resend the patch file
+
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
 
+
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
=== 2020 WB NAR paper ===
+
*So for data flow into Alliance:
* Who's contributing?
+
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
** Raymond, Chris, Ranjana, Valerio, Daniela, Kimberly
+
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
* Topics
+
* How do we handle genetic sex? Part of condition?
** Automated descriptions
+
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
** Ontology tools (SObA)
+
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
** Community curation
 
** Author first pass
 
 
 
=== 2019 IWM Workshop videos ===
 
* On YouTube, but not public yet
 
* Chris will make them public and send links to Ranjana for the blog post
 
 
 
 
 
== August 15, 2019 ==
 
 
 
=== GO Alliance slim terms ===
 
* We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance
 
* May need to watch out for terms that don't apply to worms
 
* Raymond gets slim terms into Solr from OBO release file; Sibyl collecting from different source; should make the same (pull from WB FTP site?)
 
 
 
=== Phenotype ontology patternization ===
 
* Now have 676 terms patternized (27% of 2,506 terms total)
 
* Have reviewed the class hierarchy, collecting list of unexpected class subsumptions
 
* Issues to address collected here: https://docs.google.com/document/d/1IWtQbEQ-elM-U5SQyU4VfIH3vdJp6taVMGViIjGyVks/edit?usp=sharing
 
 
 
 
 
== August 22, 2019 ==
 
 
 
=== Obsolete ontology terms in Postgres ===
 
* There are currently 172 GO annotations in the GO OA, 94 in Expr OA, and 54 in Pic OA referring to obsolete GO terms
 
** https://docs.google.com/spreadsheets/d/14iG3-s0GrZ3_W87iOjD6tZiQiUJklRRjgs6ARFWi9E4/edit?usp=sharing
 
* We would like a mechanism for detecting and alerting curators to obsolete ontology terms in the OA/Postgres
 
 
 
=== Community phenotype requests ===
 
* Sent out new round of phenotype requests on August 20, 21, and 22 (today) 2019
 
* 2,627 emails/papers requested
 
* 112 emails bounced; 4 resent to new addresses
 
* 205 Phenotype OA community annotations; 55 RNAi OA annotations, from 47 papers, by 42 distinct community curators (so far)
 
* Also, 3 worksheets submitted, for 4 papers
 
* 35 papers flagged as not having phenotypes
 
* 86 papers with responses (3% response; still early)
 
* Need to coordinate with the AFP request pipeline
 
 
 
=== GO slim terms ===
 
* SObA highlights Alliance slim terms, but doesn't correspond to ribbon
 
* Want to use same slim terms used for ribbons
 
* Add slim terms into ACEDB? One option
 
* Ribbon order of slim terms is an issue
 
* Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
 
* Will have to manually synchronize with Alliance if Alliance changes its ribbon
 
 
 
== August 29, 2019 ==
 
 
 
=== Caltech use of Hinxton name service ===
 
* Name service :  
 
** https://names.wormbase.org/gene
 
* API documentation :
 
** https://names.wormbase.org/api-docs/index.html#!
 
* Sibyl is wondering :
 
** "it would be nice to know when and how curators use the name service. And does any script managed by Caltech write data into the name services?"
 
** "what needs to be done to adopt the new name service. For example, what concern do you or the curators have about adopting the new name service, what kind of tests will allow the curators to trust that the new name service is working correctly, what changes to the new name service is needed for Caltech to be able to use it."
 
* Daniela, Chris, Karen are the only Caltech curators who use it.
 
* Daniela's workflow is :
 
** Look up variation through OA
 
** Look up variation through name service (what's the URL for that ?)
 
** Create object through name service, then enter information
 
** Create temporary entry for OA through Caltech postgres services
 
* Juancarlos has emailed Sibyl + Matt + Caltech with what we know so far.  Karen and Chris, please reply if you have other name service uses beyond what Daniela does.
 
* Name service google/wormbase login doesn't work right now for Caltech curators, Matt's been asked to add people.
 
 
 
===Anatomy term names===
 
* While going through the concise descriptions text Daniela have noted down some terms that could benefit from having a more descriptive name.
 
** e.g.: Pn.p hermaphrodite -> Pn.p hermaphrodite vulval precursor cell. e.g. P3.p hermaphrodite (WBbt:0008112) -> P3.p hermaphrodite vulval precursor cell
 
List of other potential terms:
 
<pre>
 
AB -> embryonic founder cell AB
 
EMS -> embryonic founder cell EMS -> should the definition of EMS be changed from ‘Embryonic cell’ to ‘Embryonic founder cell’? See WormAtlas founder cell definition.
 
C -> embryonic founder cell C
 
D ->  embryonic founder cell D
 
E ->  embryonic founder cell E
 
MS -> embryonic founder cell MS
 
Psub1 -> embryonic founder cell Psub1 (or simply embryonic founder cell P1)
 
Psub2 -> embryonic founder cell Psub2
 
Psub3 -> embryonic founder cell Psub3
 
Psub4 -> germline founder cell Psub4
 
G1 -> Postembryonic blast cell G1
 
G2 -> Postembryonic blast cell G2
 
</pre>
 

Latest revision as of 16:36, 6 August 2020

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August 6th, 2020

Experimental conditions data flow into Alliance

  • Experimental conditions in disease annotations: WB has inducers (used to recapitulate the disease condition) and modifiers (a modifier can ameliorate, exacerbate, or have no effect, on the disease condition)
  • We use the WB Molecule CV for Inducers and Modifiers in disease annotation
  • Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
  • So for data flow into Alliance:
    • In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
    • Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
  • How do we handle genetic sex? Part of condition?
    • Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
    • Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex