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
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
= 2019 Meetings =
+
= 2022 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
[[WormBase-Caltech_Weekly_Calls_January_2022|January]]
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
[[WormBase-Caltech_Weekly_Calls_February_2022|February]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
[[WormBase-Caltech_Weekly_Calls_March_2022|March]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
[[WormBase-Caltech_Weekly_Calls_April_2022|April]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
[[WormBase-Caltech_Weekly_Calls_May_2022|May]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
 
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
= Aug 25th, 2022=
 +
* Phosphoproteomic dataset
 +
* WB grant - the new and radically different format for a “Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed)” application
 +
*
 +
*
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
 
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
 
  
[[WormBase-Caltech_Weekly_Calls_October_2019|October]]
 
  
  
== November 7, 2019 ==
+
= Aug 18th, 2022=  
 +
* Raymond reporting on meeting with Scott Emmons and neural connectivity data
  
=== ?Genotype class ===
+
= Aug 11th, 2022 =
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
 
* Several classes have a "Genotype" tag with text entry
+
Secondary species information content.
** Strain
+
* Gone through and counted number of objects in different data classes for all species
** 2_point_data
+
* https://docs.google.com/spreadsheets/d/1Q1FE7Miz0IJxultBtEq-VFoAcdz1UpxM3wfER4-qQGg/edit?usp=sharing
** Pos_neg_data
+
* Pristionchus: Talk to Ralf Sommer and see if wee can take some of the pristionchus.org data into WB -> Ranjana; Decision: after more discussion, decided to hold off on this as the plan is to focus on C. elegans for the grant. Perhaps in the future, we can seek finding and collaboration with the Pritionchus community (such as Sommer lab, etc).
** Multi_pt_data
+
 
** RNAi
+
* Brainstorm on how wee can utilize other species data -> may be a separate grant
** Phenotype_info
+
* remanei (4 genome versions) and briggsae (3 genome versions) problem -> several versions of the genome. Same problem in parasite. Will need to address in the future. Want to have multiple sequence alignments so researchers can compare different versions.
** Mass_spec_experiment (no data as of WS273)
+
* Address c elegans version assemblies in the grant. LoS from authors?
** Condition
+
* Parasite has a new RNAseq analysis pipeline (not single cells yet)
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
+
 
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
+
= July 28th, 2022 =
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
+
 
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
+
Global Core Biodata Resource application
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
+
https://docs.google.com/document/d/1juJ4mm1evay32lNt3OOsbKL36RY4_3cW/edit?usp=sharing&ouid=106019143058337411488&rtpof=true&sd=true
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
+
 
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
+
 
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
+
 
** Reference to parent strain, like "Parent strain is AG359"
+
= July 14th, 2022 =
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
+
== Reference and Person Evidence ==
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
+
* We need to know how best to move forward with ?Reference and ?Person evidence in the context of data exchange between WB and the Alliance
 +
* Does A-team need to connect those WB Persons to be able to populate data in the Alliance curation db ? 
 +
** If so, can it wait until we have proper persons ? 
 +
** If not, when we have persons later will the data be reconnected to Person objects ?
 +
* Where does data come from, which we call Person_evidence ?  Some forms ?  Direct emails ?  Other sources ? 
 +
* For author curation/verification, what evidence do we want to use?
 +
* Can we create Paper objects for the actual emails or other forms of communication (figure out details of when and what requirements), but keep Person_evidence for form submissions ?
 +
* How much will it muddy things to create Paper objects for emails, e.g. how will it affect NLP downstream, do we need PDFs ?
 +
* If we create personal communication References at Alliance only do we also want them as WBPapers, or will we just keep ?Person evidence at WB?
 +
* Are we okay with conflating Person data and Paper data in Reference at the Alliance.  That is, duplicating the same data as a Person and as a Reference.
 +
 
 +
== How to look up balancers (Df / Dp) in WB (PWS/Ryan Baugh) ==
 +
 
 +
= June 30, 2022 =
 +
 
 +
= June 23, 2022 =
 +
 
 +
Helpdesk tickets
 +
 
 +
SOba in Alliance
 +
 
 +
GCBR application due 8th Aug
 +
 
 +
Prepare for grant; nice pics for metrics eg https://pharos.nih.gov
 +
 
 +
Should Alliance gene & allele model have Clone/Sequence name as an attribute?
 +
 
 +
 
 +
= May 26, 2022 =
 +
 
 +
WormBase user survey
 +
 
 +
 
 +
 
 +
 
 +
= May 12, 2022 =
 +
 
 +
==Subcellular localization field==
 +
* WB has 2 separate free text fields to capture anatomical and subcellular localization statements but obviously the boundaries are fuzzy, see the example below where the statement belongs to both- there are many examples.
 +
“miR-228 is expressed in the germline and preferentially localizes to the nuclear periphery.”
 +
 
 +
* Other MODs do not make such distinction.
 +
* Daniela is asking the group advice to see if there is any objection in merging the 2 fields and slot the paragraph descriptions in the ExpressionExperimentStatement in LinkML.
 +
 
 +
* Decision: Keep just one field that will take care of both anatomical expression and subcellular localization
 +
 
 +
<pre>
 +
ExpressionExperimentStatement:
 +
 
 +
    is_a: EntityStatement
 +
 
 +
    description: >-
 +
 
 +
      Free-text describing some aspect(s) of a gene's expression, particularly
 +
 
 +
      nuanced information that is not readily captured in annotations.
 +
 
 +
      This statement's scope is limited to the associated ExpressionExperiment.
 +
 
 +
    notes: >-
 +
 
 +
      Inherits: statement_subject, statement_type, statement_text, references.
 +
 
 +
    slot_usage:
 +
 
 +
      statement_subject:
 +
 
 +
        range: ExpressionExperiment
 +
</pre>

Latest revision as of 13:16, 24 August 2022

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

January

February

March

April

May


Aug 25th, 2022

  • Phosphoproteomic dataset
  • WB grant - the new and radically different format for a “Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed)” application



Aug 18th, 2022

  • Raymond reporting on meeting with Scott Emmons and neural connectivity data

Aug 11th, 2022

Secondary species information content.

  • Gone through and counted number of objects in different data classes for all species
  • https://docs.google.com/spreadsheets/d/1Q1FE7Miz0IJxultBtEq-VFoAcdz1UpxM3wfER4-qQGg/edit?usp=sharing
  • Pristionchus: Talk to Ralf Sommer and see if wee can take some of the pristionchus.org data into WB -> Ranjana; Decision: after more discussion, decided to hold off on this as the plan is to focus on C. elegans for the grant. Perhaps in the future, we can seek finding and collaboration with the Pritionchus community (such as Sommer lab, etc).
  • Brainstorm on how wee can utilize other species data -> may be a separate grant
  • remanei (4 genome versions) and briggsae (3 genome versions) problem -> several versions of the genome. Same problem in parasite. Will need to address in the future. Want to have multiple sequence alignments so researchers can compare different versions.
  • Address c elegans version assemblies in the grant. LoS from authors?
  • Parasite has a new RNAseq analysis pipeline (not single cells yet)

July 28th, 2022

Global Core Biodata Resource application https://docs.google.com/document/d/1juJ4mm1evay32lNt3OOsbKL36RY4_3cW/edit?usp=sharing&ouid=106019143058337411488&rtpof=true&sd=true


July 14th, 2022

Reference and Person Evidence

  • We need to know how best to move forward with ?Reference and ?Person evidence in the context of data exchange between WB and the Alliance
  • Does A-team need to connect those WB Persons to be able to populate data in the Alliance curation db ?
    • If so, can it wait until we have proper persons ?
    • If not, when we have persons later will the data be reconnected to Person objects ?
  • Where does data come from, which we call Person_evidence ? Some forms ? Direct emails ? Other sources ?
  • For author curation/verification, what evidence do we want to use?
  • Can we create Paper objects for the actual emails or other forms of communication (figure out details of when and what requirements), but keep Person_evidence for form submissions ?
  • How much will it muddy things to create Paper objects for emails, e.g. how will it affect NLP downstream, do we need PDFs ?
  • If we create personal communication References at Alliance only do we also want them as WBPapers, or will we just keep ?Person evidence at WB?
  • Are we okay with conflating Person data and Paper data in Reference at the Alliance. That is, duplicating the same data as a Person and as a Reference.

How to look up balancers (Df / Dp) in WB (PWS/Ryan Baugh)

June 30, 2022

June 23, 2022

Helpdesk tickets

SOba in Alliance

GCBR application due 8th Aug

Prepare for grant; nice pics for metrics eg https://pharos.nih.gov

Should Alliance gene & allele model have Clone/Sequence name as an attribute?


May 26, 2022

WormBase user survey



May 12, 2022

Subcellular localization field

  • WB has 2 separate free text fields to capture anatomical and subcellular localization statements but obviously the boundaries are fuzzy, see the example below where the statement belongs to both- there are many examples.

“miR-228 is expressed in the germline and preferentially localizes to the nuclear periphery.”

  • Other MODs do not make such distinction.
  • Daniela is asking the group advice to see if there is any objection in merging the 2 fields and slot the paragraph descriptions in the ExpressionExperimentStatement in LinkML.
  • Decision: Keep just one field that will take care of both anatomical expression and subcellular localization
ExpressionExperimentStatement:

    is_a: EntityStatement

    description: >-

      Free-text describing some aspect(s) of a gene's expression, particularly

      nuanced information that is not readily captured in annotations.

      This statement's scope is limited to the associated ExpressionExperiment.

    notes: >-

      Inherits: statement_subject, statement_type, statement_text, references.

    slot_usage:

      statement_subject:

        range: ExpressionExperiment