Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2021 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
+
= 2022 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2022|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
+
[[WormBase-Caltech_Weekly_Calls_February_2022|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
+
[[WormBase-Caltech_Weekly_Calls_March_2022|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
+
[[WormBase-Caltech_Weekly_Calls_April_2022|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
+
[[WormBase-Caltech_Weekly_Calls_May_2022|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
 
  
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
+
= 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_September_2021|September]]
 
  
[[WormBase-Caltech_Weekly_Calls_October_2021|October]]
 
  
  
  
== November 4 2021 ==
+
= Aug 18th, 2022=  
 +
* Raymond reporting on meeting with Scott Emmons and neural connectivity data
  
=== Migrating Paper Pipeline to Alliance ===
+
= Aug 11th, 2022 =
*Meeting abstracts
 
**Continuing to review what we have and standardize bibliographic info before we migrate
 
**QC checks highlight some older abstracts with little-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
 
**We can always respond to individual requests to add old meeting abstracts if they arise
 
  
 +
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).
  
== November 11 2021 ==
+
* 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)
  
=== WS284 upload dates for Caltech ===
+
= July 28th, 2022 =
* When are files due for the Caltech group?
 
  
===Minutes===
+
Global Core Biodata Resource application
*WS284 upload-Better to upload before the holidays or in Jan 2022
+
https://docs.google.com/document/d/1juJ4mm1evay32lNt3OOsbKL36RY4_3cW/edit?usp=sharing&ouid=106019143058337411488&rtpof=true&sd=true
*Wen will contact Paul D/Hinxton to find out when the WS284 models will be released
 
  
  
== November 18 2021 ==
 
Proposal for upgrading tanzendra/mangolassi computing resources
 
1. Move them to Chen. (done)
 
  monitor stability of network
 
  
  Old hardware and out of support OS (Ubuntu 14.04)
+
= 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.
  
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB)
+
== How to look up balancers (Df / Dp) in WB (PWS/Ryan Baugh) ==
  (use Valerio's local server/desktop)
 
  
3. Establish a local file server for storage and download access (PDFs, dump files)
+
= June 30, 2022 =
  
4. Run dockerized services from AWS
+
= June 23, 2022 =
  
5. Continuous development and integration locally -> AWS
+
Helpdesk tickets
  
===Commercial antibodies===
+
SOba in Alliance
* Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
+
 
* TODO: Contact TAIR and see if they including commercial antibodies and if  they charge companies (Daniela sent a message on slack)
+
GCBR application due 8th Aug
* This can be an  Alliance project. Need to contact companies and see who is interested (need to have a  price in mind for that).  
+
 
* Can pilot text mining for commercial antibodies
+
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