Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
= 2020 Meetings =
+
= 2022 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_January_2022|January]]
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2022|February]]
  
== February 6, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2022|March]]
  
=== Worcester Area Worm Meeting talk ===
+
[[WormBase-Caltech_Weekly_Calls_April_2022|April]]
* Confirmed for December 2020 or February 2021
 
  
=== Alaska software ===
+
[[WormBase-Caltech_Weekly_Calls_May_2022|May]]
* 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 ==
+
= October 6th, 2022 =  
  
=== Alliance Literature Group ===
+
== Mangolassi ==
* Held first meeting on Monday, February 10th
+
* Mangolassi is down (network only?); Michael will be in the office in an hour
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
+
** Start a cronjob to check for network connections? Already set up (Raymond)
* Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
+
** Michael can log into his machine; Tazendra is OK (so, not network issue?)
* Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
+
** Michael fixed it by unplugging and reconnecting ethernet cable (network card issue)
  
=== ?Genotype class model ===
+
== GO meeting next week ==
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
+
* 7am - 11am PDT
* Can aim to implement for WS277 but may have to wait until WS278
+
* Zoom channel? Available on GO meeting agenda page:
 +
** https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M
  
=== Genotype OA ===
+
== Alliance Literature working group ==
* Will put documentation [[Genotype|here]]
+
* Subgroups; Ranjana interested in joining the search subgroup
 +
* Can sign up on the lit group page
 +
** https://docs.google.com/document/d/1hB6cft0J_DaapQ9uHUGXwbqrnsZs7wORoepQicLdhTk/edit?pli=1#bookmark=id.butj0rfl4zh1
  
=== WB All-Hands Meeting ===
+
== Persons ==
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
+
* Are there more use cases to collect?
* Any thoughts at this point? Still need to discuss with Hinxton, Toronto.
+
* Some existing use cases:
 +
** ACKnowledge attribution
 +
** Community phenotype curators
 +
** When do people need person IDs? When accessing/using some forms
 +
* Content of earlier email
 +
** When someone asks for a CGC Lab code, they must have a WBPerson ID.  To fill out some tazendra forms, I think they need a WBPerson ID.  To connect Persons to Laboratories for their WB lab page.  To track who is a PI for which Lab.  To connect to other Persons for Intellectual Lineage.  Connect authors to Persons so Papers have a list of authors in publication order, each author linked to the Person (ZFIN has two lists, sorted for authors, separate for persons).  Our users tell us they use the WB Person page for their cv.
 +
** Use of Person Contact information: I think our use case for person information is mostly to have current emails for community outreach (ACKnowledge, community phenotype forms).  It's been used in the past to send letters to PIs, so we could prioritize maintaining more information just for PIs.  Some analysis is sometimes done by region / country, but this is rare. If anyone can think of other use cases for person data, please let us know. While we mostly only use the email addresses, Cecilia uses address / webpage / ORCID to connect authors to Persons, so having that data is important to make more connections.
 +
* Knowing address and affiliation can help disambiguate similarly named persons/authors
 +
* Questions about ethics of tracking information and person lineage?
 +
** Not really a new issue; people present CVs on grants and other contexts
 +
** Can be problematic to display people's email address and physical address, from a security perspective
 +
** Email addresses: if someone has a strain/reagent not in a repository, can be helpful to connect to access materials
 +
** We and others provide email addresses in publications
 +
** We don't currently ask for permission to display the information (email, address, etc.); maybe we should?
 +
** Should we have a survey to ask users' opinions about displaying this information? Is it worthwhile? Concerning?
 +
** Should we provide a waiver that people agree their information will be in the public domain?
 +
** Person form disclaimer: "Note: Phone and fax information won't show in your Person report for privacy reasons, but we are collecting the information in case we need to contact you. We keep old email, old institution, and old registered_lab data for history, please don't remove it when updating your information."
 +
** Person form is available to public and displays personal information, e.g.: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person.cgi?action=Display&number=WBPerson51134
 +
*** Could someone scrape this information? Yes, person information is available from WB database dumps
 +
** Could institute a login; we had wanted to keep the barrier to participate low
 +
** Have 3 forms of privacy, where people can opt out of emails, hide their email address, or hide more information.  If hidden it stays in Caltech postgres, and doesn't go to acedb.
 +
* Going forward, the Alliance can implement better security for person information
  
 +
= Aug 25th, 2022=
 +
* Phosphoproteomic dataset
 +
* WB grant - the new and radically different format for a “Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed)” application
 +
*
 +
*
  
== 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 ==
+
= Aug 18th, 2022=  
 +
* Raymond reporting on meeting with Scott Emmons and neural connectivity data
  
=== WB Project meeting ===
+
= Aug 11th, 2022 =
* Early May (~May 7th, 8th)
 
* Discussion topics:
 
** Creating more transparency/communication in the Alliance DQM data submission process for QC
 
*** JSON or TSV, etc.?
 
*** Can there be a landing page for all uploaded files to check?
 
  
=== Genotype ===
+
Secondary species information content.
* [[Genotype|Genotype Wiki page]] updated
+
* Gone through and counted number of objects in different data classes for all species
* Will start building Genotype OA
+
* 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).
  
=== Outreach inbox ===
+
* Brainstorm on how wee can utilize other species data -> may be a separate grant
* 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
+
* 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.
* Many are bounced emails messages
+
* Address c elegans version assemblies in the grant. LoS from authors?
* 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.
+
* 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
 +
 
 +
<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 00:26, 7 October 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


October 6th, 2022

Mangolassi

  • Mangolassi is down (network only?); Michael will be in the office in an hour
    • Start a cronjob to check for network connections? Already set up (Raymond)
    • Michael can log into his machine; Tazendra is OK (so, not network issue?)
    • Michael fixed it by unplugging and reconnecting ethernet cable (network card issue)

GO meeting next week

Alliance Literature working group

Persons

  • Are there more use cases to collect?
  • Some existing use cases:
    • ACKnowledge attribution
    • Community phenotype curators
    • When do people need person IDs? When accessing/using some forms
  • Content of earlier email
    • When someone asks for a CGC Lab code, they must have a WBPerson ID. To fill out some tazendra forms, I think they need a WBPerson ID. To connect Persons to Laboratories for their WB lab page. To track who is a PI for which Lab. To connect to other Persons for Intellectual Lineage. Connect authors to Persons so Papers have a list of authors in publication order, each author linked to the Person (ZFIN has two lists, sorted for authors, separate for persons). Our users tell us they use the WB Person page for their cv.
    • Use of Person Contact information: I think our use case for person information is mostly to have current emails for community outreach (ACKnowledge, community phenotype forms). It's been used in the past to send letters to PIs, so we could prioritize maintaining more information just for PIs. Some analysis is sometimes done by region / country, but this is rare. If anyone can think of other use cases for person data, please let us know. While we mostly only use the email addresses, Cecilia uses address / webpage / ORCID to connect authors to Persons, so having that data is important to make more connections.
  • Knowing address and affiliation can help disambiguate similarly named persons/authors
  • Questions about ethics of tracking information and person lineage?
    • Not really a new issue; people present CVs on grants and other contexts
    • Can be problematic to display people's email address and physical address, from a security perspective
    • Email addresses: if someone has a strain/reagent not in a repository, can be helpful to connect to access materials
    • We and others provide email addresses in publications
    • We don't currently ask for permission to display the information (email, address, etc.); maybe we should?
    • Should we have a survey to ask users' opinions about displaying this information? Is it worthwhile? Concerning?
    • Should we provide a waiver that people agree their information will be in the public domain?
    • Person form disclaimer: "Note: Phone and fax information won't show in your Person report for privacy reasons, but we are collecting the information in case we need to contact you. We keep old email, old institution, and old registered_lab data for history, please don't remove it when updating your information."
    • Person form is available to public and displays personal information, e.g.: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person.cgi?action=Display&number=WBPerson51134
      • Could someone scrape this information? Yes, person information is available from WB database dumps
    • Could institute a login; we had wanted to keep the barrier to participate low
    • Have 3 forms of privacy, where people can opt out of emails, hide their email address, or hide more information. If hidden it stays in Caltech postgres, and doesn't go to acedb.
  • Going forward, the Alliance can implement better security for person information

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