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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
 +
= 2022 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2022|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_February_2022|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
[[WormBase-Caltech_Weekly_Calls_March_2022|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
[[WormBase-Caltech_Weekly_Calls_April_2022|April]]
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
[[WormBase-Caltech_Weekly_Calls_May_2022|May]]
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
 
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
= October 6th, 2022 =
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
== 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 ==
 +
* 7am - 11am PDT
 +
* Zoom channel? Available on GO meeting agenda page:
 +
** https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M
  
==August 6th, 2020==
+
== Alliance Literature working group ==
 +
* 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
  
===Experimental conditions data flow into Alliance===
+
== Persons ==
*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)
+
* Are there more use cases to collect?
*We use the WB Molecule CV for Inducers and Modifiers in disease annotation
+
* Some existing use cases:
*Experimental conditions in phenotype annotations: are free text (captured in remarks); will probably need to formalize later on
+
** ACKnowledge attribution
*So for data flow into Alliance:
+
** Community phenotype curators
**In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will work on this)
+
** When do people need person IDs? When accessing/using some forms
**Groups will switch to using common data model that works for all and common ontology/ontologies in the near future.
+
* Content of earlier email
* How do we handle genetic sex? Part of condition?
+
** 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.
** Condition has been intended for external/environmental conditions, whereas genetic sex is inherent to the organism of study
+
** 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.
** Expression pattern curation needs genetic sex; needs a model at the Alliance for capturing sex
+
* 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
 +
*
 +
*
  
== August 13, 2020 ==
 
  
=== Species in Postgres and ACEDB/Datomic ===
 
* Want to dump "Affected By Pathogen" fields in Phenotype OA and RNAi OA
 
* Want to be sure that what gets dumped aligns with species loaded into ACEDB
 
* Currently one species annotated not in WS277: Streptococcus gallolyticus subsp. gallolyticus
 
* We currently have multiple Postgres tables for storing species lists:
 
** pap_species_index (used by "Affected By Pathogen" fields, AFP); Kimberly uses to assign species to papers and occasionally adds new ones
 
** obo_name_ncbitaxonid
 
** obo_name_taxon (original, smaller list)
 
** h_pap_species_index (history for pap_species_index)
 
* How do species get loaded into ACEDB? Dumps from Postgres? Which table(s)?
 
* WS277 has 7,906 species (1,936 have no NCBI Taxon ID)
 
* Kimberly has occasionally uploaded a species.ace file in the context of GO curation; but Hinxton otherwise handles it; should ask them
 
* New species are associated with paper objects, but otherwise no additional data for those species come from Caltech
 
* It might be useful to have species pages in WB that at least list papers for which we have species associations, maybe include other information?
 
  
=== WS279 Citace upload ===
 
* When is it happening? Not sure; not on release schedule right now
 
  
=== SOLR server security (IMSS) ===
 
* IMSS network security blocked network on our server due to its open SOLR web access.
 
* Part of AMIGO stack, very old version, drives our ontology browser directly, SObA, Enrichment tools indirectly.
 
* Added some firewall/URL filter and IMSS opens up the network (for now). IMSS still gripes about its service is open to the world.
 
  
=== Alzheimer's disease portal ===
+
= Aug 18th, 2022=
* Supplement grant awarded to Alliance for an Alzheimer's disease portal
+
* Raymond reporting on meeting with Scott Emmons and neural connectivity data
* Could involve automated/concise descriptions, interactions, etc.
+
 
* Could establish useful pipelines that could be reused in other contexts
+
= 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
 +
 
 +
<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