Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
= 2014 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2014|January]]
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
== February 6, 2014 ==
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
 +
 
 +
= 2022 Meetings =
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_January_2022|January]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_February_2022|February]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_March_2022|March]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_April_2022|April]]
 +
 
 +
[[WormBase-Caltech_Weekly_Calls_May_2022|May]]
 +
 
 +
 
 +
= December 8th, 2022 =
 +
== Data Type Flagging Pipelines and Alliance Infrastructure ==
 +
*We currently run the neural network algorithms at Caltech
 +
*What will we need to do to transition this to run on Alliance infrastructure?
 +
*Can we start to run the neural networks on a more frequent basis, e.g. monthly? Could that be automated?
 +
 
 +
== WB PDF Migration ==
 +
* Daniel, Juancarlos, Kimberly continue some clean up of redundant files before moving things over to the Alliance
 +
 
 +
= November 17th, 2022 =
 +
*TEC_RED meeting. Meeting with Nikita Jahveri, Wouter Van de Berg (Gupta's lab). Participants, Valerio, Daniela, Kimberly, Magda, Stavros.
 +
identified a large number of operons in C Briggsae. Baghwathi Gupta's lab. 4200 Briggsae genes identified with SL influencers. Want to contribute the information in WormBase.
 +
* Used WS279 for the annotations
 +
* they have excel  documents with the location in the supplementary files
 +
* Magda: are the tag sequences unique? Nikita: yes. If they bind to 2 ore more genes that have classified as paralogs
 +
* Also  identified isoforms (multiple transcripts tab in the spreadsheet)
 +
 
 +
** Steps forward: need to update the gene models and the operon models on WormBase.
 +
* Can bring in data in different tracks.
 +
* Need to update gene models based on this new evidence
 +
* Nikita will send the data to Magda and Stavros (3 spreadsheets). Need to write out the categories.
 +
* they did not produce  the GFF file, all in excel sheets.
 +
* Material used: mixed stage worm population
 +
 
 +
they have excel  documents with the location
 +
 
 +
= November 3rd, 2022 =
 +
* Booth at IWM
 +
** ACKnowledge will be showcased at the WB booth
 +
** Will also advertise Alliance
 +
 
 +
= October 27, 2022 =
 +
 
 +
= 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 ==
 +
* 7am - 11am PDT
 +
* Zoom channel? Available on GO meeting agenda page:
 +
** https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M
 +
 
 +
== 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
 +
 
 +
== 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
  
=== AGENDA ===
 
* Topic Curation
 
** WS243,244: Innate immunity and response to pathogens
 
** WS242: miRNA pathway
 
** WS241: UPR pathways
 
** using the caltech FTP site for storing topic page pathway images for the web team. Where is it, what information do we want to include, can we use this to track history of pathways?
 
** model change to put topics in hierarchical structure.
 
* File cabinets in hallway?
 
* Variations that have lost a public_name due to Million Mutation processing in WS240.
 
** What to do with ones that have phenotypes attached, should they have their public_names restored, so we can see them in our OA dropdown lists?
 
 
<pre>
 
<pre>
> WBVar00249046 former public-name sy5417
+
ExpressionExperimentStatement:
> WBVar00275318 former public-name y87
+
 
> WBVar00275321 former public_name y95
+
    is_a: EntityStatement
> WBVar00000714 former public_names cb107, cbs107
 
> WBVar00000718 former public_names cb111, cbs111
 
> WBVar00000716 former public_names cb109, cbs109
 
> WBVar00000720 former public_names cb113, cbs113
 
> e2518 is an other_name of WBVar0014462
 
> g320 is an other_name of WBVar00017601
 
</pre>
 
* Models meeting in Toronto March 10-11
 
  
=== Gene Association files ===
+
    description: >-
* Life stage-gene associations
 
* Capturing relations (e.g. "involved_in") in GAF; how to do that for life stage?
 
* What search tool do we plan for e.g. "what genes are expressed in a particular neuron AND during dauer larval stage?"
 
  
we can use WormMine. Example query:
+
      Free-text describing some aspect(s) of a gene's expression, particularly
http://www.wormbase.org/tools/wormmine/template.do?name=Anatomy_LS_Genes&scope=all
 
  
* Expression data model needs updating to capture BOTH place AND time of gene expression
+
      nuanced information that is not readily captured in annotations.
  
=== Pathway images on topic pages ===
+
      This statement's scope is limited to the associated ExpressionExperiment.
* Do we store/supply a flat image file for the web team?
 
* Store image files on the FTP site? Canopus, nightly mirroring
 
* Release-specific directories/images? OICR needs to know and handle
 
* Daniela's images are collected cumulatively; Wen's are overwritten
 
* May be an issue embedding iFrame interactive viewer
 
  
=== Variations losing public names ===
+
    notes: >-
* Million Mutation project, variations getting renamed
 
* Distinguishing natural variants vs. lab-induced alleles
 
* Merging event (natural variants at same location merged), existing names become "Other_name"s
 
* Can we have a mechanism in place to decide one Public_name if there are multiple? Temporal precedence?
 
* First published name can be official Public_name?
 
* decided to leave things as they are
 
  
 +
      Inherits: statement_subject, statement_type, statement_text, references.
  
 +
    slot_usage:
  
== February 13, 2014 ==
+
      statement_subject:
  
=== AGENDA ===
+
        range: ExpressionExperiment
*Infection model discussion--Advantages/disadvantages to curating to the level of strain for pathogens like Bacteria, Fungi etc) (Ranjana)
+
</pre>
Please see http://wiki.wormbase.org/index.php/Modeling_data_for_Infectious_agents
 
*Do we create non-nematode Strain objects here at Caltech? (Ranjana)
 
** (Mary Ann) As far as I can see, no. But I don't see a reason why you can't if there is a need. We will simply need to make sure you know the right curation format, which for non-nematode strains is a bit vague. I am talking to Aric shortly about the  Db11 strain you sent me earlier this week.
 

Latest revision as of 15:50, 8 December 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


December 8th, 2022

Data Type Flagging Pipelines and Alliance Infrastructure

  • We currently run the neural network algorithms at Caltech
  • What will we need to do to transition this to run on Alliance infrastructure?
  • Can we start to run the neural networks on a more frequent basis, e.g. monthly? Could that be automated?

WB PDF Migration

  • Daniel, Juancarlos, Kimberly continue some clean up of redundant files before moving things over to the Alliance

November 17th, 2022

  • TEC_RED meeting. Meeting with Nikita Jahveri, Wouter Van de Berg (Gupta's lab). Participants, Valerio, Daniela, Kimberly, Magda, Stavros.

identified a large number of operons in C Briggsae. Baghwathi Gupta's lab. 4200 Briggsae genes identified with SL influencers. Want to contribute the information in WormBase.

  • Used WS279 for the annotations
  • they have excel documents with the location in the supplementary files
  • Magda: are the tag sequences unique? Nikita: yes. If they bind to 2 ore more genes that have classified as paralogs
  • Also identified isoforms (multiple transcripts tab in the spreadsheet)
    • Steps forward: need to update the gene models and the operon models on WormBase.
  • Can bring in data in different tracks.
  • Need to update gene models based on this new evidence
  • Nikita will send the data to Magda and Stavros (3 spreadsheets). Need to write out the categories.
  • they did not produce the GFF file, all in excel sheets.
  • Material used: mixed stage worm population

they have excel documents with the location

November 3rd, 2022

  • Booth at IWM
    • ACKnowledge will be showcased at the WB booth
    • Will also advertise Alliance

October 27, 2022

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