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]]
+
= 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?
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
== WB PDF Migration ==
 +
* Daniel, Juancarlos, Kimberly continue some clean up of redundant files before moving things over to the Alliance
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
= 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
  
== October 3, 2019 ==
+
they have excel  documents with the location
  
=== SObA comparison graphs ===
+
= November 3rd, 2022 =
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
+
* Booth at IWM
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
+
** ACKnowledge will be showcased at the WB booth
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
+
** Will also advertise Alliance
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 
* What information does a user most care about?
 
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 
* In either case users need a good legend and/or documentation
 
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
 
  
=== Germ line discussion ===
+
= October 27, 2022 =
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
 
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
 
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
 
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
 
  
=== Script to remove blank entries from Postgres ===
+
= October 6th, 2022 =  
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
 
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
 
* Does anyone object to removing these entries throughout Postgres?
 
* Juancarlos will remove all the empty fields identified by his script
 
  
 +
== 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)
  
== October 10, 2019 ==
+
== GO meeting next week ==
 +
* 7am - 11am PDT
 +
* Zoom channel? Available on GO meeting agenda page:
 +
** https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M
  
=== Biocuration 2020 ===
+
== Alliance Literature working group ==
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
+
* Subgroups; Ranjana interested in joining the search subgroup
* Dates: Sunday May 17th to Wednesday May 20th, 2020
+
* Can sign up on the lit group page
* Will have 3rd POTATO workshop
+
** https://docs.google.com/document/d/1hB6cft0J_DaapQ9uHUGXwbqrnsZs7wORoepQicLdhTk/edit?pli=1#bookmark=id.butj0rfl4zh1
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
 
* Key Dates
 
** October 31, 2019 - Paper Submission Deadline
 
** January 24, 2020 - Abstract  and Workshop Submission Deadline
 
** March 6, 2020 - Notification of Acceptance
 
** April 6, 2020 - Early Bird Registration Ends
 
** May 8, 2020 - Registration Deadline
 
* Academic ISB Member, early bird registration fee is $250
 
* Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
 
  
=== ICBO 2020 ===
+
== Persons ==
* International Conference on Biomedical Ontologies
+
* Are there more use cases to collect?
* [https://icbo2020.inf.unibz.it/ Meeting website]
+
* Some existing use cases:
* Held in Bozen-Bolzano, Italy
+
** ACKnowledge attribution
* 16 - 19 September 2020
+
** 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
  
=== SObA comparison tool ===
+
= Aug 25th, 2022=  
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
+
* Phosphoproteomic dataset
 +
* WB grant - the new and radically different format for a “Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed)” application
 +
*
 +
*
  
=== Textpresso derived paper connections ===
 
* For example for strains and constructs, maybe anatomy terms?
 
* May want to flag Textpresso predictions (as opposed to manually connected)
 
* Couple of options:
 
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
 
** 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
 
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
 
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
 
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
 
* Transgene pipeline:
 
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
 
** Another script, captures Ex transgenes as well, automatically connects to construct objects
 
** WB only displays verified papers; unverified (predicted) associations are not dumped
 
* Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
 
* Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
 
* Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
 
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
 
  
  
== October 17, 2019 ==
 
  
=== Alliance All Hands Face-to-Face ===
 
* Flights: has everyone already booked? No, not yet
 
* Any coordination of flights from Pasadena/LA?
 
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
 
  
=== SObA Comparison Tool ===
+
= Aug 18th, 2022=  
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
* Raymond reporting on meeting with Scott Emmons and neural connectivity data
* Prototype discussed last week, updated with feedback from prior discussions
+
 
* Would this be a stand-alone tool discoverable under the Tools menu?
+
= Aug 11th, 2022 =
** Possibly; could be a gene page widget, but may be out of place
+
 
** Stand-alone tool probably makes more sense
+
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 15:50, 8 December 2022

Previous Years

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2021 Meetings

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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