Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 17: Line 17:
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
== January 4, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
=== WS264 Upload ===
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
* Citace upload to Wen, Tuesday January 16th, by 10am PST
 
* Upload to Hinxton on Jan 19th
 
  
=== Strain data import to AGR for disease ===
+
= 2022 Meetings =
* Will begin to consider pulling in strains into AGR
 
* Will need to think about how genotypes are built and stored at other MODs
 
* We should encourage authors to include strain IDs
 
* Diseases are annotated to genes, alleles, and strains within WB
 
  
=== Curating phenotypes and diseases to strains or genotypes ===
+
[[WormBase-Caltech_Weekly_Calls_January_2022|January]]
* Should we generate a ?Genotype class to capture genotypes without a known strain name? Or to capture relevant/relative genotypes thought to be responsible for a phenotype or disease?
 
* We could create un-named strain objects, that use a new unique identifier as a primary identifier and represent the entire genotype of a strain used
 
** Introduction of a new ?Strain class attribute of a unique serial identifier (like WBStrain00001) would be very costly to implement; would need to consider how crucial this is before implementing
 
** We can, instead, use new strain (public) names like "WBPaper00012345_Strain1", etc. instead of creating new unique ID attribute for un-named strains
 
* When curating phenotypes to strains, we will want to specify what is the relevant/relative genotype that is causative/correlated with the disease or phenotype observation
 
** Would be best if the specification of the relevant genotype used controlled vocabularies (when possible) and free text (when needed); would need to work out the logistics/mechanics of such curation
 
** Transgene-phenotype curation currently specifies causative gene, but would be more complicated for strains
 
* Alternatively, we could create the ?Genotype class to represent the abstract "relative"/"relevant" genotype thought to be responsible for the phenotype or disease, and annotate directly to that ?Genotype object
 
* ?Strain approach:
 
** Use strain if named (but important to know if the control strain is not simply N2)
 
*** If control strain is simply N2, causative genotype (and respective components) can be inferred from strain genotype
 
*** If control strain is not N2, causative genotype and components would need to be specified at the moment of phenotype/disease curation (by mechanism to be worked out)
 
** If no strain name provided, create "un-named" strain that contains the entire genotype provided by authors
 
*** Control strain issues above would still need to be addressed
 
* ?Genotype approach:
 
** ?Genotype class could represent individual instances of relevant/relative genotypes that are suggested to be causative for a disease or phenotype
 
** ?Genotype objects would be created with formal construction, with DB associations to each component object (e.g. alleles, transgenes, etc.) as well as free text descriptions (for components with no corresponding DB object)
 
** Such ?Genotype objects could be used repeatedly throughout a paper when applicable, but would likely not be used in any other papers (we would likely accumulate redundant objects in the DB)
 
* We may want to consider strains with same public name that have diverged
 
** Apply new strain names with prefixes/suffixes? Create new strain objects? Keep original?
 
* Need to determine how each AGR member DB curates phenotypes or diseases to genotypes: is each "genotype" a relative or absolute genotype?
 
  
 +
[[WormBase-Caltech_Weekly_Calls_February_2022|February]]
  
== January 11, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_March_2022|March]]
  
=== IWM swag ===
+
[[WormBase-Caltech_Weekly_Calls_April_2022|April]]
* Eppendorf tube openers with WormBase logo?
 
  
=== Update on AFP Form ===
+
[[WormBase-Caltech_Weekly_Calls_May_2022|May]]
*[https://docs.google.com/presentation/d/1anFOFRK9Ida1UEvrXWf2OBAJ9F4xyU4lWJGy-qr6wRU/edit#slide=id.p3 In-progress mock-up of new form]
 
*[https://docs.google.com/spreadsheets/d/1sS_uAjBJ2r5H90Lam62Ai0HunjwvfjnklkFNrDoNXeU/edit#gid=1929595460 Data type spreadsheet]
 
*[http://wiki.wormbase.org/index.php/First-pass_flagging_pipelines#Author_first-pass_form_revisions Curation forms info]
 
  
*Idea is to move from author flagging to author validation of text mining and data submission wherever possible
 
*Goal is to flag all data types in a paper and either curate at WB or share with a group that does curate that data
 
*SVM flags and author flags can/will be used as filters in TPC
 
*Provide examples of what we want for each type of data to help avoid confusion
 
* Recognize entities automatically and show list to author
 
** Species, strains, genes, alleles, transgenes, etc.
 
** Ask to verify or add unrecognized
 
** Could show known/existing objects with checkboxes
 
** Possibly include unrecognized pattern matching objects? Ask author to verify if these are real?
 
** For strains:
 
*** Show recorded genotype for verification; maybe ask to update/modify if needed?
 
** For transgenes:
 
*** When author submits new transgene, send them to a transgene form, or send them an email asking for details?
 
*** Form could be for both strain and transgene
 
* Mapping data: still ask for? Maybe for balancers, but no one is reporting that. Could still ask if there's interest
 
* Maybe provide option for author to save their progress and return to the form later
 
* Phenotypes
 
** Ask for allele, RNAi and overexpression phenotypes with links to Phenotype form
 
** Also ask for drug/chemical and environmental perturbations (call treatment?); store as free text for now, accommodate with new data model when available
 
* Gene site- and time-of-action, mosaic
 
** Appears to be confusion from authors about mosaics. Should we keep this?
 
** Will keep gene site-of-action and time-of-action; leave unchecked (no SVM, yet) but allow users to indicate
 
* Cell and anatomy data
 
** Cell function ("Cell ablation (laser/genetic) data, optogenetics")
 
** Ultrastructural analysis
 
* Interaction data
 
** Genetic interactions
 
** Physical interactions
 
** Functional complementation
 
* Comparative genomics
 
* Gene expression & regulation
 
  
 +
= December 1st, 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?
  
 +
= 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)
  
== January 18, 2018 ==
+
** 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
  
=== WormBase Tutorials ===
+
they have excel  documents with the location
* May be good to get (possibly anonymous) written questions or suggestions after presenting
 
* Wen will have Skype call with Yishi Jin
 
* Micropublications
 
** how do we peer-review single experiment? No supporting information to corroborate a larger story
 
** Is the greater benefit of peer-review that the whole story is assessed by reviewers
 
** Do MPs help or hurt reproducibility?
 
** Larger papers may have lots of poor experiments that don't get much attention but still pass peer review
 
** Dedicated peer review on single experiment may be more rigorous
 
** What are the criteria/minimal requirements to micropublish?
 
* Concise descriptions
 
** SimpleMine has multiple descriptions output; people asked about the different types
 
** Yishi Jin suggested that we remind users to update manually written descriptions
 
** Showing last-updated date is important
 
** Automated descriptions relies on primary data; will rely on forms and community submissions
 
** Microreviews? Would want to guide authors what data we want; provide a template?
 
* Public/community education issues
 
** Users shouldn't assume that WormBase is comprehensively up to date
 
* Wen will also present at MidWest meeting (Ann Arbor, MI) in April and Boulder, Colorado in May
 
** Will assess topic interest ahead of time
 
  
=== New Cytoscape display for interactions ===
+
= November 3rd, 2022 =
* Sibyl developed a new Cytoscape display for interactions, now live with WS262 release
+
* Booth at IWM
* Simplified colors and subtypes
+
** ACKnowledge will be showcased at the WB booth
* Redraw button to clean up the graph based on what you want to see
+
** Will also advertise Alliance
* Play around and let Sibyl and/or Chris know about issues
 
  
 +
= October 27, 2022 =
  
== January 25, 2018 ==
+
= October 6th, 2022 =  
  
=== UCSF visit report ===
+
== 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)
  
Questions from the audience
+
== GO meeting next week ==
*Is there a way in WB to pull out verified CRISPR guides?
+
* 7am - 11am PDT
*Single cell RNAseq from Waterson lab in WB? Paper is in WB, person-paper connections might be on staging, Kimberly verifying this. Gary W will put data in WS264. Comments from Gary on this paper:
+
* Zoom channel? Available on GO meeting agenda page:
‘The main problem is that the authors can sort the cells into groups (corresponding to tissues, I think) and sometimes sort them into single cells, but it is hard to identify the tissues or cells. I think they found 29 groups, of which about 20 appear to be single cells.  
+
** https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M
I think they have a website where they invite other researchers to make suggestions about how to identify cells in their data.
 
Currently I regard this data set as still undergoing analysis and I'm waiting to see if they improve the deconvolution and identification of the cells.
 
The RNASeq data from this paper will be going into the current Build (WS264) but I will not be adding it to SPELL this Build because displaying it probably requires more thought.
 
I'm not sure that tools for displaying single-cell data have been developed very much yet. There is potentially a lot of information if eventually all 959 or 1031 somatic cells are displayed!
 
  
*List of fem-3 alleles excluding natural variants in WormMine, how to do that? The template should be fixed (checkbox)
+
== Alliance Literature working group ==
*Is the increase of published paper due to an increased number of labs? Expansion of the field? Is there a correlation between the increased number of publications and increased number of labs
+
* Subgroups; Ranjana interested in joining the search subgroup
*One user found powerful to be able to use the Galaxy server to do analysis after exporting data from WormMine
+
* Can sign up on the lit group page
*Can you do protein domain analysis with WormMine? Is the protein->motif precanned query the best option?
+
** https://docs.google.com/document/d/1hB6cft0J_DaapQ9uHUGXwbqrnsZs7wORoepQicLdhTk/edit?pli=1#bookmark=id.butj0rfl4zh1
*Enrichment: how to see which genes are expressed in a tissue or cell -> pointed user to the ontology browser
 
  
=== Skype call with Yishi Jin and Sreekanth Chalasani ===
+
== Persons ==
Participants: Daniela, Karen, Wen, Jin, Shrek
+
* 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
  
*Not all images available due to publisher agreement -> not clear to users, we should put a disclaimer somewhere
+
= Aug 25th, 2022=
*Shrek: thinks gene expression display should improve => hard to figure out all expression patterns
+
* Phosphoproteomic dataset
**Shrek and Jin feel the most important info is the reagent, and that should be displayed on the gene page/expression widget other than the Expression page
+
* WB grant - the new and radically different format for a “Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed)” application
*Images are identical -> example on the eat-4 expression page. This is normal since one image depicts multiple neurons and the association Anatomy neuron applies.
+
*
http://www.wormbase.org/species/c_elegans/gene/WBGene00001135#1860--10
+
*
**On the eat-4 expression page the problem is amplified as one picture shows 70+ neurons
+
 
**We should remove the image column and have links to images only on the panel above (as currently displayed)
+
 
**The image column should be replaced with reagent and description, if possible. Will need to talk to Sibyl and see what is duable.  
+
 
*Shrek pointed out that the eat-4 concise description is out of date, we explained that in the near future the manual descriptions will be superseded by automatic descriptions
+
 
*Neuron connectivity: missing neuron connectivity pages, there is a new reconstruction of neuroanatomy from david hall, would be great to integrate
+
 
 +
= 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
 +
 
 +
<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 00:56, 23 November 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 1st, 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?

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