WormBase-Caltech Weekly Calls 2022
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2022 Meetings
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:
Alliance Literature working group
- Subgroups; Ranjana interested in joining the search subgroup
- Can sign up on the lit group page
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
