Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchLine 47: | Line 47: | ||
* 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. | * 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? | * 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 = | = July 28th, 2022 = |
Revision as of 18:40, 11 August 2022
Contents
Previous Years
2022 Meetings
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
- 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