Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Draft Sus scrofa domesticus (domestic pig) #1122

Open
brianraymor opened this issue Nov 20, 2024 · 0 comments
Open

Draft Sus scrofa domesticus (domestic pig) #1122

brianraymor opened this issue Nov 20, 2024 · 0 comments
Labels
in review reviewing schema for species multispecies discovery Adding new species to CELLxGENE orthologous schema CELLxGENE Discover dataset schema

Comments

@brianraymor
Copy link
Contributor

brianraymor commented Nov 20, 2024 •
edited
Loading

Pending Issues

  1. Waiting on sscrdv to be submitted to OLS for use in references
  2. FAANG is the Functional Annotation of ANimal Genomes project. We are working to understand the genotype to phenotype link in domesticated animals. Per their Ontology Improver, *Dv terms are not referenced. Both UBERON and CL are in use. Their schema:
"name": "developmental stage",
"description": "Ontology for Developmental stage, UBERON is preferred to EFO.",

Design

This draft design reflects additions to corresponding sections in schema 5.2.0. Reviewers are expected to be familiar with the CELLxGENE schema.

Editorial Notes that are inlined in the design below will not be surfaced in the schema.

Required Ontologies

Ontology OBO Prefix Release Download
Unavailable SscrDv Releases TBD

Editorial Notes

This ontology is under active development. CELLxGENE pins ontology releases in each version of the schema. A specific release of the ontology above must be selected in the future.

Required Gene Annotations

Organism Source Required version Download
"NCBITaxon:9823"
for Sus scrofa domesticus		 ENSEMBL (Sus scrofa domesticus) Sscrofa11.1 (GCA_000003025.6) Sus_scrofa.Sscrofa11.1.113.gtf

Editorial Notes

obs (Cell Metadata)

cell_type_ontology_term_id

No schema changes are required.

Editorial Notes

development_stage_ontology_term_id

Key development_stage_ontology_term_id
Annotator Curator MUST annotate.
Value categorical with str categories. If unavailable, this MUST be "unknown".

If organism_ontolology_term_id is "NCBITaxon:9823" for Sus scrofa domesticus, this MUST be the most accurate descendant of SscrDv:0000000 for life cycle stage.

Editorial Notes

This may be outdated, but potential recommendations:

UBERON:0000104 life cycle
    UBERON:0000068 embryo stage
        UBERON:0000106 zygote stage
        UBERON:0000107 cleavage stage
            UBERON:0007232 2 cell stage
            UBERON:0007233 4 cell stage
            UBERON:0007236 8 cell stage
        UBERON:0000108 blastula stage
        UBERON:0000109 gastrula stage
        UBERON:0000110 neurula stage
        UBERON:0000111 organogenesis stage
            SscrDv:0000081 ridge limb stage (pig)
            SscrDv:0000082 bud limb stage (pig)
            SscrDv:0000083 paddle limb stage (pig)
        UBERON:0007220 late embryonic stage
    UBERON:0000092 post-embryonic stage
        UBERON:0000066 fully formed stage
            UBERON:0000112 sexually immature stage
                UBERON:0018685 nursing stage
                    UBERON:0007221 neonate stage
                        SscrDv:0000072 0-day-old stage (pig)
                        SscrDv:0000073 1-day-old stage (pig)
                        SscrDv:0000074 2-day-old stage (pig)
                        SscrDv:0000075 3-day-old stage (pig)
                        SscrDv:0000076 4-day-old stage (pig)
                        SscrDv:0000077 5-day-old stage (pig)
                        SscrDv:0000078 6-day-old stage (pig)
                    UBERON:0034920 infant stage
                        SscrDv:0000010 1-week-old stage (pig)
                        SscrDv:0000011 2-week-old stage (pig)
                        SscrDv:0000012 3-week-old stage (pig)
                            SscrDv:0000018 21-day-old stage (pig)
                            SscrDv:0000019 22-day-old stage (pig)
                            SscrDv:0000020 23-day-old stage (pig)
                            SscrDv:0000021 24-day-old stage (pig)
                            SscrDv:0000022 25-day-old stage (pig)
                            SscrDv:0000023 26-day-old stage (pig)
                            SscrDv:0000024 27-day-old stage (pig)
                        SscrDv:0000013 4-week-old stage (pig)
                            SscrDv:0000025 28-day-old stage (pig)
                            SscrDv:0000026 29-day-old stage (pig)
                            SscrDv:0000027 30-day-old stage (pig)
                            SscrDv:0000028 31-day-old stage (pig)
                            SscrDv:0000029 32-day-old stage (pig)
                            SscrDv:0000030 33-day-old stage (pig)
                            SscrDv:0000031 34-day-old stage (pig)
                        SscrDv:0000014 5-week-old stage (pig)
                            SscrDv:0000032 35-day-old stage (pig)
                            SscrDv:0000033 36-day-old stage (pig)
                            SscrDv:0000034 37-day-old stage (pig)
                            SscrDv:0000035 38-day-old stage (pig)
                            SscrDv:0000036 39-day-old stage (pig)
                            SscrDv:0000037 40-day-old stage (pig)
                            SscrDv:0000038 41-day-old stage (pig)
                        SscrDv:0000015 6-week-old stage (pig)
                        SscrDv:0000016 7-week-old stage (pig)
                UBERON:0034919 juvenile stage
                    SscrDv:0000039 2-month-old stage (pig)
                        SscrDv:0000017 8-week-old stage (pig)
                        SscrDv:0000040 9-week-old stage (pig)
                        SscrDv:0000041 10-week-old stage (pig)
                        SscrDv:0000042 11-week-old stage (pig)
                    SscrDv:0000043 3-month-old stage (pig)
                        SscrDv:0000044 12-week-old stage (pig)
                        SscrDv:0000045 13-week-old stage (pig)
                        SscrDv:0000046 14-week-old stage (pig)
                        SscrDv:0000047 15-week-old stage (pig)
                    SscrDv:0000048 4-month-old stage (pig)
                        SscrDv:0000049 16-week-old stage (pig)
                        SscrDv:0000050 17-week-old stage (pig)
                        SscrDv:0000051 18-week-old stage (pig)
                        SscrDv:0000052 19-week-old stage (pig)
                        SscrDv:0000053 20-week-old stage (pig)
                    SscrDv:0000054 5-month-old stage (pig)
                        SscrDv:0000055 21-week-old stage (pig)
                        SscrDv:0000056 22-week-old stage (pig)
                        SscrDv:0000057 23-week-old stage (pig)
                        SscrDv:0000058 24-week-old stage (pig)
                    SscrDv:0000059 6-month-old stage (pig)
                    SscrDv:0000060 7-month-old stage (pig)
                    SscrDv:0000061 8-month-old stage (pig)
                    SscrDv:0000062 9-month-old stage (pig)
                    SscrDv:0000063 10-month-old stage (pig)
            UBERON:0000113 post-juvenile
                UBERON:0018241 prime adult stage
                    SscrDv:0000064 11-month-old stage (pig)
                    SscrDv:0000065 1-year-old stage (pig)
                    SscrDv:0000066 2-year-old stage (pig)
                    SscrDv:0000067 3-year-old stage (pig)
                    SscrDv:0000068 4-year-old stage (pig)
                    SscrDv:0000069 5-year-old stage (pig)
                    SscrDv:0000070 6-year-old stage (pig)
                    SscrDv:0000071 7-year-old stage (pig)
                UBERON:0007222 late adult stage

disease_ontology_term_id

No schema changes are required.

Editorial Notes

organism_ontolology_term_id

organism_ontolology_term_id is "NCBITaxon:9823" for Sus scrofa domesticus

sex_ontology_term_id

No schema changes are required.

Editorial Notes

tissue_ontology_term_id

No schema changes are required.

Editorial Notes

Reference

BGEE
@brianraymor brianraymor added schema CELLxGENE Discover dataset schema multispecies discovery Adding new species to CELLxGENE drafting drafting schema for species orthologous labels Nov 20, 2024
@brianraymor brianraymor changed the title Drafting Sus scrofa domesticus (domestic pig) Draft Sus scrofa domesticus (domestic pig) Nov 20, 2024
@brianraymor brianraymor added in review reviewing schema for species and removed drafting drafting schema for species labels Nov 21, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
in review reviewing schema for species multispecies discovery Adding new species to CELLxGENE orthologous schema CELLxGENE Discover dataset schema
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@brianraymor