Draft Gallus gallus (chicken)

[brianraymor]

Pending Issues

1. Waiting on ggaldv 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.

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Required Ontologies

Ontology	OBO Prefix	Release	Download
Unavailable	GgalDv	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.

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Required Gene Annotations

Organism	Source	Required version	Download
"NCBITaxon:9031" for Gallus gallus	ENSEMBL (Gallus gallus)	bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1)	Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.113.gtf

Editorial Notes

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obs (Cell Metadata)

cell_type_ontology_term_id

No schema changes are required.

Editorial Notes

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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:9031" for Gallus gallus, this MUST be the most accurate descendant of GgalDv:0000000 for life cycle stage.

Editorial Notes

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disease_ontology_term_id

No schema changes are required.

Editorial Notes

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organism_ontolology_term_id

organism_ontolology_term_id is "NCBITaxon:9031" for Gallus gallus

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sex_ontology_term_id

No schema changes are required.

Editorial Notes

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tissue_ontology_term_id

No schema changes are required.

Editorial Notes

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Reference

BGEE