Draft Bos taurus (Cow)

[brianraymor]

Pending Issues

1. Waiting on btaudv 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	BtauDv	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:9913" for Cow	ENSEMBL (Bos Taurus)	ARS-UCD1.3 (GCA_002263795.3))	Bos_taurus.ARS-UCD1.3.113.gtf

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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:9913" for Cow, this MUST be the most accurate descendant of BtauDv:0000000 for life cycle stage.

Editorial Notes

This may be outdated, but potential recommendations:

UBERON:0000104 life cycle
    UBERON:0000068 embryo stage
        BtauDv:0000007 first trimester of gestation (cow)
            BtauDv:0000010 first month of gestation (cow)
            BtauDv:0000011 second month of gestation (cow)
            BtauDv:0000012 third month of gestation (cow)
        BtauDv:0000008 second trimester of gestation (cow)
            BtauDv:0000013 fourth month of gestation (cow)
            BtauDv:0000014 fifth month of gestation (cow)
            BtauDv:0000015 sixth month of gestation (cow)
        BtauDv:0000009 third trimester of gestation (cow)
            BtauDv:0000016 seventh month of gestation (cow)
            BtauDv:0000017 eighth month of gestation cow stage (cow)
            BtauDv:0000018 ninth and over month of gestation (cow)
    UBERON:0000092 post-embryonic stage
        UBERON:0000066 fully formed stage
            UBERON:0000112 sexually immature stage
                BtauDv:0000053 first 0-6 postnatal days (cow)
                    BtauDv:0000054 0-day-old stage (cow)
                    BtauDv:0000055 1-day-old stage (cow)
                    BtauDv:0000056 2-day-old stage (cow)
                    BtauDv:0000057 3-day-old stage (cow)
                    BtauDv:0000058 4-day-old stage (cow)
                    BtauDv:0000059 5-day-old stage (cow)
                    BtauDv:0000060 6-day-old stage (cow)
                BtauDv:0000061 1-week-old stage (cow)
                BtauDv:0000062 2-week-old stage (cow)
                BtauDv:0000063 3-week-old stage (cow)
                    BtauDv:0000064 21-day-old stage (cow)
                    BtauDv:0000065 22-day-old stage (cow)
                    BtauDv:0000066 23-day-old stage (cow)
                    BtauDv:0000067 24-day-old stage (cow)
                    BtauDv:0000068 25-day-old stage (cow)
                    BtauDv:0000069 26-day-old stage (cow)
                    BtauDv:0000070 27-day-old stage (cow)
                    BtauDv:0000071 28-day-old stage (cow)
                    BtauDv:0000072 29-day-old stage (cow)
                BtauDv:0000020 1-month-old stage (cow)
                    BtauDv:0000073 4-week-old stage (cow)
                    BtauDv:0000074 5-week-old stage (cow)
                    BtauDv:0000075 6-week-old stage (cow)
                        BtauDv:0000077 42-day-old stage (cow)
                    BtauDv:0000076 7-week-old stage (cow)
                BtauDv:0000021 2-month-old stage (cow)
                BtauDv:0000022 3-month-old stage (cow)
                BtauDv:0000023 4-month-old stage (cow)
                BtauDv:0000024 5-month-old stage (cow)
                BtauDv:0000025 6-month-old stage (cow)
                BtauDv:0000026 7-month-old stage (cow)
                BtauDv:0000027 8-month-old stage (cow)
                BtauDv:0000028 9-month-old stage (cow)
                BtauDv:0000029 10-month-old stage (cow)
                BtauDv:0000030 11-month-old stage (cow)
                BtauDv:0000031 12-month-old stage (cow)
                BtauDv:0000032 13-month-old stage (cow)
                BtauDv:0000033 14-month-old stage (cow)
                BtauDv:0000034 15-month-old stage (cow)
                BtauDv:0000035 16-month-old stage (cow)
                BtauDv:0000036 17-month-old stage (cow)
            UBERON:0000113 post-juvenile
                UBERON:0018241 prime adult stage
                    BtauDv:0000037 18-month-old stage (cow)
                    BtauDv:0000038 19-month-old stage (cow)
                    BtauDv:0000039 20-month-old stage (cow)
                    BtauDv:0000040 21-month-old stage (cow)
                    BtauDv:0000041 22-month-old stage (cow)
                    BtauDv:0000042 23-month-old stage (cow)
                    BtauDv:0000043 2-year-old stage (cow)
                    BtauDv:0000044 3-year-old stage (cow)
                    BtauDv:0000045 4-year-old stage (cow)
                    BtauDv:0000046 5-year-old stage (cow)
                    BtauDv:0000047 6-year-old stage (cow)
                    BtauDv:0000048 7-year-old stage (cow)
                    BtauDv:0000049 8-year-old stage (cow)
                    BtauDv:0000050 9-year-old stage (cow)
                    BtauDv:0000051 10-year-old stage (cow)
                    BtauDv:0000052 11-year-old stage (cow)
                UBERON:0007222 late adult stage

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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:9913" for Cow

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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