Draft Macaca fascicularis (crab-eating macaque) and Macaca mulatta (Rhesus macaque)

[brianraymor]

Caution

There are 19 Macaca mulatta datasets in the corpus allowed by the current requirement:

Organisms. Data MUST be from a Metazoan organism or SARS-COV-2 and defined in the NCBI organismal classification. For data that is neither Human, Mouse, nor SARS-COV-2, features MUST be translated into orthologous genes from the pinned Human and Mouse gene annotations.

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Pending Issues

1. Waiting on mmuldv to be submitted to OLS for use in references

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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	MmulDv	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.

There is a development stage ontology - mmuldv - not included in OLS.

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Required Gene Annotations

Organism	Source	Required version	Download
"NCBITaxon:9541" for Crab-eating macaque	ENSEMBL (Crab-eating macaque)	Macaca_fascicularis_6.0 (GCA_011100615.1)	Macaca_fascicularis.Macaca_fascicularis_6.0.113.gtf
"NCBITaxon:9544" for Rhesus macaque	ENSEMBL (Rhesus macaque)	Mmul_10	Macaca_mulatta.Mmul_10.113.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

If organism_ontolology_term_id is "NCBITaxon:9541" for Crab-eating macaque or organism_ontolology_term_id is "NCBITaxon:9544" for Rhesus macaque this MUST be the most accurate descendant of MmulDv: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This may be outdated, but potential recommendations: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
            UBERON:0004707 pharyngula stage
        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
                        UBERON:0035946 start of neonate stage
                    UBERON:0034920 infant stage
                        MmulDv:0000005 1-month-old stage (macaque)
                        MmulDv:0000006 2-month-old stage (macaque)
                        MmulDv:0000007 3-month-old stage (macaque)
                        MmulDv:0000008 4-month-old stage (macaque)
                        MmulDv:0000009 5-month-old stage (macaque)
                        MmulDv:0000010 6-month-old stage (macaque)
                        MmulDv:0000011 7-month-old stage (macaque)
                        MmulDv:0000012 8-month-old stage (macaque)
                        MmulDv:0000013 9-month-old nursing stage (macaque)
                UBERON:0034919 juvenile stage
                    MmulDv:0000015 9-month-old weaning stage (macaque)
                    MmulDv:0000016 10-month-old stage (macaque)
                    MmulDv:0000017 11-month-old stage (macaque)
                    MmulDv:0000018 1-year-old stage (macaque)
                    MmulDv:0000019 2-year-old stage (macaque)
                    MmulDv:0000020 3-year-old immature stage (macaque)
            UBERON:0000113 post-juvenile
                UBERON:0018241 prime adult stage
                    MmulDv:0000023 3-year-old mature stage (macaque)
                    MmulDv:0000024 4-year-old stage (macaque)
                    MmulDv:0000025 5-year-old stage (macaque)
                    MmulDv:0000026 6-year-old stage (macaque)
                    MmulDv:0000027 7-year-old stage (macaque)
                    MmulDv:0000028 8-year-old stage (macaque)
                    MmulDv:0000029 9-year-old stage (macaque)
                    MmulDv:0000030 10-year-old stage (macaque)
                    MmulDv:0000031 11-year-old stage (macaque)
                    MmulDv:0000032 12-year-old stage (macaque)
                    MmulDv:0000033 13-year-old stage (macaque)
                    MmulDv:0000034 14-year-old stage (macaque)
                    MmulDv:0000035 15-year-old stage (macaque)
                    MmulDv:0000036 16-year-old stage (macaque)
                    MmulDv:0000037 17-year-old stage (macaque)
                    MmulDv:0000038 18-year-old stage (macaque)
                    MmulDv:0000039 19-year-old stage (macaque)
                    MmulDv:0000040 20-year-old stage (macaque)
                    MmulDv:0000041 21-year-old stage (macaque)
                    MmulDv:0000042 22-year-old stage (macaque)
                    MmulDv:0000043 23-year-old stage (macaque)
                    MmulDv:0000044 24-year-old stage (macaque)
                UBERON:0007222 late adult stage
                    MmulDv:0000047 25-year-old stage (macaque)
                    MmulDv:0000048 26-year-old stage (macaque)
                    MmulDv:0000049 27-year-old stage (macaque)
                    MmulDv:0000050 28-year-old stage (macaque)
                    MmulDv:0000051 29 year-old and over stage (macaque)

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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:9541" for Crab-eating macaque

organism_ontolology_term_id is "NCBITaxon:9544" for Rhesus macaque

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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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References

BGEE
BGEE