Draft Pan troglodytes (chimpanzee)

[brianraymor]

Pending Issues

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

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	PtroDv	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:9598" for Pan troglodytes	ENSEMBL (Pan troglodytes)	Pan_tro_3.0 (GCA_000001515.5)	Pan_troglodytes.Pan_tro_3.0.113.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:9598" for Pan troglodytes, this MUST be the most accurate descendant of PtroDv: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This may be outdated, but potential recommendations: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
                UBERON:0034919 juvenile stage
                    PtroDv:0000006 3-year-old stage (chimpanzee)
                    PtroDv:0000007 4-year-old stage (chimpanzee)
                    PtroDv:0000008 5-year-old stage (chimpanzee)
                    PtroDv:0000009 6-year-old stage (chimpanzee)
                    PtroDv:0000010 7-year-old stage (chimpanzee)
            UBERON:0000113 post-juvenile
                UBERON:0018241 prime adult stage
                    PtroDv:0000013 8-year-old stage (chimpanzee)
                    PtroDv:0000014 9-year-old stage (chimpanzee)
                    PtroDv:0000015 10-year-old stage (chimpanzee)
                    PtroDv:0000016 11-year-old stage (chimpanzee)
                    PtroDv:0000017 12-year-old stage (chimpanzee)
                    PtroDv:0000018 13-year-old stage (chimpanzee)
                    PtroDv:0000019 14-year-old stage (chimpanzee)
                    PtroDv:0000020 15-year-old stage (chimpanzee)
                    PtroDv:0000021 16-year-old stage (chimpanzee)
                    PtroDv:0000022 17-year-old stage (chimpanzee)
                    PtroDv:0000023 18-year-old stage (chimpanzee)
                    PtroDv:0000024 19-year-old stage (chimpanzee)
                    PtroDv:0000025 20-year-old stage (chimpanzee)
                    PtroDv:0000026 21-year-old stage (chimpanzee)
                    PtroDv:0000027 22-year-old stage (chimpanzee)
                    PtroDv:0000028 23-year-old stage (chimpanzee)
                    PtroDv:0000029 24-year-old stage (chimpanzee)
                    PtroDv:0000030 25-year-old stage (chimpanzee)
                    PtroDv:0000031 26-year-old stage (chimpanzee)
                    PtroDv:0000032 27-year-old stage (chimpanzee)
                    PtroDv:0000033 28-year-old stage (chimpanzee)
                    PtroDv:0000034 29-year-old stage (chimpanzee)
                    PtroDv:0000035 30-year-old stage (chimpanzee)
                    PtroDv:0000036 31-year-old stage (chimpanzee)
                    PtroDv:0000037 32-year-old stage (chimpanzee)
                    PtroDv:0000038 33-year-old stage (chimpanzee)
                UBERON:0007222 late adult stage
                    PtroDv:0000040 34-year-old stage (chimpanzee)
                    PtroDv:0000041 35-year-old stage (chimpanzee)
                    PtroDv:0000042 36-year-old stage (chimpanzee)
                    PtroDv:0000043 37-year-old stage (chimpanzee)
                    PtroDv:0000044 38-year-old stage (chimpanzee)
                    PtroDv:0000045 39-year-old stage (chimpanzee)
                    PtroDv:0000046 40-year-old stage (chimpanzee)
                    PtroDv:0000047 41-year-old stage (chimpanzee)
                    PtroDv:0000048 42-year-old stage (chimpanzee)
                    PtroDv:0000049 43-year-old stage (chimpanzee)
                    PtroDv:0000050 44-year-old stage (chimpanzee)
                    PtroDv:0000051 45-year-old and over stage (chimpanzee)

---

disease_ontology_term_id

No schema changes are required.

Editorial Notes

---

organism_ontolology_term_id

organism_ontolology_term_id is "NCBITaxon:9598" for Pan troglodytes

---

sex_ontology_term_id

No schema changes are required.

Editorial Notes

---

tissue_ontology_term_id

No schema changes are required.

Editorial Notes

---

Reference

BGEE