Draft Callithrix jacchus (white-tufted-ear marmoset)

[brianraymor]

Caution

There are 28 Callithrix jacchus 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.

---

Pending Issues

---

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
?	?	?	?

Editorial Notes

No Callithrix jacchus ontology references were discovered, with the exception of PCL.

---

Required Gene Annotations

Organism	Source	Required version	Download
"NCBITaxon:9483" for Callithrix jacchus	ENSEMBL (Callithrix jacchus)	mCalJac1.pat.X (GCA_011100555.1)	Callithrix_jacchus.mCalJac1.pat.X.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:9483" for Callithrix jacchus, this MUST be the most accurate descendant of UBERON:0000105 for life cycle stage, excluding UBERON:0000071 for death 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This may be outdated, but potential recommendations: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
            UBERON:0000113 post-juvenile
                UBERON:0018241 prime adult stage
                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:9483" for Callithrix jacchus

---

sex_ontology_term_id

No schema changes are required.

Editorial Notes

---

tissue_ontology_term_id

No schema changes are required.

Editorial Notes

---

Reference

BGEE