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Consider having labels referencing ontology terms #60

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cconrad8 opened this issue Nov 21, 2023 · 1 comment
Open

Consider having labels referencing ontology terms #60

cconrad8 opened this issue Nov 21, 2023 · 1 comment

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@cconrad8
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  1. Could create a hover over the headers and cite where the ontology comes from - for example cellxgene uses

Cell metadata in obs (for ontology term IDs, the values MUST be the most specific term available from the specified ontology):
organism_ontology_term_id: NCBITaxon (NCBITaxon:9606for human, NCBITaxon:10090 for mouse)

donor_id: free-text identifier that distinguishes the unique individual that data were derived from. It is encouraged to be something not likely to be used in other studies (e.g. donor_1 is likely to not be unique in the data corpus)

development_stage_ontology_term_id: HsapDv if human, MmusDv if mouse, unknownif information unavailable

sex_ontology_term_id: PATO:0000384for male, PATO:0000383for female, or unknownif unavailable

self_reported_ethnicity_ontology_term_id: HANCESTRO use multiethnicif more than one ethnicity is reported. If human and information unavailable, use unknown. Use naif non-human.

disease_ontology_term_id: MONDO or PATO:0000461for 'normal'

tissue_ontology_term_id: UBERON

cell_type_ontology_term_id: CL

assay_ontology_term_id: EFO
single cell rna sequencing: EFO:0008913

suspension_type: cell, nucleus, or na, as corresponding to assay. Use this table defined in the data schema for guidance.

If the assay does not appear in this table, the most appropriate value MUST be selected and the curation team informed during submission so that the assay can be added to the table.

@cconrad8
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First step to add mappings in model

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