metadata in .uns or .obs

[davidsebfischer]

• [x] reassign attributes
• [x] document these assignments in constants class
• [ ] adopt ontology for organism
• [x] adopt ontology for disease
• [ ] define healthy attribute as property based on disease ontology entry?
• [x] adopt ontology for ethnicity
• [x] adopt ontology for protocol
• [x] adopt ontology for organ, subtissue
• [x] keep organ and subtissue separate: organ specific nodes in ontology and subtissue and sub nodes thereof?
• [x] match contributor fields cellxgene <-> sfaira: only name

per dataset: .uns and accessible in lazy mode

assay (replaces protocol)
contributors (replaces author, only takes name field from cellxgene)
has_celltypes
id
normalization
lab
organism (replaces animal)
preprint_doi (new)
publication_doi (new)
version (new)
wget_download
year
(delete) publication
(delete) protocol

per cell: .obs and accessible in lazy mode as list of unique entries (these are .obs attributes that can be represented as a categorical with a short list of entries)

dev_stage
disease (new)
healthy (might be reduced to a function of disease)
organ
sex
subtissue

per cell: .obs and not accessible in lazy mode

age
cell_types_original
cell_ontology_class
cell_ontology_id
ethnicity
state_exact

@ambrosejcarr happy to get feedback on this

[davidsebfischer]

The corresponding schema in cellxgene is documented here https://github.com/chanzuckerberg/cellxgene/blob/345306ef7b2acc23731583a0f318a37269089efd/dev_docs/schema_guide.md

uns:
    version:
        corpora_schema_version: 1.0.0
        corpora_encoding_version: 0.1.0
    contributors:
    title:
    layer_descriptions:
    preprint_doi:
    publication_doi:
    organism_ontology_term_id:
obs:
    tissue_ontology_term_id:
    assay_ontology_term_id:
    disease_ontology_term_id:
    cell_type_ontology_term_id:
    sex:
    ethnicity_ontology_term_id:
    development_stage_ontology_term_id:

[davidsebfischer]

We will try to use ontologies where possible for meta data. The suggested ontologies are:

general:

• assay: https://www.ebi.ac.uk/ols/ontologies/efo subset: https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0010183&viewMode=All&siblings=false
• organism: http://www.obofoundry.org/ontology/ncbitaxon.html

human:

• developmental stage: http://www.obofoundry.org/ontology/hsapdv.html
• tissue / anatomy (developmental annotation): http://www.obofoundry.org/ontology/ehdaa2.html or uberon https://uberon.github.io/downloads.html#subsets, uberon provides joint ontologies across organisms
• disease: https://mondo.monarchinitiative.org/
• ethnicity_ontology_term_id: https://www.ebi.ac.uk/ols/ontologies/hancestro
• cell type ontology (same base ontology for all animals): http://www.obofoundry.org/ontology/cl.html

mouse:

• developmental stage: http://www.obofoundry.org/ontology/mmusdv.html
• tissue / anatomy: http://www.obofoundry.org/ontology/emapa.html or uberon https://uberon.github.io/downloads.html#subsets, uberon provides joint ontologies across organisms
• disease: http://www.obofoundry.org/ontology/mpath.html
• cell type ontology (same base ontology for all animals): http://www.obofoundry.org/ontology/cl.html