search

brain-bican / taxonomy-development-tools

Tools to build and edit Cell Annotation Schema taxonomies.
Apache License 2.0
3 stars 1 forks source link

Support writing to Cell Annotation Schema JSON #26

Closed dosumis closed 11 months ago

dosumis commented 1 year ago

A specified in:

https://github.com/cellannotation/cell-annotation-schema

dosumis commented 1 year ago

TDT currently has one table:

image

annotation set = annotations.annotation.labelset rank = labelsets.labelset.rank # denormalised locked cell set accession = annotations.annotation.cell_set_accession cell label = annotations.annotation.cell_label parent cell set accession = annotations.annotation.parent_cell_set_accessions parent cell set name. # denormalised for view - from annotations.annotation.cell_label based on accession classifying ontology term id = annotations.annotation.cell_ontology_term_id classifying ontology term name - annotations.annotation.cell_ontology_term marker genes = marker_gene_evidence

Fields to add:

annotations.annotation.cell_fullname annotations.annotation.rationale annotations.annotation.rationale_dois annotations.annotation.synonyms

Additional tables:

  1. labelset - see https://github.com/brain-bican/taxonomy-development-tools/issues/27

    • Columns as for Labelset object

  2. Cross ontology mappings / annotation transfer - is the existing functionality for X ontology mappings hidden?

    • Columns as for Annotation_transfer object