The schema defines a unified metadata model for biological imaging datasets across three sources: IDR, SSBD, and BIA.
The top-level model representing high-level summary information about an imaging dataset (not detailed image-level information):
- Core identification:
id,source,source_url,title,description,license,release_date - Structured objects:
biosamples,image_acquisition_protocols,publications,authors,funding - Additional metadata:
data_doi,keywords,study_type,file_count,total_size_bytes
Biological sample information:
organism: list[Organism] - Species studiedsample_type: str - Type of sample (cell, tissue, organism)biological_entity_description: str | None - Specific tissue/cell type studiedstrain: str | None - Strain name (for model organisms)cell_line: str | None - Cell line name
scientific_name: str - Scientific species name (e.g., 'Homo sapiens')common_name: str | None - Common name (e.g., 'human')ncbi_taxon_id: int | None - NCBI Taxonomy ID (e.g., 9606)
Imaging methodology and equipment:
methods: list[ImagingMethod] - Imaging techniques usedprotocol_description: str | None - Description of the imaging protocolimaging_instrument_description: str | None - Description of instruments used
name: str - Method name (e.g., 'fluorescence microscopy')fbbi_id: str | None - FBbi ontology ID (e.g., 'FBbi:00000246')
| Model | Purpose | Key Fields |
|---|---|---|
Source |
Enum for data sources | IDR, SSBD, BIA |
Organisation |
Institution | display_name, rorid, address, website, country |
Author |
Study author | name, orcid, email, affiliations |
Publication |
Associated paper | doi, pubmed_id, pmc_id, title, authors_name, year |
Funding |
Grant info | funder, grant_id |
- NCBI Taxonomy:
Organism.ncbi_taxon_id(linksscientific_nameto taxonomy) - FBbi (imaging methods):
ImagingMethod.fbbi_id - ORCID:
Author.orcid - ROR:
Organisation.rorid