| Metric |
ASAP
|
ASAP v8*
|
Bgee
|
CELLxGENE
|
Single Cell Portal
|
|---|---|---|---|---|---|
| File resources | 85 | 36 | 82 | 2216 | 110 |
| Checked | 50 | 36 | 37 | 2166 | 59 |
| Passed | 0 | 36 | 0 | 0 | 0 |
| Failed validation | 50 | 0 | 35 | 2166 | 56 |
| Check run failed | 0 | 0 | 2 | 0 | 3 |
* At the moment, all currently scFAIR-valid projects are imported from CELLxGENE and automatically updated to comply with the scFAIR schema.
Pass rate among passed and failed outcomes (warnings excluded and marked with *). Not applicable checks are shown as - and excluded from the rate. Equivalent H5AD and Loom checks are shown on the same row. Click a percentage below 100% to list projects that failed or warned on that check. A clickable - lists projects with warnings only.
| Check | ASAP | ASAP v8* | Bgee | CELLxGENE | Single Cell Portal |
|---|---|---|---|---|---|
| Cross-field schema constraints | |||||
|
CF-1: Assay and suspension_type
cross-field.CF-1-assay-suspension
|
100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
|
CF-2a: Cell line ethnicity
cross-field.CF-2a-cell-line-ethnicity
|
- | - | - | 100.0% | - |
|
CF-2b: Cell line sex
cross-field.CF-2b-cell-line-sex
|
- | - | - | 100.0% | - |
|
CF-2c: Cell line development stage
cross-field.CF-2c-cell-line-development-stage
|
- | - | - | 100.0% | - |
|
CF-2d: Cell line donor_id
cross-field.CF-2d-cell-line-donor-id
|
- | - | - | 100.0% | - |
|
CF-2e: Cell line suspension_type
cross-field.CF-2e-cell-line-suspension
|
- | - | - | - | - |
|
CF-2f: Cell line tissue identifier
cross-field.CF-2f-cell-line-tissue-id
|
- | - | - | 100.0% | - |
|
CF-3: donor_id consistency
cross-field.CF-3-donor-id
|
100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
|
CF-4: Organoid tissue constraint
cross-field.CF-4-organoid-tissue
|
- | - | - | 100.0% | - |
|
CF-5: Spatial assay uniformity
cross-field.CF-5-spatial-assay-uniformity
|
- | - | - | 100.0% | - |
|
CF-6: Spatial is_primary_data
cross-field.CF-6-spatial-primary-data
|
- | - | - | 100.0% | - |
|
CF-7: Cell line cell type
cross-field.CF-7-cell-line-cell-type
|
- | - | - | - | - |
|
CF-8: Visium in_tissue spots
cross-field.CF-8-visium-in-tissue
|
- | - | - | - | - |
|
CF-9: Spatial metadata presence
cross-field.CF-9-spatial-metadata-presence
|
- | - | - | 100.0% | 0.0% |
| Ensembl release and assembly consistency | |||||
|
ensembl_assembly vs organism and release
cross-field.uns_ensembl.assembly
|
- | 100.0% | - | - | - |
|
ensembl_release vs organism
cross-field.uns_ensembl.release
|
- | 100.0% | - | - | - |
| analysis_json extension checks | |||||
|
extension.analysis_json
extension.analysis_json
|
100.0% | 100.0% | - | - | - |
| ATAC schema extension checks | |||||
|
extension.atac
extension.atac
|
- | - | - | - | - |
| Perturbation schema extension checks | |||||
|
extension.perturb
extension.perturb
|
- | - | - | - | - |
| Spatial schema extension checks | |||||
|
extension.spatial
extension.spatial
|
- | - | - | 100.0% | 100.0% |
|
extension.spatial.assets
extension.spatial.assets
|
- | - | - | 100.0% | - |
|
extension.spatial.structure
extension.spatial.structure
|
- | - | - | 100.0% | - |
| obsm/varm/obsp/varp checks | |||||
|
obsm
obsm
|
- | - | - | 100.0% | 100.0% |
| anndata_mapping manifest checks | |||||
|
anndata_mapping
/attrs/anndata_mapping
|
100.0% | 100.0% | - | - | - |
| Matrix encoding checks | |||||
|
Matrix encoding and finite value checks
X | dimensions
|
100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
| Other checks | |||||
|
Deprecated reserved names
metadata.other.deprecated
|
100.0% | 100.0% | 100.0% | 100.0% | 96.4% |
|
Reserved name prefix
metadata.other.reserved_prefix
|
100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
|
Unique obs metadata names
metadata.other.unique_names.obs
|
100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
|
Unique var metadata names
metadata.other.unique_names.var
|
100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
| Experimental condition metadata | |||||
|
obs.experimental_condition.id_values
obs.experimental_condition.id_values
|
- | - | - | 100.0% | - |
|
obs.experimental_condition.label
obs.experimental_condition.label
|
- | - | - | 100.0% | - |
|
obs.experimental_condition.label_values
obs.experimental_condition.label_values
|
- | - | - | 100.0% | - |
|
obs.experimental_condition.perturbation_type_values
obs.experimental_condition.perturbation_type_values
|
- | - | - | 100.0% | - |
|
obs.experimental_condition.perturbation_types
obs.experimental_condition.perturbation_types
|
- | - | - | 100.0% | - |
|
experimental_condition
obs/experimental_condition | /col_attrs/experimental_condition
|
100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
|
perturbation_types
obs/perturbation_types
|
- | - | - | - | - |
| Observation label / ontology ID pairs | |||||
|
assay / assay_ontology_term_id
obs.label_pairs.assay_ontology_term_id
|
- | 100.0% | - | 100.0% | 0.0% |
|
cell_type / cell_type_ontology_term_id
obs.label_pairs.cell_type_ontology_term_id
|
- | 100.0% | - | 100.0% | 0.0% |
|
development_stage / development_stage_ontology_term_id
obs.label_pairs.development_stage_ontology_term_id
|
- | 100.0% | - | 100.0% | 0.0% |
|
disease / disease_ontology_term_id
obs.label_pairs.disease_ontology_term_id
|
- | 100.0% | - | 99.3% | 0.0% |
|
self_reported_ethnicity / self_reported_ethnicity_ontology_term_id
obs.label_pairs.self_reported_ethnicity_ontology_term_id
|
- | 100.0% | - | 97.5% | 36.4% |
|
sex / sex_ontology_term_id
obs.label_pairs.sex_ontology_term_id
|
- | 100.0% | - | 100.0% | 90.9% |
|
tissue / tissue_ontology_term_id
obs.label_pairs.tissue_ontology_term_id
|
- | 100.0% | - | 100.0% | 0.0% |
| Required observation metadata fields | |||||
|
assay
obs/assay | /col_attrs/assay
|
0.0% | 100.0% | 0.0% | 100.0% | 1.8% |
|
assay_ontology_term_id
obs/assay_ontology_term_id | /col_attrs/assay_ontology_term_id
|
0.0% | 100.0% | 0.0% | 100.0% | 1.8% |
|
cell_type
obs/cell_type | /col_attrs/cell_type
|
0.0% | 100.0% | 0.0% | 100.0% | 33.9% |
|
cell_type_ontology_term_id
obs/cell_type_ontology_term_id | /col_attrs/cell_type_ontology_term_id
|
0.0% | 100.0% | 0.0% | 100.0% | 1.8% |
|
development_stage
obs/development_stage | /col_attrs/development_stage
|
0.0% | 100.0% | 0.0% | 100.0% | 0.0% |
|
development_stage_ontology_term_id
obs/development_stage_ontology_term_id | /col_attrs/development_stage_ontology_term_id
|
0.0% | 100.0% | 0.0% | 100.0% | 19.6% |
|
disease
obs/disease | /col_attrs/disease
|
0.0% | 100.0% | 0.0% | 100.0% | 71.4% |
|
disease_ontology_term_id
obs/disease_ontology_term_id | /col_attrs/disease_ontology_term_id
|
0.0% | 100.0% | 0.0% | 100.0% | 1.8% |
|
donor_id
obs/donor_id | /col_attrs/donor_id
|
0.0% | 100.0% | 0.0% | 100.0% | 71.4% |
|
is_primary_data
obs/is_primary_data | /col_attrs/is_primary_data
|
0.0% | 100.0% | 0.0% | 100.0% | 14.3% |
|
self_reported_ethnicity
obs/self_reported_ethnicity | /col_attrs/self_reported_ethnicity
|
0.0% | 100.0% | 0.0% | 100.0% | 14.3% |
|
self_reported_ethnicity_ontology_term_id
obs/self_reported_ethnicity_ontology_term_id | /col_attrs/self_reported_ethnicity_ontology_term_id
|
0.0% | 100.0% | 0.0% | 100.0% | 19.6% |
|
sex
obs/sex | /col_attrs/sex
|
100.0% | 100.0% | 100.0% | 100.0% | 69.6% |
|
sex_ontology_term_id
obs/sex_ontology_term_id | /col_attrs/sex_ontology_term_id
|
0.0% | 100.0% | 0.0% | 100.0% | 19.6% |
|
suspension_type
obs/suspension_type | /col_attrs/suspension_type
|
0.0% | 100.0% | 0.0% | 100.0% | 17.9% |
|
tissue
obs/tissue | /col_attrs/tissue
|
74.0% | 100.0% | 0.0% | 100.0% | 8.9% |
|
tissue_ontology_term_id
obs/tissue_ontology_term_id | /col_attrs/tissue_ontology_term_id
|
0.0% | 100.0% | 0.0% | 100.0% | 1.8% |
|
tissue_type
obs/tissue_type | /col_attrs/tissue_type
|
0.0% | 100.0% | 0.0% | 100.0% | 17.9% |
| Ontology identifier format checks | |||||
|
assay_ontology_term_id
obs/assay_ontology_term_id | /col_attrs/assay_ontology_term_id
|
- | 100.0% | - | 100.0% | 100.0% |
|
cell_type_ontology_term_id
obs/cell_type_ontology_term_id | /col_attrs/cell_type_ontology_term_id
|
- | 100.0% | - | 100.0% | 0.0% |
|
development_stage_ontology_term_id
obs/development_stage_ontology_term_id | /col_attrs/development_stage_ontology_term_id
|
- | 100.0% | - | 100.0% | 90.9% |
|
disease_ontology_term_id
obs/disease_ontology_term_id | /col_attrs/disease_ontology_term_id
|
- | 100.0% | - | 100.0% | 0.0% |
|
self_reported_ethnicity_ontology_term_id
obs/self_reported_ethnicity_ontology_term_id | /col_attrs/self_reported_ethnicity_ontology_term_id
|
- | 100.0% | - | 100.0% | 90.9% |
|
sex_ontology_term_id
obs/sex_ontology_term_id | /col_attrs/sex_ontology_term_id
|
- | 100.0% | - | 100.0% | 100.0% |
|
tissue_ontology_term_id
obs/tissue_ontology_term_id | /col_attrs/tissue_ontology_term_id
|
- | 100.0% | - | 98.7% | 0.0% |
|
organism_ontology_term_id
uns/organism_ontology_term_id | /attrs/organism_ontology_term_id
|
- | 100.0% | - | 100.0% | - |
| Organism-specific constraints | |||||
|
Cell type ontology prefix
ontology.organism_specific.cell_type
|
- | 100.0% | - | 100.0% | - |
|
Development stage ontology prefix
ontology.organism_specific.development_stage
|
- | 100.0% | - | 100.0% | - |
|
Ethnicity vs organism
ontology.organism_specific.ethnicity
|
- | 100.0% | - | 100.0% | - |
|
C. elegans sex terms
ontology.organism_specific.sex
|
- | - | - | - | - |
|
Tissue ontology prefix
ontology.organism_specific.tissue
|
- | 100.0% | - | 99.9% | - |
| Ontology semantic constraints | |||||
|
assay_ontology_term_id — Allowed / known terms
ontology.semantics.assay_ontology_term_id.allowed_terms
|
- | 100.0% | - | 100.0% | 100.0% |
|
assay_ontology_term_id — Banned terms
ontology.semantics.assay_ontology_term_id.banned_terms
|
- | 100.0% | - | 100.0% | 100.0% |
|
assay_ontology_term_id — Descendant / root restrictions
ontology.semantics.assay_ontology_term_id.descendants
|
- | 100.0% | - | 100.0% | 100.0% |
|
cell_type_ontology_term_id — Allowed / known terms
ontology.semantics.cell_type_ontology_term_id.allowed_terms
|
- | 100.0% | - | 100.0% | - |
|
cell_type_ontology_term_id — Banned terms
ontology.semantics.cell_type_ontology_term_id.banned_terms
|
- | 100.0% | - | 100.0% | 100.0% |
|
cell_type_ontology_term_id — Descendant / root restrictions
ontology.semantics.cell_type_ontology_term_id.descendants
|
- | 100.0% | - | 100.0% | 100.0% |
|
cell_type_ontology_term_id — Ontology term existence
ontology.semantics.cell_type_ontology_term_id.existence
|
- | - | - | - | 0.0% |
|
cell_type_ontology_term_id — Multi-value ordering
ontology.semantics.cell_type_ontology_term_id.sorted_multi
|
- | 100.0% | - | 100.0% | 100.0% |
|
cell_type_ontology_term_id — Special placeholder values
ontology.semantics.cell_type_ontology_term_id.special_values
|
- | 100.0% | - | 100.0% | 100.0% |
|
development_stage_ontology_term_id — Allowed / known terms
ontology.semantics.development_stage_ontology_term_id.allowed_terms
|
- | 100.0% | - | 100.0% | 100.0% |
|
development_stage_ontology_term_id — Banned terms
ontology.semantics.development_stage_ontology_term_id.banned_terms
|
- | 100.0% | - | 100.0% | 100.0% |
|
development_stage_ontology_term_id — Descendant / root restrictions
ontology.semantics.development_stage_ontology_term_id.descendants
|
- | 100.0% | - | 100.0% | 100.0% |
|
development_stage_ontology_term_id — Ontology term existence
ontology.semantics.development_stage_ontology_term_id.existence
|
- | - | - | - | 0.0% |
|
development_stage_ontology_term_id — Multi-value ordering
ontology.semantics.development_stage_ontology_term_id.sorted_multi
|
- | 100.0% | - | 100.0% | 100.0% |
|
development_stage_ontology_term_id — Special placeholder values
ontology.semantics.development_stage_ontology_term_id.special_values
|
- | 100.0% | - | 100.0% | 100.0% |
|
disease_ontology_term_id — Allowed / known terms
ontology.semantics.disease_ontology_term_id.allowed_terms
|
- | 100.0% | - | 100.0% | - |
|
disease_ontology_term_id — Descendant / root restrictions
ontology.semantics.disease_ontology_term_id.descendants
|
- | 100.0% | - | 100.0% | 100.0% |
|
disease_ontology_term_id — Ontology term existence
ontology.semantics.disease_ontology_term_id.existence
|
- | - | - | - | 0.0% |
|
disease_ontology_term_id — Multi-value ordering
ontology.semantics.disease_ontology_term_id.sorted_multi
|
- | 100.0% | - | 100.0% | 100.0% |
|
organism_ontology_term_id — ID / label pairs
ontology.semantics.organism_ontology_term_id.label_pair
|
- | 100.0% | - | 100.0% | - |
|
self_reported_ethnicity_ontology_term_id — Allowed / known terms
ontology.semantics.self_reported_ethnicity_ontology_term_id.allowed_terms
|
- | 100.0% | - | 100.0% | 100.0% |
|
self_reported_ethnicity_ontology_term_id — Descendant / root restrictions
ontology.semantics.self_reported_ethnicity_ontology_term_id.descendants
|
- | 100.0% | - | 100.0% | 100.0% |
|
self_reported_ethnicity_ontology_term_id — Ontology term existence
ontology.semantics.self_reported_ethnicity_ontology_term_id.existence
|
- | - | - | - | 0.0% |
|
self_reported_ethnicity_ontology_term_id — Lineage restrictions
ontology.semantics.self_reported_ethnicity_ontology_term_id.lineage
|
- | - | - | - | 0.0% |
|
self_reported_ethnicity_ontology_term_id — Multi-value ordering
ontology.semantics.self_reported_ethnicity_ontology_term_id.sorted_multi
|
- | 100.0% | - | 100.0% | 100.0% |
|
self_reported_ethnicity_ontology_term_id — Special placeholder values
ontology.semantics.self_reported_ethnicity_ontology_term_id.special_values
|
- | 100.0% | - | 100.0% | 100.0% |
|
sex_ontology_term_id — Allowed / known terms
ontology.semantics.sex_ontology_term_id.allowed_terms
|
- | 100.0% | - | 100.0% | 100.0% |
|
sex_ontology_term_id — Special placeholder values
ontology.semantics.sex_ontology_term_id.special_values
|
- | 100.0% | - | 100.0% | 100.0% |
|
tissue_ontology_term_id — Allowed / known terms
ontology.semantics.tissue_ontology_term_id.allowed_terms
|
- | 100.0% | - | 100.0% | - |
|
tissue_ontology_term_id — Descendant / root restrictions
ontology.semantics.tissue_ontology_term_id.descendants
|
- | 100.0% | - | 100.0% | 100.0% |
|
tissue_ontology_term_id — Ontology term existence
ontology.semantics.tissue_ontology_term_id.existence
|
- | - | - | - | 0.0% |
|
tissue_ontology_term_id — Lineage restrictions
ontology.semantics.tissue_ontology_term_id.lineage
|
- | - | - | 0.0% | - |
|
tissue_ontology_term_id — Multi-value ordering
ontology.semantics.tissue_ontology_term_id.sorted_multi
|
- | 100.0% | - | 100.0% | 100.0% |
| Schema reference URL | |||||
|
schema_reference
uns/schema_reference | /attrs/schema_reference
|
- | 100.0% | - | - | - |
| Schema version compatibility | |||||
|
schema_version
uns/schema_version | /attrs/schema_version
|
- | 100.0% | - | 100.0% | 0.0% |
| File structural integrity | |||||
|
AnnData structural integrity
obs
|
- | - | - | - | - |
|
CellID
/col_attrs/CellID
|
100.0% | 100.0% | - | - | - |
| Ensembl gene annotation metadata | |||||
|
ensembl_assembly
uns.ensembl.assembly
|
- | 100.0% | - | - | - |
|
ensembl_database
uns.ensembl.database
|
- | 100.0% | - | - | - |
|
ensembl_release
uns.ensembl.release
|
- | 100.0% | - | - | - |
| Required dataset metadata fields | |||||
|
ensembl_assembly
uns/ensembl_assembly | /attrs/ensembl_assembly
|
0.0% | - | 0.0% | 0.0% | 0.0% |
|
ensembl_database
uns/ensembl_database | /attrs/ensembl_database
|
0.0% | - | 0.0% | 0.0% | 0.0% |
|
ensembl_release
uns/ensembl_release | /attrs/ensembl_release
|
0.0% | - | 0.0% | 0.0% | 0.0% |
|
organism
uns/organism | /attrs/organism
|
0.0% | 100.0% | 0.0% | 100.0% | 0.0% |
|
organism_ontology_term_id
uns/organism_ontology_term_id | /attrs/organism_ontology_term_id
|
0.0% | 100.0% | 0.0% | 100.0% | 0.0% |
|
schema_reference
uns/schema_reference | /attrs/schema_reference
|
0.0% | 100.0% | 0.0% | 100.0% | 14.3% |
|
schema_version
uns/schema_version | /attrs/schema_version
|
0.0% | - | 0.0% | - | 0.0% |
|
title
uns/title | /attrs/title
|
0.0% | 100.0% | 0.0% | 100.0% | 19.6% |
| Var metadata cross-field consistency | |||||
|
feature_name vs var index
var.cross_field.feature_name.index
|
- | - | - | - | - |
|
feature_reference
var.cross_field.feature_reference
|
- | 100.0% | - | 100.0% | 100.0% |
|
var index vs ensembl_release
var.cross_field.index.release
|
- | 100.0% | - | - | - |
| Var index (feature identifiers) | |||||
|
var.index
var.index
|
100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
|
var.index
var.index.format
|
100.0% | 100.0% | 100.0% | 100.0% | 58.9% |
|
var.index
var.index.uniqueness
|
0.0% | 100.0% | 100.0% | 100.0% | 100.0% |
| Gene (var) metadata fields | |||||
|
feature_biotype
var/feature_biotype | /row_attrs/feature_biotype
|
0.0% | 100.0% | 0.0% | 100.0% | 16.1% |
|
feature_chromosome
var/feature_chromosome | /row_attrs/feature_chromosome
|
0.0% | 100.0% | 0.0% | 0.0% | 0.0% |
|
feature_is_filtered
var/feature_is_filtered | /row_attrs/feature_is_filtered
|
0.0% | 100.0% | 0.0% | 100.0% | 16.1% |
|
feature_length
var/feature_length | /row_attrs/feature_length
|
0.0% | 100.0% | 0.0% | 100.0% | 16.1% |
|
feature_name
var/feature_name | /row_attrs/feature_name
|
0.0% | 100.0% | 0.0% | 100.0% | 17.9% |
|
feature_reference
var/feature_reference | /row_attrs/feature_reference
|
0.0% | 100.0% | 0.0% | 100.0% | 16.1% |
|
feature_type
var/feature_type | /row_attrs/feature_type
|
0.0% | 100.0% | 0.0% | 100.0% | 3.6% |
* At the moment, all currently scFAIR-valid projects are imported from CELLxGENE and automatically updated to comply with the scFAIR schema.