Working with Open Targets evidence data 🧐
Where do evidence strings come from?
Source |
Source file |
Generated by |
Count |
Sample |
phewas_catalog |
phewas_catalog-2018-11-28.json.gz |
phewascat |
56,014 |
|
crispr |
crispr-2019-04-08.json.gz |
CRISPR.py |
1,641 |
|
gene2phenotype |
gene2phenotype-2019-05-30.json.gz |
Gene2Phenotype.py |
1,589 |
|
genomics_england |
genomics_england-2018-10-02.json.gz |
GenomicsEnglandPanelApp.py |
10,533 |
|
intogen |
intogen-2018-07-23.json.gz |
IntOGen.py |
2,371 |
|
phenodigm |
phenodigm-2019-05-31.json.gz |
MouseModels.py |
500,462 |
animal_model.json |
progeny |
progeny-2018-07-23.json.gz |
PROGENY.py |
308 |
|
slapenrich |
slapenrich-2018-11-29.json.gz |
SLAPEnrich.py |
74,575 |
|
sysbio |
sysbio-2019-01-31.json.gz |
SystemsBiology.py |
408 |
|
expression_atlas |
atlas-2019-06-04.json.gz |
external |
381,141 |
rna_expression.json |
chembl |
chembl-2019-03-25.json.gz |
external |
384,783 |
known_drug.json |
cancer_gene_census |
cosmic-2019-05-15.json.gz |
external |
59,992 |
somatic_mutation.json |
europepmc |
epmc-2019-05-24.json.gz |
external |
5,438,280 |
literature.json |
eva; eva_somatic |
eva-2019-06-03.json.gz |
external |
89,636; 7,057 |
|
gwas_catalog |
gwas-2019-05-29.json.gz |
external |
157,008 |
genetic_association.json |
reactome |
reactome-2019-05-29.json.gz |
external |
10,083 |
affected_pathway.json |
uniprot; uniprot_literature; uniprot_somatic |
uniprot-2019-05-20.json.gz |
external |
28,743; 4,567; 284 |
|
Key |
Required? |
Details |
sourceID |
Y |
|
access_level |
Y |
|
type |
N |
|
validated_against_schema_version |
N |
|
target |
Y |
required: id, target_type, activity; optional: activity, complex_id, target_name, target_class |
disease |
Y |
required: id |
unique_association_fields |
Y |
Composite key to hash for duplicate detection |
evidence |
Y |
Where most of the variability lives |
Unique association fields
- sample_size
- gwas_panel_resolution
- pubmed_refs
- target
- object
- variant
- study_name
- pvalue
- confidence_interval
- odd_ratio
Additional top-level keys
literature.references.[]
variant.{type, id}
variant2disease
gwas_sample_size
unique_experiment_reference
gwas_panel_resolution
provenance_type
is_associated
resource_score
evidence_codes
date_asserted
gene2variant
functional_consequence
provenance_type
is_associated
evidence_codes
date_asserted