ot-ev

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 https://github.com/ebi-uniprot/open-targets-core-db	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