Disease Information

Index of files

• Disease information (EFO): disease_data.json or disease_data.tsv

• Disease tissue location (EFO to Uberon): disease_uberon_location.csv

• EFO to MeSH and UMLS mappings: UMLS_MeSH_disease_mappings.tsv

Disease information (EFO)

Open Targets represent rare and common diseases, phenotypes, measurements using the Experimental Factor Ontology (EFO). The following files contains basic information about the diseases (label, subclass relationships and associated phenotypes from HPO).

Column name	Description
disease_id	disease identifier
disease_label	preferred name for the disease
path_to_root	parent-child relationship defining the classification. There can be several paths
phenotypes	list of phenotypes associated to the disease when available

Disease tissue location (EFO to Uberon)

Filename: disease_uberon_location.csv

Open Targets integrates disease, phenotype and anatomical information using controlled vocabularies organised in ontologies. The Experimental Factor Ontology (EFO) developed and maintained at EMBL-EBI is used extensively in Open Targets to annotate the evidence linking a gene to a disease, GWAS trait or phenotype. EFO contains information about the relevant tissue for a disease too. In this case, tissues are annotated using the Uberon cross-species ontology which covers anatomical structures. The following file is an index of disease and the 'location' of the disease in a tissue.

Column name	Description
disease_id	disease identifier
disease_location_id	UBERON location identifier
disease_location_label	UBERON location corresponding name

For instance, the following rows:

41,EFO_0003760,UBERON_0000955,brain
42,EFO_1000310,UBERON_0000160,intestine

corresponds to

• central nervous system cyst (EFO_0003760) located in the brain
• Juvenile Polyp (EFO_1000310) located in the intestine

You can use the anatomical location feature in your drug repurposing prediction method.

EFO to MeSH and UMLS mappings

source_id destination dest_id dest_label path EFO_1001268 MeSH MeSH:D001019 Aortic Rupture EFO:1001268 (Aortic Rupture) -> MeSH:D001019 (Aortic Rupture)

Column name	Description
source_id	EFO disease identifier, e.g. EFO_1001268
destination	targeted thesaurus e.g. MeSH
dest_id	identifier in the targeted thesaurus, e.g. MeSH:D001019
dest_label	label in the targeted thesaurus, e.g. Aortic Rupture
path	transitive closure from EFO to targeted thesaurus, e.g. EFO:1001268 (Aortic Rupture) -> MeSH:D001019 (Aortic Rupture)