Data Packages
Curated third party data packages
Open Targets Safety Liabilities
This data pack contains manually curated experimental data and insights from publications and other well-known sources of target safety, extracted from the Open Targets Database.
Documentation https://platform-docs.opentargets.org/target/safety
Concepts
Gene
Safety Liabilities
Relationships
(Gene)- Associated with-> Safety Liability
Open Targets Drug Annotation
Drug and drug annotation data extracted from curated data in the Open Targets platform. This data package incorporates basic molecule information, clinical trial and indication details associated with diseases, and mechanism of action annotation associated with genes.
Documentation https://platform-docs.opentargets.org/drug
Concepts
Gene
Drug
Disease
Relationships
(Gene) - Acts on -> (Drug)
(Drug) -is approved for -> (Disease)
(Drug) -has clinical precedence for -> (Disease)
Open Target Genetics
This data package contains information extracted from Open Targets Genetics (OTG) to enhance your graph with GWAS semantics and observations. Contents of this package provides an evidence-based connection between known GWAS traits and their relatedness to variants and genes. Assignment of variants to their lead and/or causal genes is achieved through OTG Locus2Gene machine learning model.
Documentation https://platform-docs.opentargets.org/evidence#open-targets-genetics
Concepts
Trait
Variant
Variant Association
Relationships
(Variant Association) - protective against -> (Trait)
(Variant Association) - risk of trait -> (Trait)
(Variant Association) -of trait -> (Trait)
(Variant Association)-when variant is -> (Trait)
(Variant Association)-increased gene product level ->(Trait)
(Variant Association)-decreased gene product level of -> (Trait)
(Variant Association) -altered gene product level of -> (Trait)
(Variant Association) -has association -> (Trait)
Clinical Trials - Intervention Studies
A subset of the clinical trials database that captures all intervention studies.
Documentation https://clinicaltrials.gov/about-site/about-ctg
Concepts
Clinical Trial
Relationships
(Clinical Trial) - Studies Condition -> (Disease)
Alliance Genome- Animal Models of Disease
This data package provides information in regards to the animal models available for various diseases and their associated genotype.
Documentation https://www.informatics.jax.org/
Concepts
Allele
Genotype
Relationships
(Genotype) - has allele -> (Allele)
(Genotype) - is model of -> (Disease)
Alliance - Disease Gene Associations
A consortium of 7 model organism databases (MODs) and the Gene Ontology (GO) Consortium whose goal is to provide an integrated view of their data to all biologists, clinicians and other interested parties. This data package contains edges between Genes and Diseases. It will require you to have loaded in EFO and MONDO ontologies.
Documentation https://www.alliancegenome.org/downloads
Concepts
There are no concepts associated with this relationship
Reactome Events
A data package containing partial information extracted from Reactome. Reactome Events and adjacent nodes with the label 'Event', 'Pathway', 'Drug', 'GO', 'Gene', and 'Disease' labels were extracted. Diseases were mapped from DOID to EFO, Drugs were mapped from Reactome to ChEMBL, and Ensembl genes mapping were external ontologies used. Graph db dump: reactome neo4j 4.3.6. Neo4j dump was restored from the dump and migrated to be compatible with new range instead of index.
Documentation https://reactome.org/
Concepts
Event
Pathway
Drug
Biological Process
Cellular Component
Gene
Disease
Relationship
(Event)-in compartment -> (cellular component)
(Event)- relates to GO process -> (Biological Process)
(Pathway)- has encapsulated event ->(Pathway)
(Event) - has event-> (Event)
(Event) - uses drug as input -> (Drug)
(Event)- related to normal pathway-> (Event)
(Event) -produces drug-> (Drug)
(Event)- preceding event -> (Event)
(Event) - has reversible reaction -> (Event)
(Event) - found in disease -> (Disease)
(Gene)- involved in -> (Biological Process)
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