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These files contain the current CTD data release: June 2016.

For customized data sets, use our Batch Query.

CTD data is provided without warranty, and its use is subject to certain terms.

Contents

  1. Chemical–gene interactions
  2. Chemical–gene interaction types
  3. Chemical–disease associations
  4. Chemical–GO enriched associations
  5. Chemical–pathway enriched associations
  6. Gene–disease associations
  7. Gene–pathway associations
  8. Disease–pathway associations
  9. Exposure–event associations New!
  10. GO–Disease–Gene Inference Networks New!
  11. Chemical vocabulary
  12. Disease vocabulary (MEDIC)
  13. Gene vocabulary
  14. Pathway vocabulary
  15. Exposure Ontology (ExO)

Top ↑ Chemical–gene interactions

CTD_chem_gene_ixns.csv.gz Jun 28 2016 17:27 EDT 17 MB
CTD_chem_gene_ixns.tsv.gz Jun 28 2016 17:27 EDT 17 MB
CTD_chem_gene_ixns.xml.gz Jun 28 2016 17:26 EDT 20 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number, if available)
  4. GeneSymbol
  5. GeneID (NCBI Gene identifier)
  6. GeneForms ('|'-delimited list)
  7. Organism (scientific name)
  8. OrganismID (NCBI Taxonomy identifier)
  9. Interaction
  10. InteractionActions ('|'-delimited list)
  11. PubMedIDs ('|'-delimited list)

Structured XML:

CTD_chem_gene_ixns_structured.xml.gz Jun 28 2016 17:27 EDT 56 MB
CTD_chem_gene_ixns_structured.xsd Apr 06 2015 11:42 EDT 9 KB

Top ↑ Chemical–gene interaction types

CTD_chem_gene_ixn_types.csv Jun 07 2016 13:59 EDT 4 KB
CTD_chem_gene_ixn_types.obo Jun 07 2016 13:59 EDT 20 KB
CTD_chem_gene_ixn_types.tsv Jun 07 2016 13:59 EDT 4 KB
CTD_chem_gene_ixn_types.xml Jun 07 2016 13:59 EDT 9 KB

Fields (non-OBO):

  1. TypeName
  2. Code
  3. Description
  4. ParentCode

CTD curates chemical–gene and –protein interactions in vertebrates and invertebrates using this hierarchical vocabulary of interaction types. More…

Top ↑ Chemical–disease associations

CTD_chemicals_diseases.csv.gz Jun 28 2016 17:25 EDT 73 MB
CTD_chemicals_diseases.tsv.gz Jun 28 2016 17:24 EDT 73 MB
CTD_chemicals_diseases.xml.gz Jun 28 2016 17:24 EDT 86 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number, if available)
  4. DiseaseName
  5. DiseaseID (MeSH or OMIM identifier)
  6. DirectEvidence ('|'-delimited list)
  7. InferenceGeneSymbol
  8. InferenceScore
  9. OmimIDs ('|'-delimited list)
  10. PubMedIDs ('|'-delimited list)

Top ↑ Chemical–GO enriched associations

CTD_chem_go_enriched.csv.gz Jun 28 2016 17:16 EDT 96 MB
CTD_chem_go_enriched.tsv.gz Jun 28 2016 17:15 EDT 96 MB
CTD_chem_go_enriched.xml.gz Jun 28 2016 17:15 EDT 127 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number, if available)
  4. Ontology
  5. GOTermName
  6. GOTermID
  7. HighestGOLevel
  8. PValue
  9. CorrectedPValue
  10. TargetMatchQty
  11. TargetTotalQty
  12. BackgroundMatchQty
  13. BackgroundTotalQty

To provide insight into the biological properties that may be affected by chemicals, CTD calculates which GO terms are statistically enriched among the genes/proteins that interact with each chemical or its descendants. More…

Top ↑ Chemical–pathway enriched associations

CTD_chem_pathways_enriched.csv.gz Jun 28 2016 17:17 EDT 5 MB
CTD_chem_pathways_enriched.tsv.gz Jun 28 2016 17:17 EDT 5 MB
CTD_chem_pathways_enriched.xml.gz Jun 28 2016 17:16 EDT 8 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number, if available)
  4. PathwayName
  5. PathwayID (KEGG or REACTOME identifier)
  6. PValue
  7. CorrectedPValue
  8. TargetMatchQty
  9. TargetTotalQty
  10. BackgroundMatchQty
  11. BackgroundTotalQty

Top ↑ Gene–disease associations

CTD_genes_diseases.csv.gz Jun 28 2016 20:00 EDT 1 GB
CTD_genes_diseases.tsv.gz Jun 28 2016 19:55 EDT 1 GB
CTD_genes_diseases.xml.gz Jun 28 2016 19:50 EDT 1 GB

Fields:

  1. GeneSymbol
  2. GeneID (NCBI Gene identifier)
  3. DiseaseName
  4. DiseaseID (MeSH or OMIM identifier)
  5. DirectEvidence ('|'-delimited list)
  6. InferenceChemicalName
  7. InferenceScore
  8. OmimIDs ('|'-delimited list)
  9. PubMedIDs ('|'-delimited list)

Top ↑ Gene–pathway associations

CTD_genes_pathways.csv.gz Jun 28 2016 17:17 EDT 414 KB
CTD_genes_pathways.tsv.gz Jun 28 2016 17:17 EDT 414 KB
CTD_genes_pathways.xml.gz Jun 28 2016 17:17 EDT 523 KB

Fields:

  1. GeneSymbol
  2. GeneID (NCBI Gene identifier)
  3. PathwayName
  4. PathwayID (KEGG or REACTOME identifier)

Top ↑ Disease–pathway associations

CTD_diseases_pathways.csv.gz Jun 28 2016 17:17 EDT 910 KB
CTD_diseases_pathways.tsv.gz Jun 28 2016 17:17 EDT 905 KB
CTD_diseases_pathways.xml.gz Jun 28 2016 17:17 EDT 1 MB

Fields:

  1. DiseaseName
  2. DiseaseID (MeSH or OMIM identifier)
  3. PathwayName
  4. PathwayID (KEGG or REACTOME identifier)
  5. InferenceGeneSymbol (a gene via which the association is inferred)

Top ↑ Exposure–event associations New!

CTD_exposure_events.csv.gz Jun 28 2016 20:00 EDT 2 MB
CTD_exposure_events.tsv.gz Jun 28 2016 20:00 EDT 2 MB
CTD_exposure_events.xml.gz Jun 28 2016 20:00 EDT 4 MB

Fields:

  1. StressorAgentName
  2. StressorAgentID (MeSH identifier)
  3. NumberOfReceptors
  4. ReceptorDescription
  5. ReceptorNotes
  6. StudyLocation
  7. AssayMediums
  8. AssayedTermName
  9. AssayedTermID (MeSH or NCBI Gene identifier)
  10. AssayLevel
  11. AssayUnitsOfMeasurement
  12. AssayMeasurementStatistic
  13. AssayNotes
  14. OutcomeRelationship
  15. DiseaseName
  16. DiseaseID (MeSH or OMIM identifier)
  17. PhenotypeName
  18. PhenotypeID (GO identifier)
  19. Reference

Top ↑ GO–Disease–Gene Inference Networks New!

CTD_Disease-GO_biological_process_associations.csv.gz Jun 28 2016 20:05 EDT 7 MB
CTD_Disease-GO_biological_process_associations.tsv.gz Jun 28 2016 20:05 EDT 7 MB
CTD_Disease-GO_biological_process_associations.xml.gz Jun 28 2016 20:05 EDT 9 MB
CTD_Disease-GO_cellular_component_associations.csv.gz Jun 28 2016 20:06 EDT 1 MB
CTD_Disease-GO_cellular_component_associations.tsv.gz Jun 28 2016 20:06 EDT 1 MB
CTD_Disease-GO_cellular_component_associations.xml.gz Jun 28 2016 20:06 EDT 2 MB
CTD_Disease-GO_molecular_function_associations.csv.gz Jun 28 2016 20:07 EDT 1 MB
CTD_Disease-GO_molecular_function_associations.tsv.gz Jun 28 2016 20:07 EDT 1 MB
CTD_Disease-GO_molecular_function_associations.xml.gz Jun 28 2016 20:07 EDT 2 MB

Fields:

  1. DiseaseName
  2. DiseaseID (MeSH or OMIM identifier)
  3. GOName
  4. GOID (GO identifier)
  5. InferenceGeneQty
  6. InferenceGeneSymbols ('|'-delimited list)

Top ↑ Chemical vocabulary

CTD_chemicals.csv.gz Jun 28 2016 17:06 EDT 8 MB
CTD_chemicals.tsv.gz Jun 28 2016 17:06 EDT 8 MB
CTD_chemicals.xml.gz Jun 28 2016 17:06 EDT 9 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number, if available)
  4. Definition
  5. ParentIDs (identifiers of the parent terms; '|'-delimited list)
  6. TreeNumbers (identifiers of the chemical's nodes; '|'-delimited list)
  7. ParentTreeNumbers (identifiers of the parent nodes; '|'-delimited list)
  8. Synonyms ('|'-delimited list)
  9. DrugBankIDs ('|'-delimited list)

Each chemical occurs in one or more nodes of this hierarchical vocabulary. More…

See also: Linking to CTD chemicals.

Top ↑ Disease vocabulary (MEDIC)

CTD_diseases.csv.gz Jun 28 2016 17:06 EDT 1 MB
CTD_diseases.obo.gz Jun 28 2016 17:06 EDT 1 MB
CTD_diseases.tsv.gz Jun 28 2016 17:06 EDT 1 MB
CTD_diseases.xml.gz Jun 28 2016 17:06 EDT 1 MB

Fields (non-OBO):

  1. DiseaseName
  2. DiseaseID (MeSH or OMIM identifier)
  3. Definition
  4. AltDiseaseIDs (alternative identifiers; '|'-delimited list)
  5. ParentIDs (identifiers of the parent terms; '|'-delimited list)
  6. TreeNumbers (identifiers of the disease's nodes; '|'-delimited list)
  7. ParentTreeNumbers (identifiers of the parent nodes; '|'-delimited list)
  8. Synonyms ('|'-delimited list)
  9. SlimMappings (MEDIC-Slim mappings; '|'-delimited list)

CTD's MEDIC disease vocabulary is a modified subset of descriptors from the “Diseases” [C] branch of the U.S. National Library of Medicine's Medical Subject Headings (MeSH®), combined with genetic disorders from the Online Mendelian Inheritance in Man® (OMIM®) database. Each disease occurs in one or more nodes of this hierarchical vocabulary. More…

MEDIC-Slim classifies MEDIC diseases into high-level categories.

See also: Linking to CTD diseases.

Top ↑ Gene vocabulary

CTD_genes.csv.gz Jun 28 2016 17:08 EDT 22 MB
CTD_genes.tsv.gz Jun 28 2016 17:08 EDT 22 MB
CTD_genes.xml.gz Jun 28 2016 17:07 EDT 23 MB

Fields:

  1. GeneSymbol
  2. GeneName
  3. GeneID (NCBI Gene identifier)
  4. AltGeneIDs (alternative NCBI Gene identifiers; '|'-delimited list)
  5. Synonyms ('|'-delimited list)
  6. BioGRIDIDs ('|'-delimited list)
  7. PharmGKBIDs ('|'-delimited list)
  8. UniprotIDs ('|'-delimited list)

See also: Linking to CTD genes.

Top ↑ Pathway vocabulary

CTD_pathways.csv.gz Jun 28 2016 17:05 EDT 4 KB
CTD_pathways.tsv.gz Jun 28 2016 17:05 EDT 4 KB
CTD_pathways.xml.gz Jun 28 2016 17:05 EDT 4 KB

Fields:

  1. PathwayName
  2. PathwayID (OMIM or REACTOME identifier)

See also: Linking to CTD pathways.

Top ↑ Exposure Ontology (ExO)

CTD_exposure_ontology.obo Jun 07 2016 13:59 EDT 27 KB

The draft Exposure Ontology (ExO) will provide exposure context for CTD data. More…