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These files contain the current CTD data release: November 2018.

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. Phenotype–chemical interactions
  10. Exposure–study associations
  11. Exposure–event associations
  12. Phenotype (GO)–Disease Inference NetworksNew!
  13. Chemical vocabulary
  14. Disease vocabulary (MEDIC)
  15. Gene vocabulary
  16. Pathway vocabulary
  17. Exposure Ontology (ExO)

Top ↑ Chemical–gene interactions

CTD_chem_gene_ixns.csv.gz Nov 08 2018 14:29 EST 22 MB
CTD_chem_gene_ixns.tsv.gz Nov 08 2018 14:29 EST 22 MB
CTD_chem_gene_ixns.xml.gz Nov 08 2018 14:29 EST 26 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 Nov 08 2018 14:30 EST 74 MB
CTD_chem_gene_ixns_structured.xsd May 15 2017 11:50 EDT 9 KB

Top ↑ Chemical–gene interaction types

CTD_chem_gene_ixn_types.csv Aug 12 2016 14:59 EDT 4 KB
CTD_chem_gene_ixn_types.obo Aug 12 2016 15:04 EDT 20 KB
CTD_chem_gene_ixn_types.tsv Aug 12 2016 15:04 EDT 4 KB
CTD_chem_gene_ixn_types.xml Aug 12 2016 14:59 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 Nov 08 2018 14:28 EST 95 MB
CTD_chemicals_diseases.tsv.gz Nov 08 2018 14:27 EST 94 MB
CTD_chemicals_diseases.xml.gz Nov 08 2018 14:27 EST 112 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 Nov 08 2018 14:22 EST 112 MB
CTD_chem_go_enriched.tsv.gz Nov 08 2018 14:21 EST 112 MB
CTD_chem_go_enriched.xml.gz Nov 08 2018 14:21 EST 149 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 Nov 08 2018 14:23 EST 27 MB
CTD_chem_pathways_enriched.tsv.gz Nov 08 2018 14:23 EST 27 MB
CTD_chem_pathways_enriched.xml.gz Nov 08 2018 14:23 EST 37 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 Nov 08 2018 15:50 EST 1 GB
CTD_genes_diseases.tsv.gz Nov 08 2018 15:45 EST 1 GB
CTD_genes_diseases.xml.gz Nov 08 2018 15:39 EST 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 Nov 08 2018 14:23 EST 1 MB
CTD_genes_pathways.tsv.gz Nov 08 2018 14:23 EST 1 MB
CTD_genes_pathways.xml.gz Nov 08 2018 14:23 EST 1 MB

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 Nov 08 2018 14:23 EST 5 MB
CTD_diseases_pathways.tsv.gz Nov 08 2018 14:23 EST 5 MB
CTD_diseases_pathways.xml.gz Nov 08 2018 14:23 EST 6 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 ↑ Phenotype–chemical interactions

CTD_pheno_term_ixns.csv.gz Nov 08 2018 15:56 EST 8 MB
CTD_pheno_term_ixns.tsv.gz Nov 08 2018 15:56 EST 8 MB
CTD_pheno_term_ixns.xml.gz Nov 08 2018 15:56 EST 9 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CASRN (CAS Registry Number, if available)
  4. PhenotypeName
  5. PhenotypeID (GO identifier)
  6. CoMentionedTerms ('|'-delimited list ) entries formatted as Name^Id^Source
  7. Organism (scientific name)
  8. OrganismID (NCBI Taxonomy identifier)
  9. Interaction
  10. InteractionActions ('|'-delimited list)
  11. AnatomyTerms (MeSH term; '|'-delimited list) entries formatted as SequenceOrder^Name^Id
  12. InferenceGeneSymbols ('|'-delimited list) entries formatted as Name^Id
  13. PubMedIDs ('|'-delimited list)

Top ↑ Exposure–study associations

CTD_exposure_studies.csv.gz Nov 08 2018 15:51 EST 316 KB
CTD_exposure_studies.tsv.gz Nov 08 2018 15:51 EST 313 KB
CTD_exposure_studies.xml.gz Nov 08 2018 15:51 EST 348 KB

Fields:

  1. Reference
  2. StudyFactors ( | delimited list)
  3. ExposureStressors ( | delimited list ) entries formatted as Name^Id^Source
  4. Receptors ( | delimited list) formatted as Name^Id^Source^description
  5. StudyCountries (| delimited list)
  6. Mediums (| delimited list)
  7. ExposureMarkers ( | delimited list) entries formatted as Name^Id^Source
  8. Diseases ( | delimited list) entries formatted as Name^Id^Source
  9. Phenotypes ( | delimited list) entries formatted as Name^Id^Source
  10. AuthorSummary

Top ↑ Exposure–event associations

CTD_exposure_events.csv.gz Nov 08 2018 15:50 EST 2 MB
CTD_exposure_events.tsv.gz Nov 08 2018 15:50 EST 2 MB
CTD_exposure_events.xml.gz Nov 08 2018 15:50 EST 3 MB

Fields:

  1. ExposureStressorName
  2. ExposureStressorID (MeSH identifier)
  3. StressorSourceCategory ('|'-delimited list)
  4. StressorSourceDetails
  5. NumberOfStressorSamples
  6. StressorNotes
  7. NumberOfReceptors
  8. Receptors
  9. ReceptorNotes
  10. SmokingStatus ('|'-delimited list)
  11. Age
  12. AgeUnitsOfMeasurement
  13. AgeQualifier
  14. Sex
  15. Race ('|'-delimited list)
  16. Methods ('|'-delimited list)
  17. DetectionLimit
  18. DetectionLimitUnitsOfMeasurement
  19. DetectionFrequency
  20. Medium
  21. ExposureMarker
  22. ExposureMarkerID (MeSH or NCBI Gene identifier)
  23. MarkerLevel
  24. MarkerUnitsOfMeasurement
  25. MarkerMeasurementStatistic
  26. AssayNotes
  27. StudyCountries ('|'-delimited list)
  28. StateOrProvince ('|'-delimited list)
  29. City,Town,Region,Area ('|'-delimited list)
  30. ExposureEventNotes
  31. OutcomeRelationship
  32. DiseaseName
  33. DiseaseID (MeSH or OMIM identifier)
  34. PhenotypeName
  35. PhenotypeID (GO identifier)
  36. PhenotypeActionDegreeType
  37. Anatomy (MeSH term; '|'-delimited list)
  38. ExposureOutcomeNotes
  39. Reference
  40. AssociatedStudyTitles ('|'-delimited list)
  41. EnrollmentStartYear
  42. EnrollmentEndYear
  43. StudyFactors ('|'-delimited list)

Top ↑ Phenotype (GO)–Disease Inference Networks

CTD_Phenotype-Disease_biological_process_associations.csv.gz Nov 08 2018 16:35 EST 25 MB
CTD_Phenotype-Disease_biological_process_associations.tsv.gz Nov 08 2018 16:35 EST 25 MB
CTD_Phenotype-Disease_biological_process_associations.xml.gz Nov 08 2018 16:35 EST 32 MB
CTD_Phenotype-Disease_cellular_component_associations.csv.gz Nov 08 2018 16:35 EST 2 MB
CTD_Phenotype-Disease_cellular_component_associations.tsv.gz Nov 08 2018 16:35 EST 2 MB
CTD_Phenotype-Disease_cellular_component_associations.xml.gz Nov 08 2018 16:35 EST 2 MB
CTD_Phenotype-Disease_molecular_function_associations.csv.gz Nov 08 2018 16:35 EST 3 MB
CTD_Phenotype-Disease_molecular_function_associations.tsv.gz Nov 08 2018 16:35 EST 3 MB
CTD_Phenotype-Disease_molecular_function_associations.xml.gz Nov 08 2018 16:35 EST 3 MB

Fields:

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

Top ↑ Chemical vocabulary

CTD_chemicals.csv.gz Nov 08 2018 14:13 EST 9 MB
CTD_chemicals.tsv.gz Nov 08 2018 14:13 EST 8 MB
CTD_chemicals.xml.gz Nov 08 2018 14:13 EST 10 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 Nov 08 2018 14:13 EST 1 MB
CTD_diseases.obo.gz Nov 08 2018 14:13 EST 1 MB
CTD_diseases.tsv.gz Nov 08 2018 14:13 EST 1 MB
CTD_diseases.xml.gz Nov 08 2018 14:13 EST 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 Nov 08 2018 14:15 EST 31 MB
CTD_genes.tsv.gz Nov 08 2018 14:15 EST 31 MB
CTD_genes.xml.gz Nov 08 2018 14:15 EST 32 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 Nov 08 2018 14:12 EST 37 KB
CTD_pathways.tsv.gz Nov 08 2018 14:12 EST 37 KB
CTD_pathways.xml.gz Nov 08 2018 14:12 EST 41 KB

Fields:

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

See also: Linking to CTD pathways.

Top ↑ Exposure Ontology (ExO)

CTD_exposure_ontology.obo May 15 2017 11:50 EDT 88 KB

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