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These files contain the current CTD data release: November 2024.

For customized data sets, use our Batch Query.

CTD data is provided without warranty, and its use is subject to certain terms. Commercial users should direct licensing-related questions here.

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. Curated Gene–disease associations New!
  7. Aggregate Gene–disease associations
  8. Gene–pathway associations
  9. Disease–pathway associations
  10. Chemical–phenotype interactions
  11. Exposure–study associations
  12. Exposure–event associations
  13. Phenotype (GO)–Disease Inference Networks
  14. Chemical vocabulary
  15. Disease vocabulary (MEDIC)
  16. Anatomy vocabulary
  17. Gene vocabulary
  18. Pathway vocabulary
  19. Exposure Ontology (ExO)

Top ↑ Chemical–gene interactions

CTD_chem_gene_ixns.csv.gz Oct 31 2024 09:58 EDT 36 MB
CTD_chem_gene_ixns.tsv.gz Oct 31 2024 09:58 EDT 36 MB
CTD_chem_gene_ixns.xml.gz Oct 31 2024 09:58 EDT 43 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 Oct 31 2024 09:59 EDT 122 MB
CTD_chem_gene_ixns_structured.xsd May 24 2023 10:24 EDT 9 KB

Top ↑ Chemical–gene interaction types

CTD_chem_gene_ixn_types.csv Feb 12 2024 14:47 EST 4 KB
CTD_chem_gene_ixn_types.obo Feb 12 2024 15:28 EST 20 KB
CTD_chem_gene_ixn_types.tsv Feb 12 2024 14:47 EST 4 KB
CTD_chem_gene_ixn_types.xml Feb 12 2024 14:47 EST 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 Oct 31 2024 09:56 EDT 144 MB
CTD_chemicals_diseases.tsv.gz Oct 31 2024 09:55 EDT 143 MB
CTD_chemicals_diseases.xml.gz Oct 31 2024 09:55 EDT 168 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 Oct 31 2024 09:49 EDT 142 MB
CTD_chem_go_enriched.tsv.gz Oct 31 2024 09:49 EDT 142 MB
CTD_chem_go_enriched.xml.gz Oct 31 2024 09:48 EDT 189 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 Oct 31 2024 09:51 EDT 36 MB
CTD_chem_pathways_enriched.tsv.gz Oct 31 2024 09:50 EDT 36 MB
CTD_chem_pathways_enriched.xml.gz Oct 31 2024 09:50 EDT 50 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 ↑ Curated Gene–disease associations

CTD_curated_genes_diseases.csv.gz Oct 31 2024 09:59 EDT 516 KB
CTD_curated_genes_diseases.tsv.gz Oct 31 2024 09:59 EDT 511 KB
CTD_curated_genes_diseases.xml.gz Oct 31 2024 09:59 EDT 677 KB

Fields:

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

Top ↑ Aggregate Gene–disease associations

CTD_genes_diseases.csv.gz Oct 31 2024 11:34 EDT 2 GB
CTD_genes_diseases.tsv.gz Oct 31 2024 11:26 EDT 2 GB
CTD_genes_diseases.xml.gz Oct 31 2024 11:18 EDT 2 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 Oct 31 2024 09:51 EDT 1 MB
CTD_genes_pathways.tsv.gz Oct 31 2024 09:51 EDT 1 MB
CTD_genes_pathways.xml.gz Oct 31 2024 09:51 EDT 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 Oct 31 2024 09:51 EDT 6 MB
CTD_diseases_pathways.tsv.gz Oct 31 2024 09:51 EDT 6 MB
CTD_diseases_pathways.xml.gz Oct 31 2024 09:51 EDT 7 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 ↑ Chemical–phenotype interactions

CTD_pheno_term_ixns.csv.gz Oct 31 2024 11:37 EDT 19 MB
CTD_pheno_term_ixns.tsv.gz Oct 31 2024 11:37 EDT 19 MB
CTD_pheno_term_ixns.xml.gz Oct 31 2024 11:37 EDT 22 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 Oct 31 2024 11:34 EDT 520 KB
CTD_exposure_studies.tsv.gz Oct 31 2024 11:34 EDT 515 KB
CTD_exposure_studies.xml.gz Oct 31 2024 11:34 EDT 571 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 Oct 31 2024 11:34 EDT 4 MB
CTD_exposure_events.tsv.gz Oct 31 2024 11:34 EDT 3 MB
CTD_exposure_events.xml.gz Oct 31 2024 11:34 EDT 6 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('|'-delimited list)
  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 Oct 31 2024 11:41 EDT 44 MB
CTD_Phenotype-Disease_biological_process_associations.tsv.gz Oct 31 2024 11:40 EDT 43 MB
CTD_Phenotype-Disease_biological_process_associations.xml.gz Oct 31 2024 11:40 EDT 54 MB
CTD_Phenotype-Disease_cellular_component_associations.csv.gz Oct 31 2024 11:41 EDT 2 MB
CTD_Phenotype-Disease_cellular_component_associations.tsv.gz Oct 31 2024 11:41 EDT 2 MB
CTD_Phenotype-Disease_cellular_component_associations.xml.gz Oct 31 2024 11:41 EDT 3 MB
CTD_Phenotype-Disease_molecular_function_associations.csv.gz Oct 31 2024 11:41 EDT 4 MB
CTD_Phenotype-Disease_molecular_function_associations.tsv.gz Oct 31 2024 11:41 EDT 4 MB
CTD_Phenotype-Disease_molecular_function_associations.xml.gz Oct 31 2024 11:41 EDT 6 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 Oct 31 2024 09:42 EDT 9 MB
CTD_chemicals.tsv.gz Oct 31 2024 09:42 EDT 9 MB
CTD_chemicals.xml.gz Oct 31 2024 09:42 EDT 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)

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 Oct 31 2024 09:42 EDT 1 MB
CTD_diseases.obo.gz Oct 31 2024 09:42 EDT 1 MB
CTD_diseases.tsv.gz Oct 31 2024 09:42 EDT 1 MB
CTD_diseases.xml.gz Oct 31 2024 09:42 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 ↑ Anatomy vocabulary

CTD_anatomy.csv.gz Oct 31 2024 11:41 EDT 319 KB
CTD_anatomy.tsv.gz Oct 31 2024 11:41 EDT 316 KB
CTD_anatomy.xml.gz Oct 31 2024 11:41 EDT 343 KB

Fields:

  1. AnatomyName
  2. AnatomyID (MeSH identifier)
  3. Definition
  4. AltAnatomyIDs (alternative identifiers; '|'-delimited list)
  5. ParentIDs (identifiers of the parent terms; '|'-delimited list)
  6. TreeNumbers (identifiers of the anatomical term's nodes; '|'-delimited list)
  7. ParentTreeNumbers (identifiers of the parent nodes; '|'-delimited list)
  8. Synonyms ('|'-delimited list)
  9. ExternalSynonyms ('|'-delimited list)

CTD's anatomy vocabulary is a modified subset of descriptors from the “Anatomy” [A] branch of the U.S. National Library of Medicine's Medical Subject Headings (MeSH®), manually integrated by CTD curators with the Uberon Multi-Species Anatomy Ontology (UBERON®), and the Cell Ontology (CL®). UBERON and CL terms are cross-referenced to the MeSH terms as synonyms to the terms, and via direct, accession-based cross-reference hyperlinks. Each anatomical term occurs in one or more nodes of this hierarchical vocabulary.

See also: Linking to CTD anatomical terms.

Top ↑ Gene vocabulary

CTD_genes.csv.gz Oct 31 2024 09:45 EDT 77 MB
CTD_genes.tsv.gz Oct 31 2024 09:44 EDT 77 MB
CTD_genes.xml.gz Oct 31 2024 09:44 EDT 79 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 Oct 31 2024 09:42 EDT 41 KB
CTD_pathways.tsv.gz Oct 31 2024 09:42 EDT 41 KB
CTD_pathways.xml.gz Oct 31 2024 09:42 EDT 46 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 24 2023 10:24 EDT 59 KB

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