Illuminating how chemicals affect human health.
Comparative Toxicogenomics Database

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

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)

Top ↑ Chemical–gene interaction types

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

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

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

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

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

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

Fields:

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

Top ↑ Disease–pathway associations

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

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

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

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

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

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)

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

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

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

Fields:

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

See also: Linking to CTD pathways.

Top ↑ Exposure Ontology (ExO)

Exposure Ontology

The Exposure Ontology (ExO) provides exposure context for CTD data. More…