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CTD releases new data each month. Use of CTD data is subject to certain terms.

For customized data sets, use the Batch Query.

Index

  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. Chemical vocabulary
  10. Disease vocabulary (MEDIC)
  11. Gene vocabulary
  12. Pathway vocabulary
  13. Exposure Ontology (ExO)

Top Chemical–gene interactions

CTD_chem_gene_ixns.csv.gz May 07 2012 07:39 7 MB
CTD_chem_gene_ixns.tsv.gz May 07 2012 07:39 7 MB
CTD_chem_gene_ixns.xml.gz May 07 2012 07:39 8 MB

Fields:

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

Structured XML:

CTD_chem_gene_ixns_structured.xml.gz May 07 2012 07:39 21 MB
CTD_chem_gene_ixns_structured.xsd Mar 12 2012 08:23 9 KB

Top Chemical–gene interaction types

CTD_chem_gene_ixn_types.csv May 07 2012 07:29 4 KB
CTD_chem_gene_ixn_types.obo Feb 27 2012 14:10 20 KB
CTD_chem_gene_ixn_types.tsv May 07 2012 07:29 4 KB
CTD_chem_gene_ixn_types.xml May 07 2012 07:29 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. To navigate this hierarchy, use the ParentCode. More…

Top Chemical–disease associations

CTD_chemicals_diseases.csv.gz May 07 2012 07:38 27 MB
CTD_chemicals_diseases.tsv.gz May 07 2012 07:38 27 MB
CTD_chemicals_diseases.xml.gz May 07 2012 07:38 32 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number)
  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 May 07 2012 07:35 42 MB
CTD_chem_go_enriched.tsv.gz May 07 2012 07:34 42 MB
CTD_chem_go_enriched.xml.gz May 07 2012 07:34 57 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number)
  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 one of its descendants. More…

Top Chemical–pathway enriched associations

CTD_chem_pathways_enriched.csv.gz May 07 2012 07:35 3 MB
CTD_chem_pathways_enriched.tsv.gz May 07 2012 07:35 3 MB
CTD_chem_pathways_enriched.xml.gz May 07 2012 07:35 5 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number)
  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 May 07 2012 11:51 468 MB
CTD_genes_diseases.tsv.gz May 07 2012 11:49 465 MB
CTD_genes_diseases.xml.gz May 07 2012 11:46 543 MB

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 May 07 2012 07:35 407 KB
CTD_genes_pathways.tsv.gz May 07 2012 07:35 407 KB
CTD_genes_pathways.xml.gz May 07 2012 07:35 516 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 May 07 2012 07:35 574 KB
CTD_diseases_pathways.tsv.gz May 07 2012 07:35 571 KB
CTD_diseases_pathways.xml.gz May 07 2012 07:35 800 KB

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 vocabulary

CTD_chemicals.csv.gz May 07 2012 07:30 7 MB
CTD_chemicals.tsv.gz May 07 2012 07:30 7 MB
CTD_chemicals.xml.gz May 07 2012 07:30 8 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier; use to link to CTD chemical pages)
  3. CasRN (CAS Registry Number)
  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 at least one node of the hierarchy. To navigate the hierarchy, use ParentIDs or ParentTreeNumbers. More…

Top Disease vocabulary (MEDIC)

CTD_diseases.csv.gz May 07 2012 07:30 1 MB
CTD_diseases.obo.gz May 07 2012 07:30 1 MB
CTD_diseases.tsv.gz May 07 2012 07:30 1 MB
CTD_diseases.xml.gz May 07 2012 07:30 1 MB

Fields (non-OBO):

  1. DiseaseName
  2. DiseaseID (MeSH or OMIM identifier; use for linking to CTD disease pages)
  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)

CTD's “MEDIC” disease vocabulary is a modified subset of descriptors from the “Diseases” category of the U.S. National Library of Medicine (NLM) Medical Subject Headings (MeSH®), combined with genetic disorders from the Online Mendelian Inheritance in Man® (OMIM®) database.

Each disease in the MEDIC vocabulary occurs in at least one node of the hierarchy. To navigate the hierarchy, use ParentIDs or ParentTreeNumbers. More…

Top Gene vocabulary

CTD_genes.csv.gz May 07 2012 07:31 5 MB
CTD_genes.tsv.gz May 07 2012 07:31 5 MB
CTD_genes.xml.gz May 07 2012 07:31 5 MB

Fields:

  1. GeneSymbol
  2. GeneName
  3. GeneID (NCBI Gene identifier; use for linking to CTD gene pages)
  4. AltGeneIDs (alternative NCBI Gene identifiers; '|'-delimited list)
  5. Synonyms ('|'-delimited list)

Top Pathway vocabulary

CTD_pathways.csv.gz May 07 2012 07:29 5 KB
CTD_pathways.tsv.gz May 07 2012 07:29 5 KB
CTD_pathways.xml.gz May 07 2012 07:29 5 KB

Fields:

  1. PathwayName
  2. PathwayID (OMIM or REACTOME identifier; use for linking to CTD pathway pages)

Top Exposure Ontology (ExO)

CTD_exposure_ontology.obo Feb 27 2012 14:10 27 KB

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