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These files contain the current CTD data release: September 2014.

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. 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 Sep 03 2014 10:26 EDT 13 MB
CTD_chem_gene_ixns.tsv.gz Sep 03 2014 10:26 EDT 13 MB
CTD_chem_gene_ixns.xml.gz Sep 03 2014 10:26 EDT 15 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 Sep 03 2014 10:27 EDT 41 MB
CTD_chem_gene_ixns_structured.xsd Mar 12 2012 08:23 EDT 9 KB

Top ↑ Chemical–gene interaction types

CTD_chem_gene_ixn_types.csv Jul 06 2012 11:10 EDT 4 KB
CTD_chem_gene_ixn_types.obo Feb 27 2012 14:10 EST 20 KB
CTD_chem_gene_ixn_types.tsv Jul 06 2012 11:10 EDT 4 KB
CTD_chem_gene_ixn_types.xml Jul 06 2012 11:10 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 Sep 03 2014 10:24 EDT 55 MB
CTD_chemicals_diseases.tsv.gz Sep 03 2014 10:24 EDT 55 MB
CTD_chemicals_diseases.xml.gz Sep 03 2014 10:24 EDT 66 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 Sep 03 2014 10:18 EDT 72 MB
CTD_chem_go_enriched.tsv.gz Sep 03 2014 10:17 EDT 72 MB
CTD_chem_go_enriched.xml.gz Sep 03 2014 10:17 EDT 95 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 Sep 03 2014 10:18 EDT 4 MB
CTD_chem_pathways_enriched.tsv.gz Sep 03 2014 10:18 EDT 4 MB
CTD_chem_pathways_enriched.xml.gz Sep 03 2014 10:18 EDT 7 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 Sep 03 2014 12:11 EDT 830 MB
CTD_genes_diseases.tsv.gz Sep 03 2014 12:07 EDT 826 MB
CTD_genes_diseases.xml.gz Sep 03 2014 12:03 EDT 964 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 Sep 03 2014 10:18 EDT 413 KB
CTD_genes_pathways.tsv.gz Sep 03 2014 10:18 EDT 413 KB
CTD_genes_pathways.xml.gz Sep 03 2014 10:18 EDT 522 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 Sep 03 2014 10:18 EDT 823 KB
CTD_diseases_pathways.tsv.gz Sep 03 2014 10:18 EDT 819 KB
CTD_diseases_pathways.xml.gz Sep 03 2014 10:18 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 ↑ Chemical vocabulary

CTD_chemicals.csv.gz Sep 03 2014 10:08 EDT 8 MB
CTD_chemicals.tsv.gz Sep 03 2014 10:08 EDT 8 MB
CTD_chemicals.xml.gz Sep 03 2014 10:08 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) New!

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 Sep 03 2014 10:08 EDT 1 MB
CTD_diseases.obo.gz Sep 03 2014 10:08 EDT 1 MB
CTD_diseases.tsv.gz Sep 03 2014 10:08 EDT 1 MB
CTD_diseases.xml.gz Sep 03 2014 10:08 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 Sep 03 2014 10:09 EDT 13 MB
CTD_genes.tsv.gz Sep 03 2014 10:09 EDT 13 MB
CTD_genes.xml.gz Sep 03 2014 10:09 EDT 14 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) New!
  7. PharmGKBIDs ('|'-delimited list) New!
  8. UniprotIDs ('|'-delimited list) New!

See also: Linking to CTD genes.

Top ↑ Pathway vocabulary

CTD_pathways.csv.gz Sep 03 2014 10:07 EDT 4 KB
CTD_pathways.tsv.gz Sep 03 2014 10:07 EDT 4 KB
CTD_pathways.xml.gz Sep 03 2014 10:07 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 Feb 27 2012 14:10 EST 27 KB

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