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These files contain the current CTD data release: May 2013.

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 May 06 2013 10:55 EDT 11 MB
CTD_chem_gene_ixns.tsv.gz May 06 2013 10:55 EDT 11 MB
CTD_chem_gene_ixns.xml.gz May 06 2013 10:54 EDT 13 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  3. CasRN (CAS Registry Number)
  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 May 06 2013 10:55 EDT 34 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 May 06 2013 10:53 EDT 46 MB
CTD_chemicals_diseases.tsv.gz May 06 2013 10:53 EDT 46 MB
CTD_chemicals_diseases.xml.gz May 06 2013 10:53 EDT 55 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 06 2013 10:48 EDT 60 MB
CTD_chem_go_enriched.tsv.gz May 06 2013 10:47 EDT 59 MB
CTD_chem_go_enriched.xml.gz May 06 2013 10:47 EDT 79 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 its descendants. More…

Top ↑ Chemical–pathway enriched associations

CTD_chem_pathways_enriched.csv.gz May 06 2013 10:48 EDT 3 MB
CTD_chem_pathways_enriched.tsv.gz May 06 2013 10:48 EDT 3 MB
CTD_chem_pathways_enriched.xml.gz May 06 2013 10:48 EDT 6 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 06 2013 12:19 EDT 672 MB
CTD_genes_diseases.tsv.gz May 06 2013 12:16 EDT 668 MB
CTD_genes_diseases.xml.gz May 06 2013 12:13 EDT 778 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 06 2013 10:48 EDT 417 KB
CTD_genes_pathways.tsv.gz May 06 2013 10:48 EDT 417 KB
CTD_genes_pathways.xml.gz May 06 2013 10:48 EDT 527 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 06 2013 10:48 EDT 737 KB
CTD_diseases_pathways.tsv.gz May 06 2013 10:48 EDT 733 KB
CTD_diseases_pathways.xml.gz May 06 2013 10:48 EDT 1011 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 06 2013 10:41 EDT 8 MB
CTD_chemicals.tsv.gz May 06 2013 10:41 EDT 8 MB
CTD_chemicals.xml.gz May 06 2013 10:40 EDT 9 MB

Fields:

  1. ChemicalName
  2. ChemicalID (MeSH identifier)
  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 one or more nodes of this hierarchical vocabulary. More…

See also: Linking to CTD chemicals.

Top ↑ Disease vocabulary (MEDIC)

CTD_diseases.csv.gz May 06 2013 10:41 EDT 1 MB
CTD_diseases.obo.gz May 06 2013 10:41 EDT 1 MB
CTD_diseases.tsv.gz May 06 2013 10:41 EDT 1 MB
CTD_diseases.xml.gz May 06 2013 10:41 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) New!

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 is a high-level set of terms that classifies CTD’s MEDIC diseases into 36 categories.

See also: Linking to CTD diseases.

Top ↑ Gene vocabulary

CTD_genes.csv.gz May 06 2013 10:41 EDT 6 MB
CTD_genes.tsv.gz May 06 2013 10:41 EDT 6 MB
CTD_genes.xml.gz May 06 2013 10:41 EDT 7 MB

Fields:

  1. GeneSymbol
  2. GeneName
  3. GeneID (NCBI Gene identifier)
  4. AltGeneIDs (alternative NCBI Gene identifiers; '|'-delimited list)
  5. Synonyms ('|'-delimited list)

See also: Linking to CTD genes.

Top ↑ Pathway vocabulary

CTD_pathways.csv.gz May 06 2013 10:40 EDT 4 KB
CTD_pathways.tsv.gz May 06 2013 10:40 EDT 4 KB
CTD_pathways.xml.gz May 06 2013 10:40 EDT 5 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…