Illuminating how chemicals affect human health.
Comparative Toxicogenomics Database

Contents

1. Chemicals
2. Diseases
3. Genes
4. Gene Ontology (GO) Terms
5. Organisms/Taxonomy
6. Anatomical Terms
7. Pathways
8. References
9. Keyword Queries
10. Batch Queries/CTD API
11. CTD Logos

Use these instructions to link to CTD data, keyword queries, and the Batch Query tool. CTD Logos are available, too.

Use of CTD data is subject to certain terms.

Chemicals

URL: https://ctdbase.org/detail.go?type=chem&acc={ID}

Parameters:

• {ID} - the MeSH^® Unique ID of the chemical (e.g., “D001151”). Download the CTD chemical vocabulary.

Diseases

URL: https://ctdbase.org/detail.go?type=disease&acc={ID}

Parameters:

• {ID} - the MeSH^® Unique ID or OMIM ID of the disease (e.g., “MESH:D018270” or “OMIM:211750”). You must include the MESH: or OMIM: database prefix. Download the CTD disease vocabulary.

Genes

URL: https://ctdbase.org/detail.go?type=gene&acc={ID}

Parameters:

• {ID} - the NCBI Gene ID of the gene (e.g., “196”). Download the CTD gene vocabulary.

Gene Ontology (GO) Terms

URL: https://ctdbase.org/detail.go?type=go&acc={ID}

Parameters:

• {ID} - the GO ID of the term (e.g., “GO:0005215”).

Organisms/Taxonomy

Base URL: https://ctdbase.org/detail.go?type=taxon&acc={ID}

Parameters:

• {ID} - the NCBI Taxonomy ID of the organism or taxon (e.g., “9606”).

Anatomical Terms

URL: https://ctdbase.org/detail.go?type=anatomy&acc={ID}

Parameters:

• {ID} - the MeSH^® Unique ID of the anatomical term (e.g., “D007866”). Download the CTD anatomy vocabulary.

Pathways

URL: https://ctdbase.org/detail.go?type=pathway&acc={ID}

Parameters:

• {ID} - the KEGG or Reactome ID of the pathway (e.g., “KEGG:02010” or “REACT:11163”). You must include the KEGG: or REACT: database prefix. Download the CTD pathway vocabulary.

References

URL: https://ctdbase.org/detail.go?type=reference&acc={ID}

Parameters:

• {ID} - the PubMed^® ID of the reference (e.g., “17869316”).

Keyword Queries

URL: https://ctdbase.org/basicQuery.go?bqCat={CATEGORY}&bq={QUERY}

Parameters:

• {CATEGORY} - the body of data to query:
  • all
  • chem
  • disease
  • gene
  • go
  • pathway
  • reference
  • taxon
• {QUERY} - the keyword or accession identifier for which to search.

Batch Queries/CTD API

To retrieve data via CTD's Batch Query API tool, send an HTTP GET or POST request to the following URL with the following parameters:

URL: https://ctdbase.org/tools/batchQuery.go

Example: https://ctdbase.org/tools/batchQuery.go?inputType=chem&inputTerms=D003634|mercury&report=genes_curated&format=tsv

Parameters:

• inputType - the category of your input data:
  • chem: chemicals
  • disease: diseases
  • gene: genes
  • go: Gene Ontology (GO) terms
  • pathway: pathways
  • phenotype: phenotype
  • reference: references
• inputTerms is your list of query terms, delimited by newlines, tabs, or | characters. Optional if a queryFile is provided. See the Batch Query Help for permissible input data.
• report - the data you would like returned:

  Report Parameter	Contents	Valid inputs
  		Chemicals	Diseases	Genes	GO terms	Pathways	Phenotypes	References
  cgixns	Curated chemical–gene interactions. Requires at least one actionTypes parameter; see below.	✓		✓				✓
  chems	All chemical associations.		✓
  chems_curated	Curated chemical associations.		✓	✓			✓	✓
  chems_inferred	Inferred chemical associations.		✓
  genes	All gene associations.		✓
  genes_curated	Curated gene associations.	✓	✓	✓	✓	✓		✓
  genes_inferred	Inferred gene associations.		✓
  diseases	All disease associations.	✓		✓
  diseases_curated	Curated disease associations.	✓		✓				✓
  diseases_inferred	Inferred disease associations.	✓		✓	✓	✓	✓
  pathways_curated	Curated pathway associations.			✓
  pathways_inferred	Inferred pathway associations.	✓	✓
  pathways_enriched	Enriched pathway associations.	✓
  phenotypes_curated	Curated phenotype associations.	✓						✓
  phenotypes_inferred	Inferred phenotype associations.		✓
  go	All Gene Ontology (GO) associations. Requires at least one ontology parameter (see below).	✓		✓
  go_enriched	Enriched GO associations. Requires at least one ontology parameter (see below).	✓

• format - the output format of the results:
  • tsv (tab-separated values)
  • csv (comma-separated values)
  • json (JavaScript Object Notation)
  • xml
• inputTermSearchType - the search method to be used in the searches:
  • hierarchicalAssociations: use hierarchical associations to the search term(s), extracting child terms
  • directAssociations: use only direct associations to the search term(s)
• actionTypes is either ANY or one or more interaction types by which to filter your results for cgixns reports. Optional other than for cgixns reports.
• ontology is one or more ontologies by which to filter go and go_enriched reports:
  • go_bp: Biological Process
  • go_cc: Cellular Component
  • go_mf: Molecular Function
  Optional other than for go and go_enriched reports.
• queryFile - the data file you are uploading (if you are not providing data via the inputTerms parameter). Optional. Requires the POST method with multipart/form-data enctype.
• queryFileColumn - the number of the column that contains your query terms in the queryFile. Optional unless a queryFile is provided.

CTD Logos

You may download and use these logos for linking to CTD, or for referencing us in a presentation or publication. Please do not link to them directly.

45 x 21 px (transparent background)
90 x 42 px (transparent background)
118 x 55 px (transparent background)
230 x 79 px (white background)
300 PPI, print-ready (white background)