Giving insight into how chemicals affect our health.
Comparative Toxicogenomics Database

Contents

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

This page describes how to create links to CTD data pages, keyword queries, and the Batch Query tool. It also provides downloadable CTD logos.

Chemicals

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

Where:

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

Diseases

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

Where:

• {ID} is 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 list.

Genes

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

Where:

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

Gene Ontology (GO) Terms

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

Where:

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

Organisms/Taxonomy

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

Where:

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

Pathways

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

Where:

• {ID} is 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 list.

References

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

Where:

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

Keyword Queries

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

Where:

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

Batch Queries

To fetch data via CTD's Batch Query tool, send an HTTP request using the post method and multipart/form-data enctype to the following URL with the following parameters:

URL: http://ctdbase.org/tools/batchQuery.go?q

Parameters:

• inputType is the category of your input data:
  • chem: chemicals
  • disease: diseases
  • gene: genes
  • go: Gene Ontology (GO) terms
  • pathway: pathways
  • reference: references
• inputTerms is your tab- or newline-delimited data. Optional if specifying a queryFile. See the Batch Query Help for permissible input data.
• queryFile is the data file you are uploading (if you are not providing data via the inputTerms argument). Optional.
• queryFileColumn is the number of the column that contains your query terms in the queryFile. Optional.
• report is the data you would like returned:

  Report	Contents	Valid inputs
  		Chemicals	Diseases	Genes	GO terms	Pathways	References
  cgixns	Curated curated chemical–gene interactions. Requires at least one of the actionTypes values; 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.	✓
  go	All Gene Ontology (GO) associations. Requires at least one ontology value (see below).	✓		✓
  go_enriched	Enriched GO associations. Requires at least one ontology value (see below).	✓

• format is the output format of the results:
  • tsv: tab-separated values
  • csv: comma-separated values
  • xml: XML
• actionTypes is either ANY or one or more interaction types by which to filter your results for cgixns reports. Optional except 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 except for go and go_enriched reports.

CTD Logos

You may use these logos for linking to CTD, or referencing us in a poster, presentation or publication. If you do not see what you need, please contact us.

45 x 20 px (transparent background)
90 x 37 px (transparent background)
118 x 50 px (transparent background)
230 x 50 px (white background)
300 PPI, print-ready (white background)