Contents

  1. Overview
  2. Batch Query API
  3. Select your input type
  4. Downloading chemical–gene interactions
  5. Downloading chemical associations
  6. Downloading gene associations
  7. Downloading disease associations
  8. Downloading pathway associations
  9. Downloading Gene Ontology associations

Overview

The Batch Query tool allows you to download data for up to 4,000 chemicals, diseases, genes, GO terms, pathways, or references simultaneously. Enter or paste your query terms into the text box (return-, tab- or |-delimited), or upload a tab-separated-values (TSV) file containing the terms.

See also: Data Downloads to obtain complete CTD data sets.

Batch Query API

Your applications may retrieve data directly by sending HTTP requests to the Batch Query API.

Select your input type

Select the type of the query terms you are providing in Step 2.

Chemicals

Retrieve data associated with the chemicals that you specify in Step 2. You may identify chemicals by MeSH® name, synonym, or accession ID (“MESH:…”), or by CAS RN. To limit your search to official names, use the “name:” prefix.

Diseases

Retrieve data associated with the diseases that you specify in Step 2. You may identify diseases by MeSH or OMIM name, synonym, or accession ID (“MESH:…” or “OMIM:…”). To limit your search to official names, use the “name:” prefix.

Genes

Retrieve data associated with the genes that you specify in Step 2. You may identify genes by NCBI (Entrez Gene) symbols (“name:…”) or accession IDs (“GENE:…”).

Gene Ontology terms

Retrieve data associated with the GO terms that you specify in Step 2. You may identify GO terms by name, synonym, or ID (e.g., “GO:0008219” or “8219”).

Pathways

Retrieve data associated with the pathways that you specify in Step 2. You may identify pathways by KEGG or REACTOME name or accession ID (“KEGG:…” or “REACT:…”).

References

Retrieve data associated with the references that you specify in Step 2. You may identify references by PubMed® IDs or DOIs.

Downloading chemical–gene interactions

Valid input to retrieve curated chemical–gene interactions are chemicals, genes, and references.

CTD chemical–gene and protein interactions are curated in vertebrates and invertebrates from the published literature. Interactions may be direct (e.g., “chemical binds to protein”) or indirect (e.g., “chemical results in increased phosphorylation of a protein” via intermediate events).

You may select one or more interaction types to filter the interactions in your results. ANY is the default selection and does not cause any items to be filtered out. Definitions of each term are provided below.

Degree. Each chemical–gene interaction is qualified by a degree: increases, decreases, affects, or does not affect (e.g., “Chemical X increases expression of Gene Y mRNA”). The affects degree is used when the reference does not describe a more specific degree. Interactions having the does not affect degree are excluded from our public data.

An interaction type must be selected in order to filter by degree(s). At least one degree must be checked.

Type. To select or deselect multiple interaction types, hold the Ctrl key (PC) or ⌘/Open-Apple/Command key (Mac) while clicking. Interaction types are searched in this hierarchy:

abundance
The abundance of a chemical (if chemical synthesis is not known).
activity
An elemental function of a molecule.
binding
A molecular interaction.
cotreatment
Involving the use of two or more chemicals simultaneously.
expression
The expression of a gene product.
folding
The bending and positioning of a molecule to achieve conformational integrity.
localization
Part of the cell where a molecule resides.
metabolic processing
The biochemical alteration of a molecule's structure (does not include changes in expression, stability, folding, localization, splicing, or transport).
—  acetylation
The addition of an acetyl group.
—  acylation
The addition of an acyl group.
—  alkylation
The addition of an alkyl group.
—  amination
The addition of an amine group.
—  carbamoylation
The addition of a carbamoyl group.
—  carboxylation
The addition of a carboxyl group.
—  chemical synthesis
A biochemical event resulting in a new chemical product.
—  degradation
Catabolism or breakdown.
    —  cleavage
The processing or splitting of a molecule, not necessarily leading to the destruction of the molecule.
        —  hydrolysis
The splitting of a molecule via the specific use of water.
—  ethylation
The addition of an ethyl group.
—  glutathionylation
The addition of a glutathione group.
—  glycation
The non-enzymatic addition of a sugar.
—  glycosylation
The addition of a sugar group.
    —  glucuronidation
The addition of a sugar group to form a glucuronide, typically part of an inactivating or detoxifying reaction.
    —  N-linked glycosylation
The addition of a sugar group to an amide nitrogen.
    —  O-linked glycosylation
The addition of a sugar group to a hydroxyl group.
—  hydroxylation
The addition of a hydroxy group.
—  lipidation
The addition of a lipid group.
    —  farnesylation
The addition of a farnesyl group.
    —  geranoylation
The addition of a geranoyl group.
    —  myristoylation
The addition of a myristoyl group.
    —  palmitoylation
The addition of a palmitoyl group.
    —  prenylation
The addition of a prenyl group.
—  methylation
The addition of a methyl group.
—  nitrosation
The addition of a nitroso or nitrosyl group.
—  nucleotidylation
The addition of a nucleotidyl group.
—  oxidation
The loss of electrons.
—  phosphorylation
The addition of a phosphate group.
—  reduction
The gain of electrons.
—  ribosylation
The addition of a ribosyl group.
    —  ADP-ribosylation
The addition of a ADP-ribosyl group.
—  sulfation
The addition of a sulfate group.
—  sumoylation
The addition of a SUMO group.
—  ubiquitination
The addition of an ubiquitin group.
mutagenesis
The genetic alteration of a gene product.
reaction
Any general biochemical or molecular event.
response to substance
Resistance or sensitivity to a substance.
splicing
The removal of introns to generate mRNA.
stability
Overall molecular integrity.
transport
The movement of a molecule into or out of a cell.
—  secretion
The movement of a molecule out of a cell (by less specific means than export).
    —  export
The movement of a molecule out of a cell (by more specific means than secretion).
—  uptake
The movement of a molecule into a cell (by less specific means than import).
    —  import
The movement of a molecule into a cell (by more specific means than uptake).

Downloading chemical associations

Gene inputs retrieve chemicals involved in curated interactions with specified genes.

Disease inputs retrieve chemicals involved in curated and/or inferred associations with specified diseases. Curated chemical–disease associations are extracted from the published literature by CTD curators. Inferred associations are established via CTD-curated chemical–gene interactions (e.g., chemical A is associated with disease B because chemical A has a curated interaction with gene C, and gene C has a curated association with disease B).

Reference inputs retrieve chemicals involved in gene interactions or disease associations curated from the specified references.

Downloading gene associations

Chemical inputs retrieve genes involved in curated interactions with specified chemicals.

Disease inputs retrieve genes involved in curated and/or inferred associations with specified diseases. Curated gene–disease associations are extracted from the published literature by CTD curators, or are derived from the OMIM database using the mim2gene file from the NCBI Gene database. Inferred associations are established via CTD-curated chemical–gene interactions (e.g., gene A is associated with disease B because gene A has a curated interaction with chemical C, and chemical C has a curated association with disease B).

Gene inputs retrieve associated gene/protein interactions.

GO term inputs retrieve genes annotated to that GO term or one of its descendants.

Pathway inputs retrieve genes annotated to that pathway by KEGG or REACTOME curation.

Reference inputs retrieve genes involved in chemical interactions or disease associations curated from the specified references.

Downloading disease associations

Chemical inputs retrieve diseases involved in curated and/or inferred associations. Curated chemical–disease associations are extracted from the published literature by CTD curators. Inferred associations are established via CTD-curated chemical–gene interactions (e.g., chemical A is associated with disease B because chemical A has a curated interaction with gene C, and gene C has a curated association with disease B).

Gene inputs retrieve diseases involved in curated and/or inferred associations. Curated gene–disease associations are extracted from the published literature by CTD curators, or are derived from the OMIM database using the mim2gene file from the NCBI Gene database. Inferred associations are established via CTD-curated chemical–gene interactions (e.g., gene A is associated with disease B because gene A has a curated interaction with chemical C, and chemical C has a curated association with disease B).

GO term inputs retrieve disease associations inferred between the input GO term or one of its descendants.

Disease inputs retrieve disease associations inferred based on shared genes among CTD-curated gene–disease associations and gene–pathway associations established by KEGG and REACTOME curation.

Reference inputs retrieve chemical– and gene–disease associations curated from the specified references.

Downloading pathway associations

Chemical inputs will identify genes involved in curated interactions and retrieve pathways containing these genes. Alternatively, only those pathways found to be enriched significantly among genes that interact with a chemical may be retrieved. More…

Gene inputs will identify pathways involving these genes based on annotation from the KEGG and REACTOME databases.

Disease inputs will identify pathways inferred to be associated with these diseases based on shared genes among CTD-curated gene–disease associations and gene–pathway associations established by KEGG and REACTOME curation.

Downloading Gene Ontology associations

You must select at least one ontology (i.e., Biological Process, Molecular Function, and Cellular Component).

Chemical inputs will identify genes involved in curated interactions and retrieve a cross–species summary of GO terms used to annotate any of the UniProt sequences encoded by these genes. Alternatively, only those GO terms found to be enriched significantly among genes that interact with a chemical may be retrieved. More…

Gene inputs retrieve a cross–species summary of GO terms used to annotate any of the UniProt sequences encoded by specified genes.