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Help: Advanced Reference Query

Contents

  1. Overview
  2. Query Fields
  3. Results

Overview

The reference query is used to retrieve scientific literature. CTD contains a subset of PubMed® articles that discuss chemicals, diseases, and genes and proteins of interest.

See also: Advanced Queries.

Top ↑ Query Fields

Chemical

The name, symbol, CAS Registry Number, or MeSH accession ID (prefixed with “MESH:”) of a chemical cited in the title, abstract, or MeSH annotation of a reference, or involved in an interaction curated from a reference. Synonyms are also matched. To limit your search to official names, use the “name:” prefix.

Examples: dioxin, name:mercury, 1746-01-6, MESH:D001151

CTD's chemical vocabulary consists of a subset of the Medical Subject Headings (MeSH®), the hierarchical vocabulary from the U.S. National Library of Medicine. More…

The chemical vocabulary is hierarchical, so you may search by a narrow (e.g., “copper”) or broad term (e.g., “heavy metals”). Queries that use broad terms retrieve results matching the broad terms as well as related, more specific terms.

Enter your query term in the open field or choose a term from the hierarchical vocabulary by clicking the Select button and navigating through the tree.

Chemical–gene interaction

CTD curates specific chemical–gene and protein interactions in vertebrates and invertebrates from the published literature. You may search exclusively references that have curated interactions by selecting a term in this field. Selecting ANY will match any interaction type, and effectively limits your query to references with curated interactions. Each interaction has a degree and type as defined 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).

Gene

A gene or protein name, symbol, or accession ID (prefixed with “GENE:”) cited in the title, abstract, or MeSH annotation of a reference, or involved in an interaction curated from a reference. Synonyms are also matched. To limit your search to official symbols, use the “name:” prefix.

Examples: ahr, name:brca1, aryl hydrocarbon receptor, GENE:196

The cross-species gene vocabulary (symbols, names, and synonyms) in CTD is derived from the Gene database at the National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine. CTD curators may add to this vocabulary as required (e.g., to represent a species-specific gene that is not curated in NCBI Gene).

Gene form

Each curated chemical–gene interaction includes the form of the gene that is involved (e.g., promoter, mRNA, protein). Gene forms may be specified when searching for curated interaction data.

An interaction type must be selected in order to specify gene forms.

To select or deselect multiple gene forms, hold the Ctrl key (PC) or ⌘/Open-Apple/Command key (Mac) while clicking. Gene forms are searched in the hierarchy shown on the query form.

Disease

The name, synonym, or MeSH or OMIM accession ID (prefixed with “MESH:” or “OMIM:”) of a disease involved in a curated chemical or gene relationship. To limit your search to official names, use the “name:” prefix.

Examples: breast neoplasms, name:breast neoplasms, MESH:D001321, OMIM:612100

Organism

The common or scientific name of an organism or higher-order taxon in which a chemical–gene interaction was curated from a reference. To limit your search to official scientific names, use the “name:” prefix.

Examples: zebrafish, name:homo sapiens, felis catus, TAXON:9685

CTD's organism vocabulary consists of the Eumetazoa (vertebrates and invertebrates) component of the Taxonomy Database from NCBI, a division of the U.S. National Library of Medicine. The vocabulary is hierarchical, so you may search by a specific organism (e.g., “homo sapiens”) or a higher-order taxon (e.g., “mammalia”). A query that uses a higher-order taxon will retrieve results that match that taxon as well as the more specific taxa included within it.

Enter your query term in the open field or choose a term from the hierarchical vocabulary by clicking the Select button and navigating through the tree.

Author

The last name and optional first initials of any author of a reference. Use the format: “lastname initials”.

Example: Ross M

Title/abstract

Words contained in the title or abstract of a reference. You may use Boolean operators.

Examples: estrogen & endometrial, estrogen | endometrial

Year

The publication year or range of years for the references you seek. To specify a single year, select the same year in both the “from” and “through” fields. To specify a range of years, select different years in each field. To specify only the lower bound of a range, select a year in the “from” field and leave the “through” field blank. To specify only the upper bound of a range, select a year in the “through” field and leave the “from” field blank.

PubMed® IDs

The PubMed accession identifiers for references. You may specify multiple IDs by separating them with spaces.

Example: 11748833 16882451

Show curated only?

Check this box to include only CTD-curated references.

Results per page

The number of results displayed per page. A lower number provides faster response.

Clear

Click the Clear button to clear and reset all fields to their default values.

Top ↑ Results

Reference query results are presented in a summary format, which includes citation information as well as the associated genes and cited chemicals for each matching reference. From results pages, you can access individual reference detail pages which provide information about a selected reference.

By default, results are sorted by:

  1. Publication date (most recent first);
  2. Author names (in order of citation); and then
  3. Title.

Reference

The reference's complete author list, title, and bibliographic citation. Click the title to view more information about the reference.

Cited Chemicals

The chemicals cited in the title, abstract, or MeSH annotations of the reference and identified by text mining or manual curation. Terms (and descendants of terms) that matched your query are highlighted. Click a chemical to view more information about it.

CTD's chemical vocabulary consists of a subset of the Medical Subject Headings (MeSH®), the hierarchical vocabulary from the U.S. National Library of Medicine. More…

Cited Genes

Symbols of the genes cited in the title, abstract, or MeSH annotations of the reference and identified by text mining or manual curation. Click a gene to view more information about it.

Cited Diseases

Diseases cited in the reference and extracted by manual curation. Click a disease to view more information about it.

Cited Phenotypes

Phenotypes cited in the reference and extracted by manual curation. Click a phenotype to view more information about it.

Sorting

Sort these data differently by clicking a column heading.

Download

Save these data into a comma-separated values (CSV), Excel, XML, or tab-separated values (TSV) file by clicking a Download link at the bottom of the table.