Chemical Pathway Vocabulary

$79 / year

This dataset contains the terms of the vocabulary used in the Comparative Toxicogenomics Database (CTD) to describe the biological or pathological process or reaction (pathway) involved in the interaction between a chemical and disease or gene. These pathways are identified through their codes in the KEGG and REACTOME databases. This dataset is part of the CTD and can be better understood and used along with the other datasets that belong to the CTD.

Complexity

The Comparative Toxicogenomics Database (CTD) purpose is to provide a tool to generate new hypotheses on the mechanism of chemicals in the development of diseases by collecting curated data reported in the scientific literature on chemicals, genes and diseases, and making inferences on the relationships of these three elements.

The CTD datasets can be used to create a tool for input of queries to obtain inferred relationships between genes, chemicals and diseases and the significance of the inferences. When a query is run, the terms on this dataset are used in the result to describe the action of a chemical over a respective gene or disease.

Date Created

2004-01-20

Last Modified

2018-10-05

Version

2018-10-05

Update Frequency

Monthly

Temporal Coverage

N/A

Spatial Coverage

N/A

Source

John Snow Labs => Comparative Toxicogenomics Database

Source License URL

John Snow Labs Standard License

Source License Requirements

Publicly available and free for research application but citation is required. Permission asked for commercial uses

Source Citation

Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database update 2017. Nucleic Acids Res. 2016 Sep 19;[Epub ahead of print]

Keywords

Toxicogenomics, Gene Disease Association, Gene Chemical Pathways, Interaction Between Chemicals and Diseases, KEGG and REACTOME Databases, Comparative Toxicogenomics Database, Relationships Between Chemicals and Diseases, Chemical and Disease Inferences, Chemical Disease Hypotheses

Other Titles

Pathway Definitions, Pathway Types Database

Name Description Type Constraints
Pathway_NameName of the pathway, which is a series of steps in biological processes at a molecular level that leads to a biological change; a pathway is possible due to the activities of multiple gene products and other elements. Pathways involve molecular interactions and reactions pertaining to metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems, human diseases and drug development. Every pathway has a generic or standardized name that helps on obtaining an overview of the pathway’s nature, others have unique but well-known names, for example, the Krebs cycle.stringrequired : 1
Pathway_IDKEGG or REACTOME identifier. Alphanumerical code that identifies the pathway in the lookup of the KEGG or the REACTOME databases. KEGG Pathway Database is a collection of manually drawn pathway maps representing the knowledge on the molecular interaction and reaction networks for metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems, human diseases and drug development. The Reactome Pathway Database is a curated database of pathways and reactions (pathway steps) in human biology. The Reactome definition of a 'reaction' includes many events in biology that change in state, such as binding, activation, translocation and degradation, in addition to classical biochemical reactions. Information in the database is authored by expert biologist researchers, maintained by Reactome editorial staff, and extensively cross-referenced to other resources e.g. NCBI, Ensembl, UniProt, UCSC Genome Browser, HapMap, KEGG (Gene and Compound), ChEBI, PubMed and GO.stringrequired : 1
Pathway_NamePathway_ID
AsthmaKEGG:hsa05310
GliomaKEGG:hsa05214
MalariaKEGG:hsa05144
MeaslesKEGG:hsa05162
LysosomeKEGG:hsa04142
MelanomaKEGG:hsa05218
RibosomeKEGG:hsa03010
ApoptosisKEGG:hsa04210
PertussisKEGG:hsa05133
PhagosomeKEGG:hsa04145