Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks

By Allan Peter Davis, Cynthia G. Murphy, Cynthia A. Saraceni-Richards, Michael C. Rosenstein, Thomas C. Wiegers, Carolyn J. Mattingly. Nucleic Acids Res., 2008

320 citations recorded by the source corpus.

The Comparative Toxicogenomics Database (CTD) is a curated database that promotes understanding about the effects of environmental chemicals on human health. Biocurators at CTD manually curate chemical–gene interactions, chemical–disease relationships and gene–disease relationships from the literature. This strategy allows data to be integrated to construct chemical–gene–disease networks. CTD is unique in numerous respects: curation focuses on environmental chemicals; interactions are manually curated; interactions are constructed using controlled vocabularies and hierarchies; additional gene attributes (such as Gene Ontology, taxonomy and KEGG pathways) are integrated; data can be viewed from the perspective of a chemical, gene or disease; results and batch queries can be downloaded and saved; and most importantly, CTD acts as both a knowledgebase (by reporting data) and a discovery tool (by generating novel inferences). Over 116 000 interactions between 3900 chemicals and 13 300 genes have been curated from 270 species, and 5900 gene–disease and 2500 chemical–disease direct relationships have been captured. By integrating these data, 350 000 gene–disease relationships and 77 000 chemical–disease relationships can be inferred. This wealth of chemical–gene–disease information yields testable hypotheses for understanding the effects of environmental chemicals on human health. CTD is freely available at http://ctd.mdibl.org.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dbfff2e86d96b8f3d4020fc5ea761a043a318eb8

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

In Molecular Biology

Citations in the corpus

A CTD–Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug–disease and drug–phenotype interactions (2013, background): “This enhanced curated content can now be used to fill in the molecular gaps and find putative genes and pathways for developing testable hypotheses for drug–disease processes since CTD provides inference networks of genes that connect chemicals to diseases (11).”
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015 (2014, background): “5-fold increase since our 2013 update (8) and a 16-fold increase since our original report in 2009 (6).”
STITCH 3: zooming in on protein–chemical interactions (2011, background): “Second, manually curated sources of drug targets: DrugBank (12), GLIDA (13), Matador (14), TTD (15) and CTD (16).”
Chemical-induced disease relation extraction via convolutional neural network (2017, background): “Although some well-known manual curation efforts like the Comparative Toxicogenomics Database (CTD) project (4, 5) have already curated thousands of documents for CDRs, the manual curation from literature into structured knowledge databases is time-consuming and insufficient to keep up to date.”
The Comparative Toxicogenomics Database: update 2019 (2018, background): “While CTD has been curating chemical-induced diseases since 2007 (1), many toxicology articles do not report a disease as an endpoint, but rather describe molecular, cellular, or physiological systems that are altered, such as signal transduction, cell proliferation, apoptosis, and immune system pro”
BioCreative V CDR task corpus: a resource for chemical disease relation extraction (2016, methodology): “Because of their critical significance, CDRs are being manually curated by resources such as the Comparative Toxicogenomic Database (CTD; http://ctdbase.org) (2,3).”
The Comparative Toxicogenomics Database: update 2011 (2010, methodology): “(i) Batch Query has been previously described (22) and still represents an efficient way to download any type of data associated with a user’s input list of chemicals, genes or diseases.”
The Comparative Toxicogenomics Database: update 2017 (2016, background): “Over the last decade (4), CTD has successfully generated novel connections between different types of data by integrating diverse information through a common intermediate (1,6,7).”
ChemProt: a disease chemical biology database (2010, methodology): “In addition, we integrated chemical–protein associations from CTD (version 2009) (27) and STITCH (version STITCH 2.”
Comparative Toxicogenomics Database (CTD): update 2023 (2022, background): “org/) provides curated content relating chemical exposures with genetic, molecular, and biological outcomes to help understand and formulate testable hypotheses regarding environmental health (1).”
The Comparative Toxicogenomics Database: update 2013 (2012, methodology): “We have previously described the Batch Query, VennViewer and MyGeneVenn tools (4,5).”
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016, background): “CTD Gene-Chemical Interactions (48, 49) SILAC Phosphoproteomics Signatures of”