The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015
Open accessAbstract
Ten years ago, the Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) was developed out of a need to formalize, harmonize and centralize the information on numerous genes and proteins responding to environmental toxic agents across diverse species. CTD's initial approach was to facilitate comparisons of nucleotide and protein sequences of toxicologically significant genes by curating these sequences and electronically annotating them with chemical terms from their associated references. Since then, however, CTD has vastly expanded its scope to robustly represent a triad of chemical-gene, chemical-disease and gene-disease interactions that are manually curated from the scientific literature by professional biocurators using controlled vocabularies, ontologies and structured notation. Today, CTD includes 24 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, Gene Ontology annotations, pathways and interaction modules. In this 10th year anniversary update, we outline the evolution of CTD, including our increased data content, new 'Pathway View' visualization tool, enhanced curation practices, pilot chemical-phenotype results and impending exposure data set. The prototype database originally described in our first report has transformed into a sophisticated resource used actively today to help scientists develop and test hypotheses about the etiologies of environmentally influenced diseases.
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Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Self-citationThe BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745 · cited 2×
“The appeal and utility of structured notations are evident nowadays with the emergence of other bio-languages, such as BioPax (15) and BEL (http: //www.”
BackgroundPhenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms
Kleinstreuer, N. C., Yang, J., Berg, E. L., Knudsen, T. B., Richard, A. M., Martin, M. T., Reif, D. M., Judson, R. S., Polokoff, M., Dix, D. J., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2914 · Cited by 211
Cited by
Piñero, J., Bravo, À., Queralt-Rosinach, N., Gutiérrez-Sacristán, A., Deu-Pons, J., Centeno, E., García-García, J., Sanz, F., & Furlong, L. I. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw943 · Cited by 2,680
Rouillard, A. D., Gundersen, G. W., Fernandez, N. F., Wang, Z., Monteiro, C. D., McDermott, M. G., & Ma’ayan, A. (2016) · Database · doi:10.1093/database/baw100 · Cited by 1,515
Comparative Toxicogenomics Database (CTD): update 2021
Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., Wiegers, J., Wiegers, T. C., & Mattingly, C. J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa891 · Cited by 1,107
Self-citationThe BioGRID interaction database: 2017 update
Chatr-aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas, N. K., O'Donnell, L., Oster, S., Theesfeld, C., Sellam, A., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1102 · Cited by 965
Network-based approach to prediction and population-based validation of in silico drug repurposing
Cheng, F., Desai, R. J., Handy, D. E., Wang, R., Schneeweiss, S., Barabási, A.-L., & Loscalzo, J. (2018) · Nature Communications · doi:10.1038/s41467-018-05116-5 · Cited by 552
“For each CV event, we collected disease-associated genes from 8 commonly used data sources: The OMIM database (Online Mendelian Inheritance in Man) (66), The Comparative Toxicogenomics Database (67), HuGE Navigator (68), DisGeNET (69), ClinVar (70), GWAS Catalog (71), GWASdb (72), and PheWAS Catalog (phewas.”
Method
Metadata
- Authors
- Davis, A. P., Grondin, C. J., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., Wiegers, T. C., & Mattingly, C. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-10-17
- Volume
- 43
- Issue
- D1
- Pages
- D914-D920
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1992442866
- Cited by
- 387
- References
- 3
- FWCI
- 25.19
- Type
- journal article
- Language
- en
- Open access
- gold
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- Davis, A. P., Grondin, C. J., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., Wiegers, T. C., & Mattingly, C. J. (2015). The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. Nucleic Acids Research. https://doi.org/10.1093/nar/gku935
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
