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: update 2013
Open accessAbstract
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate expanded networks and predict many novel associations between different data types. CTD now contains over 15 million toxicogenomic relationships. To navigate this sea of data, we added several new features, including DiseaseComps (which finds comparable diseases that share toxicogenomic profiles), statistical scoring for inferred gene-disease and pathway-chemical relationships, filtering options for several tools to refine user analysis and our new Gene Set Enricher (which provides biological annotations that are enriched for gene sets). To improve data visualization, we added a Cytoscape Web view to our ChemComps feature, included color-coded interactions and created a 'slim list' for our MEDIC disease vocabulary (allowing diseases to be grouped for meta-analysis, visualization and better data management). CTD continues to promote interoperability with external databases by providing content and cross-links to their sites. Together, this wealth of expanded chemical-gene-disease data, combined with novel ways to analyze and view content, continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases.
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Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
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-citationReactome: a database of reactions, pathways and biological processes
Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1018 · Cited by 1,751
Cited by
A circadian gene expression atlas in mammals: Implications for biology and medicine
Zhang, R., Lahens, N. F., Ballance, H. I., Hughes, M. E., & Hogenesch, J. B. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1408886111 · Cited by 2,304
The support of human genetic evidence for approved drug indications
Nelson, M. R., Tipney, H., Painter, J. L., Shen, J., Nicoletti, P., Shen, Y., Floratos, A., Sham, P. C., Li, M. J., Wang, J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3314 · Cited by 1,666
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
Pinero, J., Queralt-Rosinach, N., Bravo, A., Deu-Pons, J., Bauer-Mehren, A., Baron, M., Sanz, F., & Furlong, L. I. (2015) · Database · doi:10.1093/database/bav028 · Cited by 1,124
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-citationLuo, Y., Zhao, X., Zhou, J., Yang, J., Zhang, Y., Kuang, W., Peng, J., Chen, L., & Zeng, J. (2017) · Nature Communications · doi:10.1038/s41467-017-00680-8 · Cited by 916
Metadata
- Authors
- Davis, A. P., Murphy, C. G., Johnson, R., Lay, J. M., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-10-23
- Volume
- 41
- Issue
- D1
- Pages
- D1104-D1114
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2124001239
- Cited by
- 497
- References
- 3
- FWCI
- 19.40
- Type
- journal article
- Language
- en
- Open access
- gold
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- Davis, A. P., Murphy, C. G., Johnson, R., Lay, J. M., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2013). The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Research. https://doi.org/10.1093/nar/gks994
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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.
