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| Item Type: | Article |
|---|---|
| Title: | CART - a chemical annotation retrieval toolkit |
| Creators Name: | Deghou, S., Zeller, G., Iskar, M., Driessen, M., Castillo, M., van Noort, V. and Bork, P. |
| Abstract: | MOTIVATION: Data on bioactivities of drug-like chemicals is rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases. RESULTS: To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data. |
| Keywords: | Automatic Data Processing, Computational Biology, Computer Graphics, Data Curation, Factual Databases, Information Storage and Retrieval, Programming Languages, Software |
| Source: | Bioinformatics |
| ISSN: | 1367-4803 |
| Publisher: | Oxford University Press |
| Volume: | 32 |
| Number: | 18 |
| Page Range: | 2869-2871 |
| Date: | 15 September 2016 |
| Additional Information: | Availability and Implementation: CART is available as a Galaxy web service (cart.embl.de). Source code and an easy-to-install command line tool can also be obtained from cart.embl.de CONTACT: bork@embl.de. |
| Official Publication: | https://doi.org/10.1093/bioinformatics/btw233 |
| PubMed: | View item in PubMed |
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