Helmholtz Gemeinschaft


CART - a chemical annotation retrieval toolkit

[img] PDF (Article) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
[img] MS Word (Supplementary data)

Item Type:Article
Title:CART - a chemical annotation retrieval toolkit
Creators Name:Deghou, S. and Zeller, G. and Iskar, M. and Driessen, M. and Castillo, M. and 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
Publisher:Oxford University Press
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

Repository Staff Only: item control page


Downloads per month over past year

Open Access
MDC Library