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2016 ; 32
(18
): 2869-71
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CART-a chemical annotation retrieval toolkit
#MMPMID27256313
Deghou S
; Zeller G
; Iskar M
; Driessen M
; Castillo M
; van Noort V
; Bork P
Bioinformatics
2016[Sep]; 32
(18
): 2869-71
PMID27256313
show ga
MOTIVATION: Data on bioactivities of drug-like chemicals are 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. 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 the web
site. CONTACT: bork@embl.de SUPPLEMENTARY INFORMATION: Supplementary data are
available at Bioinformatics online.
free
free
free
