Dataset Information

CART-a chemical annotation retrieval toolkit.

ABSTRACT:

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.

SUBMITTER: Deghou S

PROVIDER: S-EPMC5018367 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

CART-a chemical annotation retrieval toolkit.

Deghou Samy S Zeller Georg G Iskar Murat M Driessen Marja M Castillo Mercedes M van Noort Vera V Bork Peer P

Bioinformatics (Oxford, England) 20160602 18

<h4>Motivation</h4>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.<h4>Results</h4>To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality ...[more]

PMID: 27256313

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Dataset Information

CART-a chemical annotation retrieval toolkit.

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

CART-a chemical annotation retrieval toolkit.

Similar Datasets

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