{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T03:31:47Z","timestamp":1778643107521,"version":"3.51.4"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":132,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: bork@embl.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw233","type":"journal-article","created":{"date-parts":[[2016,6,3]],"date-time":"2016-06-03T01:12:51Z","timestamp":1464916371000},"page":"2869-2871","source":"Crossref","is-referenced-by-count":8,"title":["CART\u2014a chemical annotation retrieval toolkit"],"prefix":"10.1093","volume":"32","author":[{"given":"Samy","family":"Deghou","sequence":"first","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georg","family":"Zeller","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Murat","family":"Iskar","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marja","family":"Driessen","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mercedes","family":"Castillo","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vera","family":"van Noort","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany"},{"name":"2 Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peer","family":"Bork","sequence":"additional","affiliation":[{"name":"1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany"},{"name":"3 Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany"},{"name":"4 Max Delbr\u00fcck Centre for Molecular Medicine, Berlin, Germany"},{"name":"5 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, W\u00fcrzburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,6,2]]},"reference":[{"key":"2023020113385666000_btw233-B1","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1093\/bioinformatics\/btt628","article-title":"The fuctional therapeutic chemical classification system","volume":"30","author":"Croset","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020113385666000_btw233-B111","doi-asserted-by":"crossref","first-page":"D914","DOI":"10.1093\/nar\/gku935","article-title":"The Comparative Toxicogenomics Database s 10th year anniversary: update 2015","volume":"43","author":"Davis","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020113385666000_btw233-B2","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1093\/bioinformatics\/btv557","article-title":"Cytoscape. js: a graph theory library for visualisation and analysis","volume":"32","author":"Franz","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020113385666000_btw233-B3","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biol"},{"key":"2023020113385666000_btw233-B4","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. 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