{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T06:41:04Z","timestamp":1759992064937},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Searching for certain compounds in literature can be an elaborate task, with many compounds having several different synonyms. Often, only the structure is known but not its name. Furthermore, rarely investigated compounds may not be described in the available literature at all. In such cases, preceding searches for described similar compounds facilitate literature mining. Highlighted names of proteins in selected texts may further accelerate the time-consuming process of literary research. Compounds In Literature (CIL) provides a web interface to automatically find names, structures, and similar structures in over 28 million compounds of PubChem and more than 18 million citations provided by the PubMed service. CIL's pre-calculated database contains more than 56 million parent compound\u2013abstract relations. Found compounds, relatives and abstracts are related to proteins in a concise \u2018heat map\u2019-like overview. Compounds and proteins are highlighted in their respective abstracts, and are provided with links to PubChem and UniProt.<\/jats:p>\n               <jats:p>Availability: An easy-to-use web interface with detailed descriptions, help and statistics is available from http:\/\/cil.pharmaceutical-bioinformatics.de.<\/jats:p>\n               <jats:p>Contact: \u00a0stefan.guenther@pharmazie.uni-freiburg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr130","type":"journal-article","created":{"date-parts":[[2011,3,18]],"date-time":"2011-03-18T01:09:30Z","timestamp":1300410570000},"page":"1341-1342","source":"Crossref","is-referenced-by-count":11,"title":["Compounds In Literature (CIL): screening for compounds and relatives in PubMed"],"prefix":"10.1093","volume":"27","author":[{"given":"Bj\u00f6rn A.","family":"Gr\u00fcning","sequence":"first","affiliation":[{"name":"Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, D-79104 Freiburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Senger","sequence":"additional","affiliation":[{"name":"Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, D-79104 Freiburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anika","family":"Erxleben","sequence":"additional","affiliation":[{"name":"Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, D-79104 Freiburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephan","family":"Flemming","sequence":"additional","affiliation":[{"name":"Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, D-79104 Freiburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"G\u00fcnther","sequence":"additional","affiliation":[{"name":"Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, D-79104 Freiburg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,3,16]]},"reference":[{"key":"2023012512190611200_B1","doi-asserted-by":"crossref","first-page":"2983","DOI":"10.1093\/bioinformatics\/btp535","article-title":"A dictionary to identify small molecules and drugs in free text","volume":"25","author":"Hettne","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512190611200_B2","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1093\/bioinformatics\/btp049","article-title":"SciMiner: web-based literature mining tool for target identification and functional enrichment analysis","volume":"25","author":"Hur","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512190611200_B3","doi-asserted-by":"crossref","first-page":"D552","DOI":"10.1093\/nar\/gkp937","article-title":"STITCH 2: an interaction network database for small molecules and proteins","volume":"38","author":"Kuhn","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512190611200_B4","doi-asserted-by":"crossref","first-page":"e237","DOI":"10.1093\/bioinformatics\/btl302","article-title":"EBIMed\u2013text crunching to gather facts for proteins from medline","volume":"23","author":"Rebholz-Schuhmann","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512190611200_B5","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1093\/bioinformatics\/btm557","article-title":"Text processing through web services: calling whatizit","volume":"24","author":"Rebholz-Schuhmann","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512190611200_B6","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1758-2946-2-6","article-title":"WENDI: a tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications","volume":"2","author":"Zhu","year":"2010","journal-title":"J. Cheminformat."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1341\/48869616\/bioinformatics_27_9_1341.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1341\/48869616\/bioinformatics_27_9_1341.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:13:18Z","timestamp":1674659598000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/9\/1341\/242950"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,3,16]]},"references-count":6,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2011,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr130","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,5,1]]},"published":{"date-parts":[[2011,3,16]]}}}