{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:34:40Z","timestamp":1732034080884},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Specific information on newly discovered proteins is often difficult to find in literature. Particularly if only sequences and no common names of proteins or genes are available, preceding sequence similarity searches can be crucial for the process of information collection. In drug research, it is important to know whether a small molecule targets only one specific protein or whether similar or homologous proteins are also influenced that may account for possible side effects.<\/jats:p>\n               <jats:p>Results: \u00a0prolific (protein-literature investigation for interacting compounds) provides a one-step solution to investigate available information on given protein names, sequences, similar proteins or sequences on the gene level. Co-occurrences of UniProtKB\/Swiss-Prot proteins and PubChem compounds in all PubMed abstracts are retrievable. Concise \u2018heat-maps\u2019 and tables display frequencies of co-occurrences. They provide links to processed literature with highlighted found protein and compound synonyms. Evaluation with manually curated drug\u2013protein relationships showed that up to 69% could be discovered by automatic text-processing. Examples are presented to demonstrate the capabilities of prolific.<\/jats:p>\n               <jats:p>Availability: The web-application is available at http:\/\/prolific.pharmaceutical-bioinformatics.de and a web service at http:\/\/www.pharmaceutical-bioinformatics.de\/prolific\/soap\/prolific.wsdl.<\/jats:p>\n               <jats:p>Contact: \u00a0stefan.guenther@pharmazie.uni-freiburg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts026","type":"journal-article","created":{"date-parts":[[2012,1,14]],"date-time":"2012-01-14T01:50:47Z","timestamp":1326505847000},"page":"709-714","source":"Crossref","is-referenced-by-count":7,"title":["Mining and evaluation of molecular relationships in literature"],"prefix":"10.1093","volume":"28","author":[{"given":"Christian","family":"Senger","sequence":"first","affiliation":[{"name":"1 Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9 and 2Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany"}]},{"given":"Bj\u00f6rn A.","family":"Gr\u00fcning","sequence":"additional","affiliation":[{"name":"1 Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9 and 2Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany"}]},{"given":"Anika","family":"Erxleben","sequence":"additional","affiliation":[{"name":"1 Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9 and 2Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany"}]},{"given":"Kersten","family":"D\u00f6ring","sequence":"additional","affiliation":[{"name":"1 Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9 and 2Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany"}]},{"given":"Hitesh","family":"Patel","sequence":"additional","affiliation":[{"name":"1 Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9 and 2Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany"}]},{"given":"Stephan","family":"Flemming","sequence":"additional","affiliation":[{"name":"1 Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9 and 2Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany"}]},{"given":"Irmgard","family":"Merfort","sequence":"additional","affiliation":[{"name":"1 Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9 and 2Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany"}]},{"given":"Stefan","family":"G\u00fcnther","sequence":"additional","affiliation":[{"name":"1 Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9 and 2Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2012,1,13]]},"reference":[{"key":"2023012512192016000_B1","first-page":"556","article-title":"Assisted curation: does text mining really help?","author":"Alex","year":"2008","journal-title":"Pac. Symp. Biocomput."},{"key":"2023012512192016000_B2","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1093\/bib\/bbr005","article-title":"Literature mining, ontologies and information visualization for drug repurposing","volume":"12","author":"Andronis","year":"2011","journal-title":"Brief. Bioinform."},{"issue":"Database issue","key":"2023012512192016000_B3","doi-asserted-by":"crossref","first-page":"D525","DOI":"10.1093\/nar\/gkp878","article-title":"The IntAct molecular interaction database in 2010","volume":"38","author":"Aranda","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512192016000_B4","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"issue":"Database issue","key":"2023012512192016000_B5","doi-asserted-by":"crossref","first-page":"D396","DOI":"10.1093\/nar\/gkn803","article-title":"The GOA database in 2009-an integrated Gene Ontology Annotation resource","volume":"37","author":"Barrell","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012512192016000_B6","doi-asserted-by":"crossref","first-page":"267","DOI":"10.5772\/6419","article-title":"Biomedical literature mining for biological databases annotation","volume-title":"Data Mining in Medical and Biological Research","author":"Berardi","year":"2008"},{"key":"2023012512192016000_B7","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/j.ccr.2011.08.019","article-title":"Short hairpin RNA screen reveals bromodomain proteins as novel targets in acute myeloid leukemia","volume":"20","author":"Blobel","year":"2011","journal-title":"Cancer Cell"},{"key":"2023012512192016000_B8","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/S1574-1400(08)00012-1","article-title":"Chapter 12 - PubChem: Integrated platform of small molecules and biological activities","volume":"4","author":"Bolton","year":"2008","journal-title":"Ann. Rep. Comput. Chem."},{"key":"2023012512192016000_B9","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"Web Server issue","key":"2023012512192016000_B10","doi-asserted-by":"crossref","first-page":"W450","DOI":"10.1093\/nar\/gkr310","article-title":"CoPub update: CoPub 5.0 a text mining system to answer biological questions","volume":"39","author":"Fleuren","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512192016000_B11","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1093\/bioinformatics\/btr130","article-title":"Compounds in literature (CIL): screening for compounds and relatives in PubMed","volume":"27","author":"Gr\u00fcning","year":"2011","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"2023012512192016000_B12","first-page":"D919","article-title":"SuperTarget and Matador: resources for exploring drug-target relationships","volume":"36","author":"G\u00fcnther","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012512192016000_B13","doi-asserted-by":"crossref","first-page":"D1113","DOI":"10.1093\/nar\/gkr912","article-title":"SuperTarget goes quantitative: update on drug-target interactions","volume":"40","author":"Hecker","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012512192016000_B14","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"},{"issue":"Database issue","key":"2023012512192016000_B15","doi-asserted-by":"crossref","first-page":"D211","DOI":"10.1093\/nar\/gkn785","article-title":"InterPro: the integrative protein signature database","volume":"37","author":"Hunter","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023012512192016000_B16","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"},{"issue":"Database issue","key":"2023012512192016000_B17","doi-asserted-by":"crossref","first-page":"D1035","DOI":"10.1093\/nar\/gkq1126","article-title":"DrugBank 3.0: a comprehensive resource for \u2018omics\u2019 research on drugs","volume":"39","author":"Knox","year":"2011","journal-title":"Nucleic Acids Res."},{"issue":"Suppl. 2","key":"2023012512192016000_B18","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/gb-2008-9-s2-s1","article-title":"Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge","volume":"9","author":"Krallinger","year":"2008","journal-title":"Genome Biol."},{"issue":"Database issue","key":"2023012512192016000_B19","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":"2023012512192016000_B20","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bar009","article-title":"UniProt Knowledgebase: a hub of integrated protein data","volume":"2011","author":"Magrane","year":"2011","journal-title":"Database"},{"issue":"Database issue","key":"2023012512192016000_B21","doi-asserted-by":"crossref","first-page":"D220","DOI":"10.1093\/nar\/gkq1157","article-title":"MIPS: curated databases and comprehensive secondary data resources in 2010","volume":"39","author":"Mewes","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023012512192016000_B22","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":"2023012512192016000_B23","doi-asserted-by":"crossref","first-page":"e237","DOI":"10.1093\/bioinformatics\/btl302","article-title":"EBIMed-text crunching to gather facts for proteins from Medline","volume":"23","author":"Rebholz-Schuhmann","year":"2007","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"2023012512192016000_B24","doi-asserted-by":"crossref","first-page":"D534","DOI":"10.1093\/nar\/gkq1062","article-title":"IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data","volume":"39","author":"Sharman","year":"2011","journal-title":"Nucleic Acids Res."},{"issue":"Database issue","key":"2023012512192016000_B25","doi-asserted-by":"crossref","first-page":"D787","DOI":"10.1093\/nar\/gkp1014","article-title":"Update of TTD: Therapeutic Target Database","volume":"38","author":"Zhu","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512192016000_B26","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. Cheminform."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/5\/709\/48876770\/bioinformatics_28_5_709.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/5\/709\/48876770\/bioinformatics_28_5_709.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:22:53Z","timestamp":1674660173000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/5\/709\/248441"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,13]]},"references-count":26,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2012,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts026","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,3,1]]},"published":{"date-parts":[[2012,1,13]]}}}