{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T23:57:43Z","timestamp":1773446263504,"version":"3.50.1"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,2,1]],"date-time":"2012-02-01T00:00:00Z","timestamp":1328054400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BioData Mining"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that the user judges to be 'interesting'. Some methods go further by allowing the user to provide a second input set of 'uninteresting' abstracts; these two input sets are then used to search and rank literature by relevance. In this work we present the service 'Caipirini' (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/caipirini.org\" ext-link-type=\"uri\">http:\/\/caipirini.org<\/jats:ext-link>) that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>To evaluate the usefulness of Caipirini, we used two test cases, one related to the human cell cycle, and a second related to disease defense mechanisms in <jats:italic>Arabidopsis thaliana<\/jats:italic>. In both cases, the new method achieved high precision in finding literature related to the biological mechanisms underlying the input data sets.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>To our knowledge Caipirini is the first service enabling literature search directly based on biological relevance to gene sets; thus, Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via high-throughput experiments.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1756-0381-5-1","type":"journal-article","created":{"date-parts":[[2012,2,1]],"date-time":"2012-02-01T19:21:07Z","timestamp":1328124067000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Caipirini: using gene sets to rank literature"],"prefix":"10.1186","volume":"5","author":[{"given":"Theodoros G","family":"Soldatos","sequence":"first","affiliation":[]},{"given":"Se\u00e1n I","family":"O'Donoghue","sequence":"additional","affiliation":[]},{"given":"Venkata P","family":"Satagopam","sequence":"additional","affiliation":[]},{"given":"Adriano","family":"Barbosa-Silva","sequence":"additional","affiliation":[]},{"given":"Georgios A","family":"Pavlopoulos","sequence":"additional","affiliation":[]},{"given":"Ana Carolina","family":"Wanderley-Nogueira","sequence":"additional","affiliation":[]},{"given":"Nina Mota","family":"Soares-Cavalcanti","sequence":"additional","affiliation":[]},{"given":"Reinhard","family":"Schneider","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,2,1]]},"reference":[{"key":"59_CR1","doi-asserted-by":"publisher","first-page":"S7","DOI":"10.1186\/gb-2008-9-s2-s7","volume":"9","author":"R Altman","year":"2008","unstructured":"Altman R, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L: Text mining for biology - the way forward: opinions from leading scientists. Genome Biology. 2008, 9: S7-","journal-title":"Genome Biology"},{"key":"59_CR2","doi-asserted-by":"publisher","first-page":"e1000597","DOI":"10.1371\/journal.pcbi.1000597","volume":"5","author":"R Rodriguez-Esteban","year":"2009","unstructured":"Rodriguez-Esteban R: Biomedical text mining and its applications. PLoS Comput Biol. 2009, 5: e1000597-10.1371\/journal.pcbi.1000597.","journal-title":"PLoS Comput Biol"},{"key":"59_CR3","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1093\/bib\/6.1.57","volume":"6","author":"AM Cohen","year":"2005","unstructured":"Cohen AM, Hersh WR: A survey of current work in biomedical text mining. Brief Bioinform. 2005, 6: 57-71. 10.1093\/bib\/6.1.57.","journal-title":"Brief Bioinform"},{"key":"59_CR4","doi-asserted-by":"publisher","first-page":"2298","DOI":"10.1093\/bioinformatics\/btl388","volume":"22","author":"J Lewis","year":"2006","unstructured":"Lewis J, Ossowski S, Hicks J, Errami M, Garner HR: Text similarity: an alternative way to search MEDLINE. Bioinformatics. 2006, 22: 2298-2304. 10.1093\/bioinformatics\/btl388.","journal-title":"Bioinformatics"},{"key":"59_CR5","doi-asserted-by":"publisher","first-page":"W774","DOI":"10.1093\/nar\/gki429","volume":"33","author":"T Goetz","year":"2005","unstructured":"Goetz T, von der Lieth C-W: PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts. Nucleic Acids Res. 2005, 33: W774-W778. 10.1093\/nar\/gki429.","journal-title":"Nucleic Acids Res"},{"key":"59_CR6","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/1471-2105-9-108","volume":"9","author":"GL Poulter","year":"2008","unstructured":"Poulter GL, Rubin DL, Altman RB, Seoighe C: MScanner: a classifier for retrieving Medline citations. BMC Bioinformatics. 2008, 9: 108-10.1186\/1471-2105-9-108.","journal-title":"BMC Bioinformatics"},{"key":"59_CR7","doi-asserted-by":"publisher","first-page":"W141","DOI":"10.1093\/nar\/gkp353","volume":"37","author":"JF Fontaine","year":"2009","unstructured":"Fontaine JF, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM, Andrade-Navarro MA: MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Res. 2009, 37: W141-W146. 10.1093\/nar\/gkp353.","journal-title":"Nucleic Acids Res"},{"key":"59_CR8","volume-title":"IEEE Computational Systems Bioinformatics Conference; Stanford, USA","author":"N Polavarapu","year":"2005","unstructured":"Polavarapu N, Navathe SB, Ramnarayanan R, ul Haque A, Sahay S, Liu Y: Investigation into biomedical literature classification using support vector machines. IEEE Computational Systems Bioinformatics Conference; Stanford, USA. 2005"},{"key":"59_CR9","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1093\/bioinformatics\/btk044","volume":"22","author":"PK Shah","year":"2006","unstructured":"Shah PK, Bork P: LSAT: learning about alternative transcripts in MEDLINE. Bioinformatics. 2006, 22: 857-865. 10.1093\/bioinformatics\/btk044.","journal-title":"Bioinformatics"},{"key":"59_CR10","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1186\/1471-2105-9-205","volume":"9","author":"W Yu","year":"2008","unstructured":"Yu W, Clyne M, Dolan SM, Yesupriya A, Wulf A, Liu T, Khoury MJ, Gwinn M: GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique. BMC Bioinformatics. 2008, 9: 205-10.1186\/1471-2105-9-205.","journal-title":"BMC Bioinformatics"},{"key":"59_CR11","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1197\/jamia.M2996","volume":"16","author":"H Kilicoglu","year":"2009","unstructured":"Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB: Towards automatic recognition of scientifically rigorous clinical research evidence. J Am Med Inform Assoc. 2009, 16: 25-31. 10.1197\/jamia.M2996.","journal-title":"J Am Med Inform Assoc"},{"key":"59_CR12","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1186\/1471-2105-9-406","volume":"9","author":"T Tuchler","year":"2008","unstructured":"Tuchler T, Velez G, Graf A, Kreil DP: BibGlimpse: the case for a light-weight reprint manager in distributed literature research. BMC Bioinformatics. 2008, 9: 406-10.1186\/1471-2105-9-406.","journal-title":"BMC Bioinformatics"},{"key":"59_CR13","doi-asserted-by":"publisher","first-page":"i119","DOI":"10.1093\/bioinformatics\/btn291","volume":"24","author":"S Yu","year":"2008","unstructured":"Yu S, Van Vooren S, Tranchevent LC, De Moor B, Moreau Y: Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining. Bioinformatics. 2008, 24: i119-i125. 10.1093\/bioinformatics\/btn291.","journal-title":"Bioinformatics"},{"key":"59_CR14","first-page":"787","volume-title":"31st Annual International ACM SIGIR Conference on Research and Development in Information Retrieval; Singapore","author":"C Nobata","year":"2008","unstructured":"Nobata C, Cotter P, Okazaki N, Rea B, Sasaki Y, Tsuruoka Y, Tsujii Ji, Ananiadou S: Kleio: A Knowledge-enriched Information Retrieval System for Biology. 31st Annual International ACM SIGIR Conference on Research and Development in Information Retrieval; Singapore. 2008, Association for Computing Machinery, 787-788."},{"key":"59_CR15","unstructured":"Caipirini home page. [http:\/\/caipirini.org]"},{"key":"59_CR16","unstructured":"Entrez gene database. [http:\/\/www.ncbi.nlm.nih.gov\/sites\/entrez?db=gene]"},{"key":"59_CR17","unstructured":"Ensembl. [http:\/\/ensembl.org]"},{"key":"59_CR18","unstructured":"PubMed. [http:\/\/pubmed.org]"},{"key":"59_CR19","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1093\/nar\/gkp876","volume":"38","author":"T Soldatos","year":"2010","unstructured":"Soldatos T, O'Donoghue SI, Satagopam VP, Brown NP, Jensen LJ, Schneider R: Martini: using literature keywords to compare gene sets. Nucleic Acid Res. 2010, 38: 26-38. 10.1093\/nar\/gkp876.","journal-title":"Nucleic Acid Res"},{"key":"59_CR20","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1093\/bioinformatics\/9.1.49","volume":"9","author":"T Etzold","year":"1993","unstructured":"Etzold T, Argos P: SRS - an indexing and retrieval tool for flat file data libraries. Bioinformatics. 1993, 9: 49-57. 10.1093\/bioinformatics\/9.1.49.","journal-title":"Bioinformatics"},{"key":"59_CR21","unstructured":"eUtils. [http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query\/static\/eutils_help.html]"},{"key":"59_CR22","unstructured":"LIBLINEAR- A Library for Large Linear Classification. [http:\/\/www.csie.ntu.edu.tw\/~cjlin\/liblinear\/]"},{"key":"59_CR23","unstructured":"Hsu Chih-Wei, Chang Chih-Chung, Lin Chih-Jen: A Practical Guide to Support Vector Classification. [http:\/\/www.csie.ntu.edu.tw\/~cjlin\/papers\/guide\/guide.pdf]"},{"key":"59_CR24","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1002\/gepi.20360","volume":"33","author":"KA Pattin","year":"2009","unstructured":"Pattin KA, White BC, Barney N, Gui J, Nelson HH, Kelsey KT, Andrew AS, Karagas MR, Moore JH: A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction. Genet Epidemiol. 2009, 33: 87-94. 10.1002\/gepi.20360.","journal-title":"Genet Epidemiol"},{"key":"59_CR25","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1038\/nature05186","volume":"443","author":"LJ Jensen","year":"2006","unstructured":"Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P: Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature. 2006, 443: 594-597.","journal-title":"Nature"},{"key":"59_CR26","unstructured":"Medical Subject Headings. [http:\/\/www.nlm.nih.gov\/mesh\/]"},{"key":"59_CR27","first-page":"110","volume-title":"Proceedings of the 1st International Conference of The Brazilian Association of Bioinformatics and Computational Biology (X- Meeting): 4-7 October 2005","author":"A Barbosa-Silva","year":"2005","unstructured":"Barbosa-Silva A, Mudado M, Ortega JM: Plant Defense Mechanisms Database (PDM): Building and Evaluation. Proceedings of the 1st International Conference of The Brazilian Association of Bioinformatics and Computational Biology (X- Meeting): 4-7 October 2005. 2005, Caxambu-MG, 110-"},{"key":"59_CR28","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1146\/annurev.arplant.54.031902.135035","volume":"54","author":"GB Martin","year":"2003","unstructured":"Martin GB, Bogdanove AJ, Sessa G: Understanding the functions of plant disease resistance proteins. Ann Rev Plant Biol. 2003, 54: 23-61. 10.1146\/annurev.arplant.54.031902.135035.","journal-title":"Ann Rev Plant Biol"},{"key":"59_CR29","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1146\/annurev.py.32.090194.002255","volume":"32","author":"H Kessman","year":"1994","unstructured":"Kessman H, Staub T, Hofmann C, Maetzke T, Herzog J, Ward E, Uknes S, Ryals J: Induction of Systemic Acquired Disease Resistance in Plants by Chemicals. Ann Rev Phytopathol. 1994, 32: 439-459. 10.1146\/annurev.py.32.090194.002255.","journal-title":"Ann Rev Phytopathol"},{"key":"59_CR30","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/sj.cdd.4400309","volume":"4","author":"J-B Morel","year":"1997","unstructured":"Morel J-B, Dangl JL: The hypersensitive response and the induction of cell death in plants. Cell Death & Differentiation. 1997, 4: 671-683. 10.1038\/sj.cdd.4400309.","journal-title":"Cell Death & Differentiation"},{"key":"59_CR31","unstructured":"Caipirini examples. http:\/\/caipirini.org\/caipiriniATexample.html;http:\/\/caipirini.org\/caipiriniCellCycleExampleSphase.html; http:\/\/caipirini.org\/caipiriniCellCycleExampleNotSphase.html; http:\/\/caipirini.org\/caipiriniCellCycleExampleNotMESH.html"}],"container-title":["BioData Mining"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1756-0381-5-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1756-0381-5-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1756-0381-5-1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1756-0381-5-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T18:36:41Z","timestamp":1630521401000},"score":1,"resource":{"primary":{"URL":"https:\/\/biodatamining.biomedcentral.com\/articles\/10.1186\/1756-0381-5-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,2,1]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["59"],"URL":"https:\/\/doi.org\/10.1186\/1756-0381-5-1","relation":{},"ISSN":["1756-0381"],"issn-type":[{"value":"1756-0381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,2,1]]},"assertion":[{"value":"12 October 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 February 2012","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 February 2012","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"1"}}