{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T10:10:01Z","timestamp":1775124601465,"version":"3.50.1"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Advances in biotechnology and in high-throughput methods for gene analysis have contributed to an exponential increase in the number of scientific publications in these fields of study. While much of the data and results described in these articles are entered and annotated in the various existing biomedical databases, the scientific literature is still the major source of information. There is, therefore, a growing need for text mining and information retrieval tools to help researchers find the relevant articles for their study. To tackle this, several tools have been proposed to provide alternative solutions for specific user requests.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>This paper presents QuExT, a new PubMed-based document retrieval and prioritization tool that, from a given list of genes, searches for the most relevant results from the literature. QuExT follows a concept-oriented query expansion methodology to find documents containing concepts related to the genes in the user input, such as protein and pathway names. The retrieved documents are ranked according to user-definable weights assigned to each concept class. By changing these weights, users can modify the ranking of the results in order to focus on documents dealing with a specific concept. The method's performance was evaluated using data from the 2004 TREC genomics track, producing a mean average precision of 0.425, with an average of 4.8 and 31.3 relevant documents within the top 10 and 100 retrieved abstracts, respectively.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>QuExT implements a concept-based query expansion scheme that leverages gene-related information available on a variety of biological resources. The main advantage of the system is to give the user control over the ranking of the results by means of a simple weighting scheme. Using this approach, researchers can effortlessly explore the literature regarding a group of genes and focus on the different aspects relating to these genes.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-11-212","type":"journal-article","created":{"date-parts":[[2010,5,18]],"date-time":"2010-05-18T06:17:37Z","timestamp":1274163457000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Concept-based query expansion for retrieving gene related publications from MEDLINE"],"prefix":"10.1186","volume":"11","author":[{"given":"S\u00e9rgio","family":"Matos","sequence":"first","affiliation":[]},{"given":"Joel P","family":"Arrais","sequence":"additional","affiliation":[]},{"given":"Jo\u00e3o","family":"Maia-Rodrigues","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 Luis","family":"Oliveira","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,4,28]]},"reference":[{"issue":"Suppl 2","key":"3669_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 C, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A: Text mining for biology - the way forward: opinions from leading scientists. Genome Biol 2008, 9(Suppl 2):S7. 10.1186\/gb-2008-9-s2-s7","journal-title":"Genome Biol"},{"issue":"2","key":"3669_CR2","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/nrg1768","volume":"7","author":"LJ Jensen","year":"2006","unstructured":"Jensen LJ, Saric J, Bork P: Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 2006, 7(2):119\u2013129. 10.1038\/nrg1768","journal-title":"Nat Rev Genet"},{"issue":"2","key":"3669_CR3","doi-asserted-by":"publisher","first-page":"e65","DOI":"10.1371\/journal.pbio.0030065","volume":"3","author":"D Rebholz-Schuhmann","year":"2005","unstructured":"Rebholz-Schuhmann D, Kirsch H, Couto F: Facts from text-is text mining ready to deliver? PLoS Biol 2005, 3(2):e65. 10.1371\/journal.pbio.0030065","journal-title":"PLoS Biol"},{"issue":"3","key":"3669_CR4","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1093\/bib\/6.3.222","volume":"6","author":"H Shatkay","year":"2005","unstructured":"Shatkay H: Hairpins in bookstacks: information retrieval from biomedical text. Brief Bioinform 2005, 6(3):222\u2013238. 10.1093\/bib\/6.3.222","journal-title":"Brief Bioinform"},{"issue":"7","key":"3669_CR5","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1186\/gb-2005-6-7-224","volume":"6","author":"M Krallinger","year":"2005","unstructured":"Krallinger M, Valencia A: Text-mining and information-retrieval services for molecular biology. Genome Biol 2005, 6(7):224. 10.1186\/gb-2005-6-7-224","journal-title":"Genome Biol"},{"key":"3669_CR6","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511809071","volume-title":"Introduction to Information Retrieval","author":"C Manning","year":"2008","unstructured":"Manning C, Raghavan P, Sch\u00fctze H: Introduction to Information Retrieval. New York: Cambridge University Press; 2008."},{"issue":"6","key":"3669_CR7","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1093\/bib\/bbn032","volume":"9","author":"JJ Kim","year":"2008","unstructured":"Kim JJ, Rebholz-Schuhmann D: Categorization of services for seeking information in biomedical literature: a typology for improvement of practice. Brief Bioinform 2008, 9(6):452\u2013465. 10.1093\/bib\/bbn032","journal-title":"Brief Bioinform"},{"issue":"3","key":"3669_CR8","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1093\/bib\/6.3.277","volume":"6","author":"M Weeber","year":"2005","unstructured":"Weeber M, Kors JA, Mons B: Online tools to support literature-based discovery in the life sciences. Brief Bioinform 2005, 6(3):277\u2013286. 10.1093\/bib\/6.3.277","journal-title":"Brief Bioinform"},{"key":"3669_CR9","doi-asserted-by":"crossref","unstructured":"Doms A, Schroeder M: GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res 2005, (33 Web Server):W783\u2013786. 10.1093\/nar\/gki470","DOI":"10.1093\/nar\/gki470"},{"issue":"7","key":"3669_CR10","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1038\/ng0704-664","volume":"36","author":"R Hoffmann","year":"2004","unstructured":"Hoffmann R, Valencia A: A gene network for navigating the literature. Nat Genet 2004, 36(7):664. 10.1038\/ng0704-664","journal-title":"Nat Genet"},{"issue":"19","key":"3669_CR11","doi-asserted-by":"publisher","first-page":"2444","DOI":"10.1093\/bioinformatics\/btl408","volume":"22","author":"C Plake","year":"2006","unstructured":"Plake C, Schiemann T, Pankalla M, Hakenberg J, Leser U: AliBaba: PubMed as a graph. Bioinformatics 2006, 22(19):2444\u20132445. 10.1093\/bioinformatics\/btl408","journal-title":"Bioinformatics"},{"issue":"2","key":"3669_CR12","doi-asserted-by":"publisher","first-page":"e237","DOI":"10.1093\/bioinformatics\/btl302","volume":"23","author":"D Rebholz-Schuhmann","year":"2007","unstructured":"Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Riethoven M, Stoehr P: EBIMed-text crunching to gather facts for proteins from Medline. Bioinformatics 2007, 23(2):e237\u2013244. 10.1093\/bioinformatics\/btl302","journal-title":"Bioinformatics"},{"issue":"21","key":"3669_CR13","doi-asserted-by":"publisher","first-page":"2559","DOI":"10.1093\/bioinformatics\/btn469","volume":"24","author":"Y Tsuruoka","year":"2008","unstructured":"Tsuruoka Y, Tsujii J, Ananiadou S: FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics 2008, 24(21):2559\u20132560. 10.1093\/bioinformatics\/btn469","journal-title":"Bioinformatics"},{"key":"3669_CR14","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1186\/1471-2105-5-147","volume":"5","author":"H Chen","year":"2004","unstructured":"Chen H, Sharp BM: Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics 2004, 5: 147. 10.1186\/1471-2105-5-147","journal-title":"BMC Bioinformatics"},{"key":"3669_CR15","first-page":"1017","volume-title":"Proceedings of the 21st International Conference on Computational Linguistics and 44th Annual Meeting of the Association for Computational Linguistics: 17-21 July 2006","author":"Y Miyao","year":"2006","unstructured":"Miyao Y, Ohta T, Masuda K, Tsuruoka Y, Yoshida K, Ninomiya T, Tsujii J: Semantic retrieval for the accurate identification of relational concepts in massive textbases. In Proceedings of the 21st International Conference on Computational Linguistics and 44th Annual Meeting of the Association for Computational Linguistics: 17\u201321 July 2006. Sydney, Australia. Association for Computational Linguistics; 2006:1017\u20131024."},{"key":"3669_CR16","doi-asserted-by":"crossref","unstructured":"Arrais J, Santos B, Fernandes J, Carreto L, Santos MAS, Oliveira JL: GeneBrowser: an approach for integration and functional classification of genomic data. J Integr Bioinform 2007., 4(3):","DOI":"10.1515\/jib-2007-82"},{"issue":"2","key":"3669_CR17","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/S0888-7543(02)00021-6","volume":"81","author":"S Draghici","year":"2003","unstructured":"Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA: Global functional profiling of gene expression. Genomics 2003, 81(2):98\u2013104. 10.1016\/S0888-7543(02)00021-6","journal-title":"Genomics"},{"issue":"12","key":"3669_CR18","doi-asserted-by":"publisher","first-page":"1980","DOI":"10.1093\/bioinformatics\/bth183","volume":"20","author":"M Korotkiy","year":"2004","unstructured":"Korotkiy M, Middelburg R, Dekker H, van Harmelen F, Lankelma J: A tool for gene expression based PubMed search through combining data sources. Bioinformatics 2004, 20(12):1980\u20131982. 10.1093\/bioinformatics\/bth183","journal-title":"Bioinformatics"},{"issue":"1","key":"3669_CR19","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1093\/bioinformatics\/btp597","volume":"26","author":"MJ Schuemie","year":"2010","unstructured":"Schuemie MJ, Kang N, Hekkelman ML, Kors JA: GeneE: gene and protein query expansion with disambiguation. Bioinformatics 2010, 26(1):147\u2013148. 10.1093\/bioinformatics\/btp597","journal-title":"Bioinformatics"},{"key":"3669_CR20","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1007\/978-3-540-85861-4_10","volume-title":"Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008): 22-24 October 2008; Salamanca, Spain","author":"J Arrais","year":"2009","unstructured":"Arrais J, Rodrigues J, Oliveira J: Improving Literature Searches in Gene Expression Studies. In Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008): 22\u201324 October 2008; Salamanca, Spain. Edited by: Corchado JM, De Paz JF, Rocha MP, Fern\u00e1ndez-Riverola F. Berlin: Springer; 2009:74\u201382. full_text"},{"issue":"2","key":"3669_CR21","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1093\/bioinformatics\/bth496","volume":"21","author":"L Chen","year":"2005","unstructured":"Chen L, Liu H, Friedman C: Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics 2005, 21(2):248\u2013256. 10.1093\/bioinformatics\/bth496","journal-title":"Bioinformatics"},{"issue":"3","key":"3669_CR22","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1016\/j.jbi.2006.09.002","volume":"40","author":"MJ Schuemie","year":"2007","unstructured":"Schuemie MJ, Mons B, Weeber M, Kors JA: Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification. J Biomed Inform 2007, 40(3):316\u2013324. 10.1016\/j.jbi.2006.09.002","journal-title":"J Biomed Inform"},{"key":"3669_CR23","first-page":"9","volume-title":"Proceedings of BioLINK 2004: linking biological literature, ontologies, and databases: 6 May 2004; Boston","author":"A Koike","year":"2004","unstructured":"Koike A, Takagi T: Gene\/protein\/family name recognition in biomedical literature. In Proceedings of BioLINK 2004: linking biological literature, ontologies, and databases: 6 May 2004; Boston. Association for Computational Linguistics; 2004:9\u201316."},{"issue":"1","key":"3669_CR24","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1007\/s10791-008-9075-7","volume":"12","author":"Y Lu","year":"2009","unstructured":"Lu Y, Fang H, Zhai C: An empirical study of gene synonym query expansion in biomedical information retrieval. Inf Retr 2009, 12(1):51\u201368. 10.1007\/s10791-008-9075-7","journal-title":"Inf Retr"},{"issue":"1","key":"3669_CR25","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1007\/s10791-008-9073-9","volume":"12","author":"N Stokes","year":"2009","unstructured":"Stokes N, Li Y, Cavedon L, Zobel J: Exploring criteria for successful query expansion in the genomic domain. Inf Retr 2009, 12(1):17\u201350. 10.1007\/s10791-008-9073-9","journal-title":"Inf Retr"},{"key":"3669_CR26","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1007\/978-3-540-85861-4_12","volume-title":"Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008): 22-24 October 2008; Salamanca, Spain","author":"J Pinto","year":"2009","unstructured":"Pinto J, Dias O, Louren\u00e7o A, Carneiro S, Ferreira E, Rocha I, Rocha M: Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. In Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008): 22\u201324 October 2008; Salamanca, Spain. Edited by: Corchado JM, De Paz JF, Rocha MP, Fern\u00e1ndez-Riverola F. Berlin: Springer; 2009:92\u2013101. full_text"},{"key":"3669_CR27","first-page":"850","volume-title":"Proceedings of the International Conference on Bioinformatics and Biomedicine (ICBB 2009): 26-29 October 2009; Venice, Italy","author":"J Arrais","year":"2009","unstructured":"Arrais J, Pereira JE, Fernandes J, Oliveira JL: GeNS: a biological data integration platform. Proceedings of the International Conference on Bioinformatics and Biomedicine (ICBB 2009): 26\u201329 October 2009; Venice, Italy 2009, 850\u2013855."},{"key":"3669_CR28","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1145\/160688.160713","volume-title":"Proceedings of the 16th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval: 27 June - 1 July 1993;","author":"Y Qiu","year":"1993","unstructured":"Qiu Y, Frei H-P: Concept based query expansion. In Proceedings of the 16th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval: 27 June - 1 July 1993; Pittsburgh, PA. ACM; 1993:160\u2013170. full_text"},{"key":"3669_CR29","unstructured":"Apache Lucene[http:\/\/lucene.apache.org\/]"},{"key":"3669_CR30","unstructured":"Entrez Programming Utilities[http:\/\/eutils.ncbi.nlm.nih.gov\/corehtml\/query\/static\/eutils_help.html]"},{"key":"3669_CR31","first-page":"1","volume":"13","author":"WR Hersh","year":"2006","unstructured":"Hersh WR, Bhupatiraju RT, Ross L, Roberts P, Cohen AM, Kraemer DF: Enhancing access to the Bibliome: the TREC 2004 Genomics Track. J Biomed Discov Collab 2006, 13: 1\u20133.","journal-title":"J Biomed Discov Collab"},{"issue":"1","key":"3669_CR32","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1007\/s10791-008-9074-8","volume":"12","author":"Z Lu","year":"2009","unstructured":"Lu Z, Kim W, Wilbur WJ: Evaluation of Query Expansion Using MeSH in PubMed. Inf Retr 2009, 12(1):69\u201380. 10.1007\/s10791-008-9074-8","journal-title":"Inf Retr"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-212.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T06:16:39Z","timestamp":1685600199000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-212"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,28]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3669"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-212","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,4,28]]},"assertion":[{"value":"1 July 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 April 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 April 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"212"}}