{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:14:26Z","timestamp":1764688466607},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,4,22]],"date-time":"2005-04-22T00:00:00Z","timestamp":1114128000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,4,22]],"date-time":"2005-04-22T00:00:00Z","timestamp":1114128000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>Text-mining can assist biomedical researchers in reducing information overload by extracting useful knowledge from large collections of text. We developed a novel text-mining method based on analyzing the network structure created by symbol co-occurrences as a way to extend the capabilities of knowledge extraction. The method was applied to the task of automatic gene and protein name synonym extraction.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>Performance was measured on a test set consisting of about 50,000 abstracts from one year of MEDLINE. Synonyms retrieved from curated genomics databases were used as a gold standard. The system obtained a maximum F-score of 22.21% (23.18% precision and 21.36% recall), with high efficiency in the use of seed pairs.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>The method performs comparably with other studied methods, does not rely on sophisticated named-entity recognition, and requires little initial seed knowledge.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-103","type":"journal-article","created":{"date-parts":[[2005,4,22]],"date-time":"2005-04-22T18:13:52Z","timestamp":1114193632000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts"],"prefix":"10.1186","volume":"6","author":[{"given":"AM","family":"Cohen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"WR","family":"Hersh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C","family":"Dubay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"K","family":"Spackman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,4,22]]},"reference":[{"key":"428_CR1","first-page":"460","volume-title":"Proc AMIA Symp","author":"JA Mitchell","year":"2003","unstructured":"Mitchell JA, Aronson AR, Mork JG, Folk LC, Humphrey SM, Ward JM: Gene Indexing: Characterization and Analysis of NLM's GeneRIFs. Proc AMIA Symp 2003, 460\u2013464."},{"key":"428_CR2","first-page":"642","volume-title":"Proc AMIA Symp","author":"P Srinivasan","year":"2001","unstructured":"Srinivasan P: MeSHmap: a text mining tool for MEDLINE. Proc AMIA Symp 2001, 642\u2013646."},{"key":"428_CR3","doi-asserted-by":"publisher","first-page":"i340","DOI":"10.1093\/bioinformatics\/btg1047","volume":"19","author":"H Yu","year":"2003","unstructured":"Yu H, Agichtein E: Extracting synonymous gene and protein terms from biological literature. Bioinformatics 2003, 19: i340-i349. 10.1093\/bioinformatics\/btg1047","journal-title":"Bioinformatics"},{"key":"428_CR4","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1002\/(SICI)1097-4571(1999)50:7<574::AID-ASI3>3.0.CO;2-Q","volume":"50","author":"RK Lindsay","year":"1999","unstructured":"Lindsay RK, Gordon MD: Literature-based discovery by lexical statistics. J Am Soc Inform Sci 1999, 50: 574\u2013587. Publisher Full Text 10.1002\/(SICI)1097-4571(1999)50:7<574::AID-ASI3>3.0.CO;2-Q","journal-title":"J Am Soc Inform Sci"},{"key":"428_CR5","first-page":"29","volume":"78","author":"DR Swanson","year":"1990","unstructured":"Swanson DR: Medical literature as a potential source of new knowledge. Bull Med Libr Assoc 1990, 78: 29\u201337.","journal-title":"Bull Med Libr Assoc"},{"key":"428_CR6","first-page":"415","volume-title":"Pac Symp Biocomput","author":"H Liu","year":"2003","unstructured":"Liu H, Friedman C: Mining terminological knowledge in large biomedical corpora. Pac Symp Biocomput 2003, 415\u2013426."},{"key":"428_CR7","first-page":"371","volume":"10","author":"J Pustejovsky","year":"2001","unstructured":"Pustejovsky J, Castano J, Cochran B, Kotecki M, Morrell M: Automatic extraction of acronym-meaning pairs from MEDLINE databases. Medinfo 2001, 10: 371\u2013375.","journal-title":"Medinfo"},{"key":"428_CR8","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1197\/jamia.M1139","volume":"9","author":"JT Chang","year":"2002","unstructured":"Chang JT, Schutze H, Altman RB: Creating an online dictionary of abbreviations from MEDLINE. J Am Med Inform Assoc 2002, 9: 612\u2013620. 10.1197\/jamia.M1139","journal-title":"J Am Med Inform Assoc"},{"key":"428_CR9","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/S1532-0464(03)00014-5","volume":"35","author":"L Hirschman","year":"2002","unstructured":"Hirschman L, Morgan AA, Yeh AS: Rutabaga by any other name: extracting biological names. J Biomed Inform 2002, 35: 247\u2013259. 10.1016\/S1532-0464(03)00014-5","journal-title":"J Biomed Inform"},{"key":"428_CR10","first-page":"72","volume":"9","author":"D Proux","year":"1998","unstructured":"Proux D, Rechenmann F, Julliard L, Pillet VV, Jacq B: Detecting Gene Symbols and Names in Biological Texts: A First Step toward Pertinent Information Extraction. Genome Inform Ser Workshop Genome Inform 1998, 9: 72\u201380.","journal-title":"Genome Inform Ser Workshop Genome Inform"},{"key":"428_CR11","doi-asserted-by":"crossref","unstructured":"Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S: Guidelines for Human Gene Nomenclature (2002).[http:\/\/www.gene.ucl.ac.uk\/nomenclature\/guidelines.html]","DOI":"10.1006\/geno.2002.6748"},{"key":"428_CR12","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1093\/nar\/gkg094","volume":"31","author":"FlyBase Consortium","year":"2003","unstructured":"FlyBase Consortium: The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 2003, 31: 172\u2013175. 10.1093\/nar\/gkg094","journal-title":"Nucleic Acids Res"},{"key":"428_CR13","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1093\/nar\/30.1.169","volume":"30","author":"HM Wain","year":"2002","unstructured":"Wain HM, Lush M, Ducluzeau F, Povey S: Genew: the human gene nomenclature database. Nucleic Acids Res 2002, 30: 169\u2013171. 10.1093\/nar\/30.1.169","journal-title":"Nucleic Acids Res"},{"key":"428_CR14","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1007\/s00439-001-0615-0","volume":"109","author":"S Povey","year":"2001","unstructured":"Povey S, Lovering R, Bruford E, Wright M, Lush M, Wain H: The HUGO Gene Nomenclature Committee (HGNC). Hum Genet 2001, 109: 678\u2013680. 10.1007\/s00439-001-0615-0","journal-title":"Hum Genet"},{"key":"428_CR15","unstructured":"The Human Genome Organisation: HUGO Gene Nomenclature Committee.[http:\/\/www.gene.ucl.ac.uk\/nomenclature\/]"},{"key":"428_CR16","first-page":"403","volume-title":"Pac Symp Biocomput","author":"D Hanisch","year":"2003","unstructured":"Hanisch D, Fluck J, Mevissen HT, Zimmer R: Playing biology's name game: identifying protein names in scientific text. Pac Symp Biocomput 2003, 403\u2013414."},{"key":"428_CR17","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/88213","volume":"28","author":"TK Jenssen","year":"2001","unstructured":"Jenssen TK, Laegreid A, Komorowski J, Hovig E: A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001, 28: 21\u201328. 10.1038\/88213","journal-title":"Nat Genet"},{"key":"428_CR18","first-page":"919","volume-title":"Proc AMIA Symp","author":"H Yu","year":"2002","unstructured":"Yu H, Hatzivassiloglou V, Friedman C, Rzhetsky A, Wilbur WJ: Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. Proc AMIA Symp 2002, 919\u2013923."},{"key":"428_CR19","volume-title":"Extracting patterns and relations from the World-Wide Web: March 1998.","author":"S Brin","year":"1998","unstructured":"Brin S: Extracting patterns and relations from the World-Wide Web: March 1998. 1998."},{"key":"428_CR20","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1145\/376284.375774","volume":"30","author":"E Agichtein","year":"2001","unstructured":"Agichtein E, Gravano L, Pavel J, Sokolova V, Voskoboynik A: Snowball: A prototype system for extracting relations from large text collections. Sigmod Record 2001, 30: 612\u2013612.","journal-title":"Sigmod Record"},{"key":"428_CR21","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.ymgme.2003.08.023","volume":"80","author":"R Clipsham","year":"2003","unstructured":"Clipsham R, McCabe ER: DAX1 and its network partners: exploring complexity in development. Mol Genet Metab 2003, 80: 81\u2013120. 10.1016\/j.ymgme.2003.08.023","journal-title":"Mol Genet Metab"},{"key":"428_CR22","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1210\/jc.2002-021034","volume":"88","author":"G Ozisik","year":"2003","unstructured":"Ozisik G, Mantovani G, Achermann JC, Persani L, Spada A, Weiss J, Beck-Peccoz P, Jameson JL: An alternate translation initiation site circumvents an amino-terminal DAX1 nonsense mutation leading to a mild form of X-linked adrenal hypoplasia congenita. J Clin Endocrinol Metab 2003, 88: 417\u2013423. 10.1210\/jc.2002-021034","journal-title":"J Clin Endocrinol Metab"},{"key":"428_CR23","first-page":"858","volume":"3","author":"F Klein","year":"2004","unstructured":"Klein F, Feldhahn N, Muschen M: Interference of BCR-ABL1 kinase activity with antigen receptor signaling in B cell precursor leukemia cells. Cell Cycle 2004, 3: 858\u2013860.","journal-title":"Cell Cycle"},{"key":"428_CR24","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28: 27\u201330. 10.1093\/nar\/28.1.27","journal-title":"Nucleic Acids Res"},{"key":"428_CR25","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1093\/bioinformatics\/14.6.529","volume":"14","author":"FA Kolpakov","year":"1998","unstructured":"Kolpakov FA, Ananko EA, Kolesov GB, Kolchanov NA: GeneNet: a gene network database and its automated visualization. Bioinformatics 1998, 14: 529\u2013537. 10.1093\/bioinformatics\/14.6.529","journal-title":"Bioinformatics"},{"key":"428_CR26","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1093\/bioinformatics\/18.8.1124","volume":"18","author":"L Tanabe","year":"2002","unstructured":"Tanabe L, Wilbur WJ: Tagging gene and protein names in biomedical text. Bioinformatics 2002, 18: 1124\u20131132. 10.1093\/bioinformatics\/18.8.1124","journal-title":"Bioinformatics"},{"key":"428_CR27","first-page":"280","volume-title":"Complementary structures in disjoint science literatures: ; Chicago, Illinois, United States.","author":"DR Swanson","year":"1991","unstructured":"Swanson DR: Complementary structures in disjoint science literatures: ; Chicago, Illinois, United States. ACM Press; 1991:280--289."},{"key":"428_CR28","doi-asserted-by":"publisher","first-page":"I290","DOI":"10.1093\/bioinformatics\/bth914","volume":"20 Suppl 1","author":"P Srinivasan","year":"2004","unstructured":"Srinivasan P, Libbus B: Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 2004, 20 Suppl 1: I290-I296. 10.1093\/bioinformatics\/bth914","journal-title":"Bioinformatics"},{"key":"428_CR29","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/S0169-2607(98)00033-9","volume":"57","author":"NR Smalheiser","year":"1998","unstructured":"Smalheiser NR, Swanson DR: Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. Comput Methods Programs Biomed 1998, 57: 149\u2013153. 10.1016\/S0169-2607(98)00033-9","journal-title":"Comput Methods Programs Biomed"},{"key":"428_CR30","unstructured":"Cohen AM: Genetic Optimized Synonym Extraction Gold Standard Data Files.[http:\/\/medir.ohsu.edu\/~cohenaa\/synonym-extraction-gold-standard.html]"},{"key":"428_CR31","first-page":"1028","volume":"9","author":"SL Rose","year":"2003","unstructured":"Rose SL, Goodheart MJ, DeYoung BR, Smith BJ, Buller RE: p21 expression predicts outcome in p53-null ovarian carcinoma. Clin Cancer Res 2003, 9: 1028\u20131032.","journal-title":"Clin Cancer Res"},{"key":"428_CR32","doi-asserted-by":"publisher","first-page":"2479","DOI":"10.1111\/j.1572-0241.2003.08673.x","volume":"98","author":"G Tomer","year":"2003","unstructured":"Tomer G, Ceballos C, Concepcion E, Benkov KJ: NOD2\/CARD15 variants are associated with lower weight at diagnosis in children with Crohn's disease. Am J Gastroenterol 2003, 98: 2479\u20132484. 10.1016\/S0002-9270(03)01706-4","journal-title":"Am J Gastroenterol"},{"key":"428_CR33","first-page":"2300","volume":"63","author":"T Abe","year":"2003","unstructured":"Abe T, Terada K, Wakimoto H, Inoue R, Tyminski E, Bookstein R, Basilion JP, Chiocca EA: PTEN decreases in vivo vascularization of experimental gliomas in spite of proangiogenic stimuli. Cancer Res 2003, 63: 2300\u20132305.","journal-title":"Cancer Res"},{"key":"428_CR34","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1073\/pnas.98.2.404","volume":"98","author":"MEJ Newman","year":"2001","unstructured":"Newman MEJ: The structure of scientific collaboration networks. P Natl Acad Sci USA 2001, 98: 404\u2013409. 10.1073\/pnas.021544898","journal-title":"P Natl Acad Sci USA"},{"key":"428_CR35","first-page":"116","volume-title":"The GENITOR Algorithm and Selection Pressure: Why Rank-Based Allocation of Reproductive Trials is Best","author":"D Whitley","year":"1989","unstructured":"Whitley D: The GENITOR Algorithm and Selection Pressure: Why Rank-Based Allocation of Reproductive Trials is Best. Morgan-Kaufmann; 1989:116\u2013121."},{"key":"428_CR36","volume-title":"Colorado State University, Dept of CS, TR CS-93-103","author":"D Whitley","year":"1993","unstructured":"Whitley D: A Genetic Algorithm Tutorial. Colorado State University, Dept of CS, TR CS-93\u2013103 1993."},{"key":"428_CR37","first-page":"xii, 657 p.","volume-title":"Addison-Wesley series in computer science","author":"R Sedgewick","year":"1989","unstructured":"Sedgewick R: Algorithms. In Addison-Wesley series in computer science. 2nd edition. Reading, Mass., Addison-Wesley; 1989:xii, 657 p..","edition":"2nd"},{"key":"428_CR38","unstructured":"European Bioinformatics Institute: UniProt\/Swiss-Prot.[http:\/\/www.ebi.ac.uk\/swissprot\/index.html]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-103.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-103\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-103.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:10:59Z","timestamp":1728303059000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-103"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,4,22]]},"references-count":38,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["428"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-103","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2005,4,22]]},"assertion":[{"value":"26 November 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 April 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 April 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"103"}}