{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T13:13:12Z","timestamp":1779887592488,"version":"3.53.1"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,5,31]],"date-time":"2013-05-31T00:00:00Z","timestamp":1369958400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,12]]},"DOI":"10.1186\/1471-2105-14-171","type":"journal-article","created":{"date-parts":[[2013,5,31]],"date-time":"2013-05-31T16:14:36Z","timestamp":1370016876000},"source":"Crossref","is-referenced-by-count":36,"title":["GeneRIF indexing: sentence selection based on machine learning"],"prefix":"10.1186","volume":"14","author":[{"given":"Antonio J","family":"Jimeno-Yepes","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J Caitlin","family":"Sticco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James G","family":"Mork","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan R","family":"Aronson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2013,5,31]]},"reference":[{"key":"5930_CR1","unstructured":"MEDLINE Statistics. [\n                    http:\/\/www.nlm.nih.gov\/bsd\/licensee\/baselinestats.html\n                    \n                  ]"},{"key":"5930_CR2","first-page":"14","volume-title":"Proceedings of the Text Retrieval Conference","author":"W Hersh","year":"2003","unstructured":"Hersh W, Bhupatiraju R: TREC genomics track overview. Proceedings of the Text Retrieval Conference. 2003, Gaithersburg, 14-23."},{"issue":"Suppl 8","key":"5930_CR3","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2105-12-S8-S4","volume":"12","author":"C Arighi","year":"2011","unstructured":"Arighi C, Roberts P, Agarwal S, Bhattacharya S, Cesareni G, Chatr-Aryamontri A, Clematide S, Gaudet P, Giglio M, Harrow I et al.: BioCreative III interactive task: an overview. BMC Bioinformatics. 2011, 12 (Suppl 8): S4-10.1186\/1471-2105-12-S8-S4.","journal-title":"BMC Bioinformatics"},{"key":"5930_CR4","first-page":"17","volume-title":"Proceedings of the AMIA Symposium","author":"A Aronson","year":"2000","unstructured":"Aronson A, Bodenreider O, Chang H, Humphrey S, Mork J, Nelson S, Rindflesch T, Wilbur W: The NLM indexing initiative. Proceedings of the AMIA Symposium. 2000, Los Angeles: American Medical Informatics Association, 17-21."},{"key":"5930_CR5","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1145\/2110363.2110450","volume-title":"Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium","author":"A Jimeno Yepes","year":"2012","unstructured":"Jimeno Yepes A, Mork JG, Wilkowski B, Demner Fushman D, Aronson AR: MEDLINE MeSH indexing: lessons learned from machine learning and future directions. Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium. 2012, Miami: ACM, 737-742."},{"issue":"2","key":"5930_CR6","doi-asserted-by":"publisher","first-page":"151","DOI":"10.5626\/JCSE.2012.6.2.151","volume":"6","author":"A Jimeno-Yepes","year":"2012","unstructured":"Jimeno-Yepes A, Mork JG, Demner-Fushman D, Aronson AR: A one-size-fits-all indexing method does not exist: automatic selection based on meta-learning. J Comput Sci Eng. 2012, 6 (2): 151-160. 10.5626\/JCSE.2012.6.2.151.","journal-title":"J Comput Sci Eng"},{"issue":"5","key":"5930_CR7","doi-asserted-by":"publisher","first-page":"660","DOI":"10.1136\/amiajnl-2010-000055","volume":"18","author":"M Huang","year":"2011","unstructured":"Huang M, N\u00e9v\u00e9ol A, Lu Z: Recommending MeSH terms for annotating biomedical articles. J Am Med Inform Assoc. 2011, 18 (5): 660-667. 10.1136\/amiajnl-2010-000055.","journal-title":"J Am Med Inform Assoc"},{"key":"5930_CR8","volume-title":"Database (Oxford)","author":"L Hirschman","year":"2012","unstructured":"Hirschman L, Burns G, Krallinger M, Arighi C, Cohen K, Valencia A, Wu C, Chatr-Aryamontri A, Dowell K, Huala E et al.: Text mining for the biocuration workflow. Database (Oxford). 2012, 2012,"},{"key":"5930_CR9","volume-title":"Database (Oxford)","author":"A Jimeno-Yepes","year":"2013","unstructured":"Jimeno-Yepes A, Li C, Arregui M, Kirsch H, Rebholz-Schuhmann D: PCorral - interactive mining of protein interactions from MEDLINE. Database (Oxford). 2013, 2013,"},{"key":"5930_CR10","volume-title":"Database (Oxford)","author":"Z Lu","year":"2012","unstructured":"Lu Z, Hirschman L: Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II. Database (Oxford). 2012, 2012,"},{"key":"5930_CR11","volume-title":"Database (Oxford)","author":"K Verspoor","year":"2013","unstructured":"Verspoor K, Jimeno Yepes A, Cavedon L, McIntosh T, Herten-Crabb A, Thomas Z, Plazzer J: Annotating the biomedical literature for the Human Variome. Database (Oxford). 2013, 2013,"},{"key":"5930_CR12","unstructured":"Entrez Gene site. [\n                    http:\/\/www.ncbi.nlm.nih.gov\/sites\/entrez?db=gene\n                    \n                  ]"},{"key":"5930_CR13","unstructured":"NLM Indexing Section. [\n                    http:\/\/www.nlm.nih.gov\/bsd\/indexhome.html\n                    \n                  ]"},{"key":"5930_CR14","first-page":"460","volume-title":"AMIA Annual Symposium proceedings Volume 2003","author":"J Mitchell","year":"2003","unstructured":"Mitchell J, Aronson A, Mork J, Folk L, Humphrey S, Ward J: Gene indexing: characterization and analysis of NLM\u2019s GeneRIFs. AMIA Annual Symposium proceedings Volume 2003. 2003, Washington: American Medical Informatics Association, 460-464."},{"key":"5930_CR15","first-page":"268","volume-title":"Medinfo 2004: proceedings of the 11th, World Conference on Medical Informatics","author":"A Aronson","year":"2004","unstructured":"Aronson A, Mork J, Gay C, Humphrey S, Rogers W: The NLM Indexing Initiative\u2019s Medical Text Indexer. Medinfo 2004: proceedings of the 11th, World Conference on Medical Informatics. 2004, San Francisco: OCSL Press, 268-272."},{"key":"5930_CR16","first-page":"167","volume-title":"Proceedings of the Text Retrieval Conference","author":"R Jelier","year":"2003","unstructured":"Jelier R, Schuemie M, Eijk C, Weeber M, Mulligen E, Schijvenaars B, Mons B, Kors J: Searching for GeneRIFs: concept-based query expansion and Bayes classification. Proceedings of the Text Retrieval Conference. 2003, Gaithersburg, 167-174."},{"key":"5930_CR17","first-page":"612","volume-title":"Proceedings of the Text Retrieval Conference","author":"G Bhalotia","year":"2003","unstructured":"Bhalotia G, Nakov P, Schwartz A, Hearst M: BioText team report for the TREC 2003 genomics track. Proceedings of the Text Retrieval Conference. 2003, Gaithersburg, 612-621."},{"key":"5930_CR18","first-page":"52","volume-title":"Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing","author":"Z Lu","year":"2006","unstructured":"Lu Z, Cohen K, Hunter L: Finding GeneRIFs via gene ontology annotations. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2006, Hawaii, 52-52."},{"key":"5930_CR19","first-page":"269","volume-title":"Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing","author":"Z Lu","year":"2007","unstructured":"Lu Z, Cohen K, Hunter L: GeneRIF quality assurance as summary revision. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2007, Hawaii, 269-269."},{"issue":"Suppl 3","key":"5930_CR20","doi-asserted-by":"publisher","first-page":"S9","DOI":"10.1186\/1471-2105-9-S3-S9","volume":"9","author":"J Gobeill","year":"2008","unstructured":"Gobeill J, Tbahriti I, Ehrler F, Mottaz A, Veuthey AL, Ruch P: Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. BMC Bioinformatics. 2008, 9 (Suppl 3): S9-10.1186\/1471-2105-9-S3-S9. [\n                    http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18426554?dopt=Abstract\n                    \n                  ]","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 8","key":"5930_CR21","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-12-S8-S2","volume":"12","author":"Z Lu","year":"2011","unstructured":"Lu Z, Kao H, Wei C, Huang M, Liu J, Kuo C, Hsu C, Tsai R, Dai H, Okazaki N et al.: The gene normalization task in BioCreative III. BMC Bioinformatics. 2011, 12 (Suppl 8): S2-10.1186\/1471-2105-12-S8-S2.","journal-title":"BMC Bioinformatics"},{"key":"5930_CR22","unstructured":"GeneRIF ftp file from NCBI\u2019s repository. January 2013. [\n                    http:\/\/ftp.ncbi.nih.gov\/gene\/GeneRIF\/generifs_basic.gz\n                    \n                  ]"},{"key":"5930_CR23","unstructured":"MEDLINE Baseline. [\n                    http:\/\/mbr.nlm.nih.gov\n                    \n                  ]"},{"key":"5930_CR24","unstructured":"Gene Indexing. NLM Technical Bulletin. Sep-Oct 2002. [\n                    http:\/\/www.nlm.nih.gov\/pubs\/techbull\/so02\/so02_gene_indexing.html\n                    \n                  ]"},{"key":"5930_CR25","first-page":"1269","volume-title":"Data Min Knowl Discov Handb Springer USA","author":"E Frank","year":"2010","unstructured":"Frank E, Hall M, Holmes G, Kirkby R, Pfahringer B, Witten I, Trigg L: Weka-a machine learning workbench for data mining. Data Min Knowl Discov Handb Springer USA. 2010, 1269-1277."},{"key":"5930_CR26","unstructured":"Structured Abstracts in MEDLINE. [\n                    http:\/\/structuredabstracts.nlm.nih.gov\/\n                    \n                  ]"},{"key":"5930_CR27","unstructured":"MTI ML machine learning package. [\n                    http:\/\/ii.nlm.nih.gov\/MTI_ML\/index.shtml\n                    \n                  ]"},{"key":"5930_CR28","doi-asserted-by":"publisher","first-page":"65","DOI":"10.3115\/1654415.1654427","volume-title":"Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology","author":"J Lin","year":"2006","unstructured":"Lin J, Karakos D, Demner-Fushman D, Khudanpur S: Generative content models for structural analysis of medical abstracts. Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology. 2006, Sydney: Association for, Computational Linguistics, 65-72."},{"key":"5930_CR29","first-page":"381","volume-title":"Proceedings of 3rd International Joint Conference on Natural Language Processing","author":"K Hirohata","year":"2008","unstructured":"Hirohata K, Okazaki N, Ananiadou S, Ishizuka M, Biocentre MI: Identifying sections in scientific abstracts using conditional random fields. Proceedings of 3rd International Joint Conference on Natural Language Processing. 2008, Hyderabad, 381-388."},{"key":"5930_CR30","unstructured":"Sutton C: GRMM: GRaphical Models in Mallet 2006. \n                    http:\/\/mallet.cs.umass.edu\/grmm\n                    \n                  ,"},{"key":"5930_CR31","unstructured":"McCallum A: Mallet: A machine learning for language toolkit. \n                    http:\/\/mallet.cs.umass.edu\n                    \n                  ,"},{"issue":"16","key":"5930_CR32","doi-asserted-by":"publisher","first-page":"i126","DOI":"10.1093\/bioinformatics\/btn299","volume":"24","author":"J Hakenberg","year":"2008","unstructured":"Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G: Inter-species normalization of gene mentions with GNAT. Bioinformatics. 2008, 24 (16): i126-i132. 10.1093\/bioinformatics\/btn299.","journal-title":"Bioinformatics"},{"issue":"3","key":"5930_CR33","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1136\/jamia.2009.002733","volume":"17","author":"A Aronson","year":"2010","unstructured":"Aronson A, Lang F: An overview of MetaMap: historical perspective and recent advances. J Am Med Inf Assoc. 2010, 17 (3): 229-","journal-title":"J Am Med Inf Assoc"},{"key":"5930_CR34","first-page":"451","volume-title":"Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing","author":"A Schwartz","year":"2003","unstructured":"Schwartz A, Hearst M: A simple algorithm for identifying abbreviation definitions in biomedical text. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2003, Hawaii, 451-462."},{"issue":"8","key":"5930_CR35","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1093\/bioinformatics\/btm056","volume":"23","author":"H Xu","year":"2007","unstructured":"Xu H, Fan J, Hripcsak G, Mendon\u00e7a E, Markatou M, Friedman C: Gene symbol disambiguation using knowledge-based profiles. Bioinformatics. 2007, 23 (8): 1015-1022. 10.1093\/bioinformatics\/btm056.","journal-title":"Bioinformatics"},{"key":"5930_CR36","volume-title":"ISMB: Vienna, Austria","author":"Y Lussier","year":"2007","unstructured":"Lussier Y, Friedman C: BiomedLEE: a natural-language processor for extracting and representing phenotypes, underlying molecular mechanisms and their relationships. ISMB: Vienna, Austria. 2007"},{"key":"5930_CR37","unstructured":"GOCat EAGLi site. [\n                    http:\/\/eagl.unige.ch\/GOCat\/\n                    \n                  ]"},{"issue":"6","key":"5930_CR38","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1093\/bioinformatics\/bti783","volume":"22","author":"P Ruch","year":"2006","unstructured":"Ruch P: Automatic assignment of biomedical categories: toward a generic approach. Bioinformatics. 2006, 22 (6): 658-664. 10.1093\/bioinformatics\/bti783.","journal-title":"Bioinformatics"},{"issue":"23","key":"5930_CR39","doi-asserted-by":"publisher","first-page":"3174","DOI":"10.1093\/bioinformatics\/btp548","volume":"25","author":"S Agarwal","year":"2009","unstructured":"Agarwal S, Yu H: Automatically classifying sentences in full-text biomedical articles into introduction, methods, results and discussion. Bioinformatics. 2009, 25 (23): 3174-3180. 10.1093\/bioinformatics\/btp548.","journal-title":"Bioinformatics"},{"key":"5930_CR40","first-page":"993","volume":"3","author":"D Blei","year":"2003","unstructured":"Blei D, Ng A, Jordan M: Latent dirichlet allocation. J Mach Learn Res. 2003, 3: 993-1022.","journal-title":"J Mach Learn Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-171.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-171\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-171.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T05:41:16Z","timestamp":1548135676000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-171"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,31]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["5930"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-171","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,5,31]]},"article-number":"171"}}