{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T14:17:11Z","timestamp":1790086631267,"version":"4.0.1"},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,9,9]],"date-time":"2016-09-09T00:00:00Z","timestamp":1473379200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,9,9]],"date-time":"2016-09-09T00:00:00Z","timestamp":1473379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Gene Ontology (GO) terms represent the standard for annotation and representation of molecular functions, biological processes and cellular compartments, but a large gap exists between the way concepts are represented in the ontology and how they are expressed in natural language text. The construction of highly specific GO terms is formulaic, consisting of parts and pieces from more simple terms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present two different types of manually generated rules to help capture the variation of how GO terms can appear in natural language text. The first set of rules takes into account the compositional nature of GO and recursively decomposes the terms into their smallest constituent parts. The second set of rules generates derivational variations of these smaller terms and compositionally combines all generated variants to form the original term. By applying both types of rules, new synonyms are generated for two-thirds of all GO terms and an increase in F-measure performance for recognition of GO on the CRAFT corpus from 0.498 to 0.636 is observed. Additionally, we evaluated the combination of both types of rules over one million full text documents from Elsevier; manual validation and error analysis show we are able to recognize GO concepts with reasonable accuracy (88 %) based on random sampling of annotations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>In this work we present a set of simple synonym generation rules that utilize the highly compositional and formulaic nature of the Gene Ontology concepts. We illustrate how the generated synonyms aid in improving recognition of GO concepts on two different biomedical corpora. We discuss other applications of our rules for GO ontology quality assurance, explore the issue of overgeneration, and provide examples of how similar methodologies could be applied to other biomedical terminologies. Additionally, we provide all generated synonyms for use by the text-mining community.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13326-016-0096-7","type":"journal-article","created":{"date-parts":[[2016,9,9]],"date-time":"2016-09-09T08:03:02Z","timestamp":1473408182000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition"],"prefix":"10.1186","volume":"7","author":[{"given":"Christopher S.","family":"Funk","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K. Bretonnel","family":"Cohen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lawrence E.","family":"Hunter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karin M.","family":"Verspoor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,9,9]]},"reference":[{"key":"96_CR1","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1471-2105-6-S1-S1","volume":"6","author":"L Hirschman","year":"2005","unstructured":"Hirschman L, Yeh A, Blaschke C, Valencia A. Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinforma. 2005; 6:S1.","journal-title":"BMC Bioinforma"},{"key":"96_CR2","doi-asserted-by":"publisher","first-page":"086","DOI":"10.1093\/database\/bau086","volume":"2014","author":"Y Mao","year":"2014","unstructured":"Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, et al. Overview of the gene ontology task at biocreative iv. Database. 2014; 2014:086.","journal-title":"Database"},{"key":"96_CR3","unstructured":"Verspoor C, Joslyn C, Papcun G. The Gene Ontology as a source of lexical semantic knowledge for a biological natural language processing application. In: Proceedings of the SIGIR\u201903 Workshop on Text Analysis and Search for Bioinformatics. Toronto: 2003."},{"key":"96_CR4","doi-asserted-by":"crossref","unstructured":"Cohen KB, Palmer M, Hunter L. Nominalization and alternations in biomedical language. PLoS ONE. 2008;3(9).","DOI":"10.1371\/journal.pone.0003158"},{"key":"96_CR5","doi-asserted-by":"crossref","unstructured":"Brewster C, Alani H, Dasmahapatra S, Wilks Y. Data-driven ontology evaluation. In: Proceedings of the 4th International Conference on Language Resources and Evaluation (LREC 2004). Lisbon, Portugal: 2004.","DOI":"10.63317\/4f6s9jyb29f4"},{"issue":"13","key":"96_CR6","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1093\/bioinformatics\/btm229","volume":"23","author":"W Baumgartner","year":"2007","unstructured":"Baumgartner W, Cohen K, Fox L, Acquaah-Mensah G, Hunter L. Manual curation is not sufficient for annotation of genomic databases. Bioinf. 2007; 23(13):41\u20138.","journal-title":"Bioinf"},{"key":"96_CR7","doi-asserted-by":"crossref","unstructured":"Funk CS, Hunter LE, Cohen KB. Combining heterogeneous data for prediction of disease related and pharmacogenes. In: Pacific Symposium on Biocomputing: 2014. p. 328\u201339.","DOI":"10.1142\/9789814583220_0032"},{"issue":"Suppl 3","key":"96_CR8","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1471-2105-14-S3-S10","volume":"14","author":"A Sokolov","year":"2013","unstructured":"Sokolov A, Funk C, Graim K, Verspoor K, Ben-Hur A. Combining heterogeneous data sources for accurate functional annotation of proteins. BMC Bioinforma. 2013; 14(Suppl 3):10. doi:10.1186\/1471-2105-14-S3-S10.","journal-title":"BMC Bioinforma"},{"issue":"1","key":"96_CR9","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/s13326-015-0006-4","volume":"6","author":"CS Funk","year":"2015","unstructured":"Funk CS, Kahanda I, Ben-Hur A, Verspoor KM. Evaluating a variety of text-mined features for automatic protein function prediction with gostruct. J Biomed Semant. 2015; 6(1):9.","journal-title":"J Biomed Semant"},{"key":"96_CR10","doi-asserted-by":"publisher","first-page":"S16","DOI":"10.1186\/1471-2105-6-S1-S16","volume":"6 Suppl 1","author":"C Blaschke","year":"2005","unstructured":"Blaschke C, Leon EA, Krallinger M, Valencia A. Evaluation of BioCreative assessment of task 2. BMC Bioinforma. 2005; 6 Suppl 1:S16.","journal-title":"BMC Bioinforma"},{"issue":"6","key":"96_CR11","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\u201364.","journal-title":"Bioinformatics"},{"key":"96_CR12","first-page":"4","volume":"2008","author":"S Gaudan","year":"2008","unstructured":"Gaudan S, Yepes AJ, Lee V, Rebholz-Schuhmann D. Combining evidence, specificity, and proximity towards the normalization of gene ontology terms in text. EURASIP J Bioinforma Syst Biol. 2008; 2008:4.","journal-title":"EURASIP J Bioinforma Syst Biol"},{"key":"96_CR13","doi-asserted-by":"publisher","first-page":"041","DOI":"10.1093\/database\/bat041","volume":"2013","author":"J Gobeill","year":"2013","unstructured":"Gobeill J, Pasche E, Vishnyakova D, Ruch P. Managing the data deluge: data-driven go category assignment improves while complexity of functional annotation increases. Database. 2013; 2013:041.","journal-title":"Database"},{"issue":"1","key":"96_CR14","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1186\/1471-2105-15-59","volume":"15","author":"C Funk","year":"2014","unstructured":"Funk C, Baumgartner W, Garcia B, Roeder C, Bada M, Cohen K, Hunter L, Verspoor K. Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinforma. 2014; 15(1):59.","journal-title":"BMC Bioinforma"},{"issue":"1","key":"96_CR15","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1186\/1471-2105-14-281","volume":"14","author":"D Campos","year":"2013","unstructured":"Campos D, Matos S, Oliveira JL. A modular framework for biomedical concept recognition. BMC Bioinforma. 2013; 14(1):281.","journal-title":"BMC Bioinforma"},{"issue":"3","key":"96_CR16","doi-asserted-by":"publisher","first-page":"0119091","DOI":"10.1371\/journal.pone.0119091","volume":"10","author":"T Groza","year":"2015","unstructured":"Groza T, Verspoor K. Assessing the impact of case sensitivity and term information gain on biomedical concept recognition. PloS ONE. 2015; 10(3):0119091.","journal-title":"PloS ONE"},{"key":"96_CR17","doi-asserted-by":"crossref","unstructured":"Tsuruoka Y, Tsujii J. Probabilistic term variant generator for biomedical terms. In: Proceedings of the 26th Annual International ACM SIGIR Conference on Research and Development in Informaion Retrieval. Toronto: 2003. p. 167\u201373.","DOI":"10.1145\/860435.860467"},{"issue":"5","key":"96_CR18","first-page":"1","volume":"1","author":"KM Hettne","year":"2010","unstructured":"Hettne KM, van Mulligen EM, Schuemie MJ, Schijvenaars BJ, Kors JA. Rewriting and suppressing umls terms for improved biomedical term identification. J Biomed Semant. 2010; 1(5):1\u20135.","journal-title":"J Biomed Semant"},{"key":"96_CR19","doi-asserted-by":"crossref","unstructured":"Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L. The compositional structure of Gene Ontology terms. In: Pac Symp Biocomput. NIH Public Access: 2004. p. 214\u201315.","DOI":"10.1142\/9789812704856_0021"},{"key":"96_CR20","doi-asserted-by":"crossref","unstructured":"Ogren P, Cohen K, Hunter L. Implications of compositionality in the Gene Ontology for its curation and usage. In: Pacific Symposium on Biocomputing: 2005. p. 174\u201385.","DOI":"10.1142\/9789812702456_0017"},{"issue":"12","key":"96_CR21","doi-asserted-by":"publisher","first-page":"1982","DOI":"10.1101\/gr.580102","volume":"12","author":"DP Hill","year":"2002","unstructured":"Hill DP, Blake JA, Richardson JE, Ringwald M. Extension and integration of the gene ontology (go): combining go vocabularies with external vocabularies. Genome Res. 2002; 12(12):1982\u20131991.","journal-title":"Genome Res"},{"issue":"6-7","key":"96_CR22","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1002\/cfg.435","volume":"5","author":"CJ Mungall","year":"2004","unstructured":"Mungall CJ. Obol: integrating language and meaning in bio-ontologies. Comp Funct Genom. 2004; 5(6-7):509\u201320.","journal-title":"Comp Funct Genom"},{"issue":"1","key":"96_CR23","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/1471-2105-15-155","volume":"15","author":"RP Huntley","year":"2014","unstructured":"Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, et al. A method for increasing expressivity of gene ontology annotations using a compositional approach. BMC Bioinforma. 2014; 15(1):155.","journal-title":"BMC Bioinforma"},{"issue":"1","key":"96_CR24","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1186\/2041-1480-5-48","volume":"5","author":"H Dietze","year":"2014","unstructured":"Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ. Termgenie\u2013a web-application for pattern-based ontology class generation. J Biomed Semant. 2014; 5(1):48.","journal-title":"J Biomed Semant"},{"key":"96_CR25","doi-asserted-by":"crossref","unstructured":"Hamon T, Grabar N. Acquisition of elementary synonym relations from biological structured terminology. In: Computational Linguistics and Intelligent Text Processing. Springer: 2008. p. 40\u201351.","DOI":"10.1007\/978-3-540-78135-6_4"},{"key":"96_CR26","unstructured":"Verspoor CM, Joslyn C, Papcun GJ. The gene ontology as a source of lexical semantic knowledge for a biological natural language processing application. In: SIGIR Workshop on Text Analysis and Search for Bioinformatics: 2003. p. 51\u20136."},{"issue":"12","key":"96_CR27","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1093\/bioinformatics\/btp195","volume":"25","author":"K Verspoor","year":"2009","unstructured":"Verspoor K, Dvorkin D, Cohen KB, Hunter L. Ontology quality assurance through analysis of term transformations. Bioinformatics. 2009; 25(12):77\u201384.","journal-title":"Bioinformatics"},{"key":"96_CR28","unstructured":"Blaschke C, Andrade MA, Ouzounis C, Valencia A. Automatic extraction of biological information from scientific text: protein-protein interactions. In: Intelligent Systems for Molecular Biology: 1999. p. 60\u20137."},{"key":"96_CR29","unstructured":"Choi JD, McCallum A. Transition-based dependency parsing with selectional branching. In: ACL (1): 2013. p. 1052\u20131062."},{"key":"96_CR30","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/7287.001.0001","volume-title":"WordNet: An Electronic Lexical Database (Language, Speech, and Communication)","author":"C Fellbaum","year":"1998","unstructured":"Fellbaum C. WordNet: An Electronic Lexical Database (Language, Speech, and Communication). Cambridge: The MIT Press; 1998. http:\/\/www.amazon.ca\/exec\/obidos\/redirect?tag=citeulike04-20&path=ASIN\/026206197X."},{"key":"96_CR31","unstructured":"The Lexical Systems Group. LVG: Lexical variant generator: 2012. http:\/\/lexsrv2.nlm.nih.gov\/LexSysGroup\/Projects\/lvg\/2012\/web\/index.html. Accessed 22 July 2013."},{"issue":"3","key":"96_CR32","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1147\/sj.433.0455","volume":"43","author":"D Ferrucci","year":"2004","unstructured":"Ferrucci D, Lally A. Building an example application with the unstructured information management architecture. IBM Syst J. 2004; 43(3):455\u201375.","journal-title":"IBM Syst J"},{"issue":"161","key":"96_CR33","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1186\/1471-2105-13-161","volume":"13","author":"M Bada","year":"2012","unstructured":"Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Jr WAB, Cohen KB, Verspoor K, Blake JA, Hunter LE. Concept annotation in the craft corpus. BMC Bioinforma. 2012; 13(161):161.","journal-title":"BMC Bioinforma"},{"issue":"207","key":"96_CR34","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1186\/1471-2105-13-207","volume":"13","author":"K Verspoor","year":"2012","unstructured":"Verspoor K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Jr WAB, Bada M, Palmer M, Hunter LE. A corpus of full-text journal articles i a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinforma. 2012; 13(207):207.","journal-title":"BMC Bioinforma"},{"key":"96_CR35","doi-asserted-by":"crossref","unstructured":"Tanenblatt M, Coden A, Sominsky I. The conceptmapper approach to named entity recognition. In: International Conference on Language Resources and Evaluation: 2010.","DOI":"10.63317\/22rjwr69yqqu"},{"issue":"suppl 1","key":"96_CR36","first-page":"190","volume":"36","author":"U Consortium","year":"2008","unstructured":"Consortium U, et al. The universal protein resource (uniprot). Nucleic Acids Res. 2008; 36(suppl 1):190\u20135.","journal-title":"Nucleic Acids Res"},{"key":"96_CR37","doi-asserted-by":"crossref","unstructured":"Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res. 2004;32(Database issue). http:\/\/obofoundry.org\/ontology\/bto.html. Accessed 14 June 2007.","DOI":"10.1093\/nar\/gkh081"},{"key":"96_CR38","unstructured":"Wikipedia. Wikipedia, The Free Encyclopedia. 2004. http:\/\/en.wikipedia.org\/. Accessed 22 July 2013."},{"key":"96_CR39","unstructured":"Bada M, Hunter LE, Eckert M, Palmer M. An overview of the craft concept annotation guidelines. In: Proceedings of the Fourth Linguistic Annotation Workshop. Uppsala, Sweden: 2010. p. 207\u201311."},{"issue":"suppl 1","key":"96_CR40","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1093\/nar\/gkh021","volume":"32","author":"E Camon","year":"2004","unstructured":"Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R. The gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology. Nucleic Acids Res. 2004; 32(suppl 1):262\u20136.","journal-title":"Nucleic Acids Res"},{"key":"96_CR41","unstructured":"Resnik P. Using information content to evaluate semantic similarity in a taxonomy. In: Proceedings of the 14th International Joint Committee on Artificial Intelligence (IJCAI 1995). Montreal: 1995. p. 448\u201353."},{"issue":"5","key":"96_CR42","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1016\/j.ajhg.2008.09.017","volume":"83","author":"PN Robinson","year":"2008","unstructured":"Robinson PN, K\u00f6hler S, Bauer S, Seelow D, Horn D, Mundlos S. The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet. 2008; 83(5):610\u20135.","journal-title":"Am J Hum Genet"},{"key":"96_CR43","doi-asserted-by":"crossref","unstructured":"Bollacker K, Evans C, Paritosh P, Sturge T, Taylor J. Freebase: a collaboratively created graph database for structuring human knowledge. In: Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data. ACM: 2008. p. 1247\u20131250.","DOI":"10.1145\/1376616.1376746"},{"issue":"3","key":"96_CR44","first-page":"5","volume":"33","author":"LM Fox","year":"2014","unstructured":"Fox LM, Williams LA, Hunter L, Roeder C. Negotiating a text mining license for faculty researchers. Inf Technol Libr. 2014; 33(3):5\u201321.","journal-title":"Inf Technol Libr"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-016-0096-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13326-016-0096-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-016-0096-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:23:14Z","timestamp":1790036594000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13326-016-0096-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,9]]},"references-count":44,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["96"],"URL":"https:\/\/doi.org\/10.1186\/s13326-016-0096-7","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,9]]},"assertion":[{"value":"10 April 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 August 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 September 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"52"}}