{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T15:58:15Z","timestamp":1687795095931},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"S11","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Motivation<\/jats:title>\n            <jats:p>The increasingly large amount of free, online biological text makes automatic interaction extraction correspondingly attractive. Machine learning is one strategy that works by uncovering and using useful properties that are implicit in the text. However these properties are usually not reported in the literature explicitly. By investigating specific properties of biological text passages in this paper, we aim to facilitate an alternative strategy, the use of <jats:italic>text empirics<\/jats:italic>, to support mining of biomedical texts for biomolecular interactions. We report on our application of this approach, and also report some empirical findings about an important class of passages. These may be useful to others who may also wish to use the empirical properties we describe.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We manually analyzed syntactic and semantic properties of sentences likely to describe interactions between biomolecules. The resulting empirical data were used to design an algorithm for the PathBinder system to extract biomolecular interactions from texts. PathBinder searches PubMed for sentences describing interactions between two given biomolecules. PathBinder then uses probabilistic methods to combine evidence from multiple relevant sentences in PubMed to assess the relative likelihood of interaction between two arbitrary biomolecules. A biomolecular interaction network was constructed based on those likelihoods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The text empirics approach used here supports computationally friendly, performance competitive, automatic extraction of biomolecular interactions from texts.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Availability<\/jats:title>\n            <jats:p>\n              <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.metnetdb.org\/pathbinder\" ext-link-type=\"uri\">http:\/\/www.metnetdb.org\/pathbinder<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-s11-s18","type":"journal-article","created":{"date-parts":[[2009,10,8]],"date-time":"2009-10-08T18:14:45Z","timestamp":1255025685000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["PathBinder \u2013 text empirics and automatic extraction of biomolecular interactions"],"prefix":"10.1186","volume":"10","author":[{"given":"Lifeng","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Berleant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Ding","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tuan","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eve","family":"Syrkin Wurtele","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,10,8]]},"reference":[{"key":"3400_CR1","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1093\/bioinformatics\/17.2.155","volume":"17","author":"T Ono","year":"2001","unstructured":"Ono T, Hishigaki H, Tanigami A, Takagi T: Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 2001, 17: 155\u2013161. 10.1093\/bioinformatics\/17.2.155","journal-title":"Bioinformatics"},{"issue":"19","key":"3400_CR2","doi-asserted-by":"publisher","first-page":"6083","DOI":"10.1093\/nar\/gki892","volume":"33","author":"PD Karp","year":"2005","unstructured":"Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahr\u00e9n D, Tsoka S, Darzentas N, Kunin V, L\u00f3pez-Bigas N: Expansion of the BioCyc collection of pathway\/genome databases to 160 genomes. Nucleic Acids Research 2005, 33(19):6083\u20136089. 10.1093\/nar\/gki892","journal-title":"Nucleic Acids Research"},{"key":"3400_CR3","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1007\/978-1-4020-5608-6_10","volume-title":"Concepts in Plant Metabolomics","author":"ES Wurtele","year":"2007","unstructured":"Wurtele ES, Li L, Berleant D, Cook D, Dickerson JA, Ding J, Hofmann H, Lawrence M, Lee EK, Li J, Mentzen W, Miller L, Nikolau BJ, Ransom N, Wang Y: MetNet: systems biology software for Arabidopsis. In Concepts in Plant Metabolomics. Springer; 2007:145\u2013158."},{"key":"3400_CR4","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1093\/bioinformatics\/bti115","volume":"21","author":"P Pagel","year":"2005","unstructured":"Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, St\u00fcmpflen V, Mewes H-W, Ruepp A, Frishman D: The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21: 832\u2013834. 10.1093\/bioinformatics\/bti115","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"3400_CR5","doi-asserted-by":"publisher","first-page":"D354","DOI":"10.1093\/nar\/gkj102","volume":"34","author":"M Kanehisa","year":"2006","unstructured":"Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34(Database issue):D354-D357. 10.1093\/nar\/gkj102","journal-title":"Nucleic Acids Res"},{"key":"3400_CR6","doi-asserted-by":"publisher","first-page":"D449","DOI":"10.1093\/nar\/gkh086","volume":"32","author":"L Salwinski","year":"2004","unstructured":"Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Research 2004, 32: D449-D451. 10.1093\/nar\/gkh086","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"3400_CR7","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1093\/nar\/gkg056","volume":"31","author":"GD Bader","year":"2003","unstructured":"Bader GD, Betel D, Hogue CW: BIND: the Biomolecular Interaction Network Database. Nucleic Acids Research 2003, 31(1):248\u2013250. 10.1093\/nar\/gkg056","journal-title":"Nucleic Acids Research"},{"key":"3400_CR8","first-page":"326","volume-title":"Pacific Symposium on Biocomputing","author":"J Ding","year":"2002","unstructured":"Ding J, Berleant D, Nettleton D, Wurtele E: Mining MEDLINE: abstracts, sentences, or phrases? Pacific Symposium on Biocomputing 2002, 326\u2013337."},{"key":"3400_CR9","first-page":"53","volume":"29","author":"D Yao","year":"2004","unstructured":"Yao D, Wang J, Lu Y, Noble N, Sun H, Zhu X, Payan DG, Li M, Qu K: PathwayFinder: paving the way towards automatic pathway extraction. Proceedings of the second conference on Asia-Pacific bioinformatics 2004, 29: 53\u201362.","journal-title":"Proceedings of the second conference on Asia-Pacific bioinformatics"},{"key":"3400_CR10","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1093\/bioinformatics\/bti165","volume":"21","author":"C Santos","year":"2005","unstructured":"Santos C, Eggle D, States DJ: Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction. Bioinformatics 2005, 21: 1653\u20131658. 10.1093\/bioinformatics\/bti165","journal-title":"Bioinformatics"},{"key":"3400_CR11","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1186\/1471-2105-7-373","volume":"7","author":"J Natarajan","year":"2006","unstructured":"Natarajan J, Berrar D, Dubitzky W, Hack C, Zhang Y, DeSesa C, Van Brocklyn JR, Bremer EG: Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. BMC Bioinformatics 2006, 7: 373. 10.1186\/1471-2105-7-373","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"3400_CR12","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/bioinformatics\/btl616","volume":"23","author":"K Fundel","year":"2007","unstructured":"Fundel K, K\u00fcffner R, Zimmer R: RelEx \u2013 Relation extraction using dependency parse trees. Bioinformatics 2007, 23(3):365\u2013371. 10.1093\/bioinformatics\/btl616","journal-title":"Bioinformatics"},{"key":"3400_CR13","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.artmed.2006.08.005","volume":"39","author":"F Rinaldi","year":"2007","unstructured":"Rinaldi F, Schneider G, Kaljurand K, Hess M, Andronis C, Konstandi O, Persidis A: Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach. Artificial Intelligence in Medicine 2007, 39: 127\u2013136. 10.1016\/j.artmed.2006.08.005","journal-title":"Artificial Intelligence in Medicine"},{"issue":"3","key":"3400_CR14","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1093\/bioinformatics\/btn631","volume":"25","author":"Y Miyao","year":"2009","unstructured":"Miyao Y, Sagae K, S\u00e6tre R, Matsuzaki T, Tsujii T: Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics 2009, 25(3):394\u2013400. 10.1093\/bioinformatics\/btn631","journal-title":"Bioinformatics"},{"issue":"Suppl 9","key":"3400_CR15","doi-asserted-by":"publisher","first-page":"S11","DOI":"10.1186\/1471-2105-9-S9-S11","volume":"9","author":"CB Giles","year":"2008","unstructured":"Giles CB, Wren JD: Large-scale directional relationship extraction and resolution. BMC Bioinformatics 2008, 9(Suppl 9):S11. 10.1186\/1471-2105-9-S9-S11","journal-title":"BMC Bioinformatics"},{"key":"3400_CR16","first-page":"408","volume-title":"Pac Symp Biocomput","author":"A Yakushiji","year":"2001","unstructured":"Yakushiji A, Tateisi Y, Miyao Y, Tsujii Y: Event extraction from biomedical papers using a full parser in biocomputing. Pac Symp Biocomput 2001, 408\u2013419."},{"issue":"Suppl 1","key":"3400_CR17","doi-asserted-by":"publisher","first-page":"S74","DOI":"10.1093\/bioinformatics\/17.suppl_1.S74","volume":"17","author":"C Friedman","year":"2001","unstructured":"Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A: GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 2001, 17(Suppl 1):S74\u201382.","journal-title":"Bioinformatics"},{"key":"3400_CR18","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1093\/bioinformatics\/btg369","volume":"20","author":"J Chiang","year":"2004","unstructured":"Chiang J, Yu H, Hsu H: GIS: a biomedical text-mining system for gene information discovery. Bioinformatics 2004, 20: 120\u2013121. 10.1093\/bioinformatics\/btg369","journal-title":"Bioinformatics"},{"key":"3400_CR19","doi-asserted-by":"publisher","first-page":"3582","DOI":"10.1093\/bioinformatics\/bti578","volume":"21","author":"N Domedel-Puig","year":"2005","unstructured":"Domedel-Puig N, Wernisch L: Applying GIFT, a Gene Interactions Finder in Text, to fly literature. Bioinformatics 2005, 21: 3582\u20133583. 10.1093\/bioinformatics\/bti578","journal-title":"Bioinformatics"},{"key":"3400_CR20","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.[Http:\/\/www.biomedcentral.com\/1471\u20132105\/5\/147]BMC Bioinformatics 2004, 5: 147. The Chilibot system is on-line at [http:\/\/www.chilibot.net\/] 10.1186\/1471-2105-5-147","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 2","key":"3400_CR21","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/1471-2105-10-S2-S6","volume":"10","author":"Y Garten","year":"2009","unstructured":"Garten Y, Altman RB: Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text. BMC Bioinformatics 2009, 10(Suppl 2):S6. 10.1186\/1471-2105-10-S2-S6","journal-title":"BMC Bioinformatics"},{"key":"3400_CR22","doi-asserted-by":"publisher","first-page":"3604","DOI":"10.1093\/bioinformatics\/bth451","volume":"20","author":"M Huang","year":"2004","unstructured":"Huang M, Zhu X, Hao Y, Payan DG, Qu K, Li M: Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics 2004, 20: 3604\u20133612. 10.1093\/bioinformatics\/bth451","journal-title":"Bioinformatics"},{"key":"3400_CR23","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1093\/bioinformatics\/btg452","volume":"20","author":"N Daraselia","year":"2004","unstructured":"Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I: Extracting protein function information from MEDLINE using a full-sentence parser. Bioinformatics 2004, 20: 604\u2013611. 10.1093\/bioinformatics\/btg452","journal-title":"Bioinformatics"},{"key":"3400_CR24","doi-asserted-by":"publisher","first-page":"1227","DOI":"10.1093\/bioinformatics\/bti084","volume":"21","author":"A Koike","year":"2005","unstructured":"Koike A, Niwa Y, Takagi T: Automatic extraction of gene\/protein biological functions from biomedical text. Bioinformatics 2005, 21: 1227\u20131236. 10.1093\/bioinformatics\/bti084","journal-title":"Bioinformatics"},{"key":"3400_CR25","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1093\/bioinformatics\/17.4.359","volume":"17","author":"EM Marcotte","year":"2001","unstructured":"Marcotte EM, Xenarios I, Eisenberg D: Mining literature for protein-protein interactions. Bioinformatics 2001, 17: 359\u201363. 10.1093\/bioinformatics\/17.4.359","journal-title":"Bioinformatics"},{"issue":"4","key":"3400_CR26","doi-asserted-by":"publisher","first-page":"1914","DOI":"10.1104\/pp.105.060863","volume":"138","author":"VB Bajic","year":"2005","unstructured":"Bajic VB, Veronika M, Veladandi PS, Meka A, Heng MW, Rajaraman K, Pan H, Swarup S: Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists. Plant Physiol 2005, 138(4):1914\u201325. 10.1104\/pp.105.060863","journal-title":"Plant Physiol"},{"issue":"8","key":"3400_CR27","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1210\/me.2002-0424","volume":"17","author":"S Albert","year":"2003","unstructured":"Albert S, Gaudan S, Knigge H, Raetsch A, Delgado A, Huhse B, Kirsch H, Albers M, Rebholz-Schuhmann D, Koegl M: Computer-assisted generation of a protein-interaction database for nuclear receptors. Molecular Endocrinology 2003, 17(8):1555\u20131567. 10.1210\/me.2002-0424","journal-title":"Molecular Endocrinology"},{"issue":"16","key":"3400_CR28","doi-asserted-by":"publisher","first-page":"2055","DOI":"10.1093\/bioinformatics\/btl342","volume":"22","author":"GR Grimes","year":"2006","unstructured":"Grimes GR, Wen TQ, Mewissen M, Baxter RM, Moodie S, Beattie JS, Ghazal P: PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature. Bioinformatics 2006, 22(16):2055\u20132057. 10.1093\/bioinformatics\/btl342","journal-title":"Bioinformatics"},{"key":"3400_CR29","doi-asserted-by":"publisher","first-page":"2059","DOI":"10.1093\/bioinformatics\/bti284","volume":"21","author":"O Hofmann","year":"2005","unstructured":"Hofmann O, Schomburg D: Concept-based annotation of enzyme classes. Bioinformatics 2005, 21: 2059\u20132066. 10.1093\/bioinformatics\/bti284","journal-title":"Bioinformatics"},{"key":"3400_CR30","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. Nature Genetics 2004, 36: 664. The iHOP system is on-line at [http:\/\/www.ihop-net.org\/] The iHOP system is on-line at [] 10.1038\/ng0704-664","journal-title":"Nature Genetics"},{"key":"3400_CR31","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1093\/bioinformatics\/btg390","volume":"20","author":"JD Wren","year":"2004","unstructured":"Wren JD, Garner HR: Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics 2004, 20: 191\u2013198. 10.1093\/bioinformatics\/btg390","journal-title":"Bioinformatics"},{"key":"3400_CR32","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1504\/IJBRA.2008.017164","volume":"4","author":"D Zhou","year":"2008","unstructured":"Zhou D, He Y, Kwoh CK: Extracting protein-protein interactions from MEDLINE using the Hidden Vector State model. Int J Bioinform Res Appl 2008, 4: 64\u201380. 10.1504\/IJBRA.2008.017164","journal-title":"Int J Bioinform Res Appl"},{"key":"3400_CR33","unstructured":"Empirical: Definition.Dictionary.com Unabridged, based on the Random House Dictionary, Random House, Inc; [Http:\/\/dictionary.reference.com\/browse\/empirical] (downloaded 5\/27\/09)."},{"key":"3400_CR34","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511809071","volume-title":"Introduction to Information Retrieval","author":"CD Manning","year":"2008","unstructured":"Manning CD, Raghavan R, Sch\u00fctze H: Introduction to Information Retrieval. Cambridge University Press; 2008."},{"key":"3400_CR35","volume-title":"Representations of Commonsense Knowledge","author":"E Davis","year":"1990","unstructured":"Davis E:Representations of Commonsense Knowledge. Morgan Kaufmann; 1990. [http:\/\/www.cs.nyu.edu\/faculty\/davise\/ai\/independentEvidence.pdf]"},{"key":"3400_CR36","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1007\/0-387-25739-X_17","volume-title":"Medical Informatics: Knowledge Management and Data Mining in Biomedicine","author":"JA Dickerson","year":"2005","unstructured":"Dickerson JA, Berleant D, Du P, Ding J, Foster CM, Li L, Wurtele ES: Creating, modeling, and visualizing metabolic networks. In Medical Informatics: Knowledge Management and Data Mining in Biomedicine. Volume chapter 17. Edited by: Chen H, Fuller SS, Friedman C, Hersh W. Springer; 2005:491\u2013518."},{"key":"3400_CR37","volume-title":"Combining evidence: the Na\u00efve Bayes model vs. semi-na\u00efve evidence combination, Technical Report SARD04-11","author":"D Berleant","year":"2004","unstructured":"Berleant D: Combining evidence: the Na\u00efve Bayes model vs. semi-na\u00efve evidence combination, Technical Report SARD04\u201311.2004 . [http:\/\/ifsc.ualr.edu\/jdberleant\/papers\/seminaivemodel.pdf]"},{"issue":"4","key":"3400_CR38","doi-asserted-by":"publisher","first-page":"1067","DOI":"10.1042\/bj1341067","volume":"134","author":"A McAllister","year":"1973","unstructured":"McAllister A, Allison SP, Randle PJ: Effects of dichloroacetate on the metabolism of glucose, pyruvate, acetate, 3-hydroxybutyrate and palmitate in rat diaphragm and heart muscle in vitro and on extraction of glucose, lactate, pyruvate and free fatty acids by dog heart in vivo. Biochem J 1973, 134(4):1067\u20131081.","journal-title":"Biochem J"},{"key":"3400_CR39","unstructured":"Ding J, Berleant D, Xu J, Fulmer AW: Extracting biochemical interactions from MEDLINE using a link grammar parser. Proceedings of the Fifteenth IEEE Conference on Tools with Artificial Intelligenc (ICTAI 2003), Nov. 3\u20135, Sacramento, 467\u2013471. [http:\/\/ifsc.ualr.edu\/jdberleant\/papers\/LGPmanuscript8\u20138-03a.pdf]"},{"key":"3400_CR40","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1038\/nature04718","volume":"441","author":"A Roux","year":"2006","unstructured":"Roux A, Uyhazi K, Frost A, De Camilli P: GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission. Nature 2006, 441: 528\u2013531. 10.1038\/nature04718","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S11-S18.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:40:08Z","timestamp":1630446008000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S11-S18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10]]},"references-count":40,"journal-issue":{"issue":"S11","published-print":{"date-parts":[[2009,10]]}},"alternative-id":["3400"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s11-s18","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10]]},"assertion":[{"value":"8 October 2009","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S18"}}