{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:14:46Z","timestamp":1762506886003},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,9,20]],"date-time":"2016-09-20T00:00:00Z","timestamp":1474329600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,9,20]],"date-time":"2016-09-20T00:00:00Z","timestamp":1474329600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Bio-Synergy Research Project of the Ministry of Science","award":["NRF-2013M3A9C4078138"],"award-info":[{"award-number":["NRF-2013M3A9C4078138"]}]},{"name":"Bio-Synergy Research Project of the Ministry of Science.","award":["NRF-2013M3A9C4078138"],"award-info":[{"award-number":["NRF-2013M3A9C4078138"]}]},{"name":"Bio-Synergy Research Project of the Ministry of Science","award":["NRF-2013M3A9C4078138"],"award-info":[{"award-number":["NRF-2013M3A9C4078138"]}]},{"name":"Bio-Synergy Research Project of the Ministry of Science","award":["NRF-2013M3A9C4078138"],"award-info":[{"award-number":["NRF-2013M3A9C4078138"]}]},{"name":"Bio-Synergy Research Project of the Ministry of Science","award":["NRF-2013M3A9C4078138"],"award-info":[{"award-number":["NRF-2013M3A9C4078138"]}]}],"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>Plants are natural products that humans consume in various ways including food and medicine. They have a long empirical history of treating diseases with relatively few side effects. Based on these strengths, many studies have been performed to verify the effectiveness of plants in treating diseases. It is crucial to understand the chemicals contained in plants because these chemicals can regulate activities of proteins that are key factors in causing diseases. With the accumulation of a large volume of biomedical literature in various databases such as PubMed, it is possible to automatically extract relationships between plants and chemicals in a large-scale way if we apply a text mining approach. A cornerstone of achieving this task is a corpus of relationships between plants and chemicals.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>In this study, we first constructed a corpus for plant and chemical entities and for the relationships between them. The corpus contains 267 plant entities, 475 chemical entities, and 1,007 plant\u2013chemical relationships (550 and 457 positive and negative relationships, respectively), which are drawn from 377 sentences in 245 PubMed abstracts. Inter-annotator agreement scores for the corpus among three annotators were measured. The simple percent agreement scores for entities and trigger words for the relationships were 99.6 and 94.8 %, respectively, and the overall kappa score for the classification of positive and negative relationships was 79.8 %. We also developed a rule-based model to automatically extract such plant\u2013chemical relationships. When we evaluated the rule-based model using the corpus and randomly selected biomedical articles, overall F-scores of 68.0 and 61.8 % were achieved, respectively.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>We expect that the corpus for plant\u2013chemical relationships will be a useful resource for enhancing plant research. The corpus is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/combio.gist.ac.kr\/plantchemicalcorpus\">http:\/\/combio.gist.ac.kr\/plantchemicalcorpus<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1249-5","type":"journal-article","created":{"date-parts":[[2016,9,20]],"date-time":"2016-09-20T02:47:41Z","timestamp":1474339661000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["A corpus for plant-chemical relationships in the biomedical domain"],"prefix":"10.1186","volume":"17","author":[{"given":"Wonjun","family":"Choi","sequence":"first","affiliation":[]},{"given":"Baeksoo","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Hyejin","family":"Cho","sequence":"additional","affiliation":[]},{"given":"Doheon","family":"Lee","sequence":"additional","affiliation":[]},{"given":"Hyunju","family":"Lee","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,9,20]]},"reference":[{"issue":"1","key":"1249_CR1","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1007\/BF02866603","volume":"54","author":"BC Bennett","year":"2000","unstructured":"Bennett BC, Prance GT. Introduced plants in the indigenous pharmacopoeia of northern south america. Econ Bot. 2000; 54(1):90\u2013102.","journal-title":"Econ Bot"},{"issue":"1","key":"1249_CR2","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.jep.2005.06.004","volume":"100","author":"JB Calixto","year":"2005","unstructured":"Calixto JB. Twenty-five years of research on medicinal plants in latin america: a personal view. J Ethnopharmacol. 2005; 100(1):131\u20134.","journal-title":"J Ethnopharmacol"},{"issue":"6","key":"1249_CR3","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1001\/archfami.7.6.523","volume":"7","author":"M O\u2019Hara","year":"1998","unstructured":"O\u2019Hara M, Kiefer D, Farrell K, Kemper K. A review of 12 commonly used medicinal herbs. Arch Fam Med. 1998; 7(6):523.","journal-title":"Arch Fam Med"},{"issue":"1","key":"1249_CR4","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1016\/j.nut.2012.06.004","volume":"29","author":"AY Esmat","year":"2013","unstructured":"Esmat AY, Said MM, Soliman AA, El-Masry KS, Badiea EA. Bioactive compounds, antioxidant potential, and hepatoprotective activity of sea cucumber (holothuria atra) against thioacetamide intoxication in rats. Nutrition. 2013; 29(1):258\u201367.","journal-title":"Nutrition"},{"issue":"2","key":"1249_CR5","doi-asserted-by":"publisher","first-page":"191","DOI":"10.3109\/08923973.2011.590499","volume":"34","author":"JH Han","year":"2012","unstructured":"Han JH, Koh W, Lee HJ, Lee HJ, Lee EO, Lee SJ, Khil JH, Kim JT, Jeong SJ, Kim SH. Analgesic and anti-inflammatory effects of ethyl acetate fraction of polygonum cuspidatum in experimental animals. Immunopharmacol Immunotoxicol. 2012; 34(2):191\u20135.","journal-title":"Immunopharmacol Immunotoxicol"},{"issue":"1","key":"1249_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1472-6882-13-1","volume":"13","author":"J Bjorne","year":"2013","unstructured":"Bjorne J, Ginter F, Pyysalo S, Tsujii J, Salakoski T. Ganghwaljetongyeum, an anti-arthritic remedy, attenuates synoviocyte proliferation and reduces the production of proinflammatory mediators in macrophages: the therapeutic effect of ghjty on rheumatoid arthritis. BMC Complement Altern Med. 2013; 13(1):1.","journal-title":"BMC Complement Altern Med"},{"issue":"3","key":"1249_CR7","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/nrd1657","volume":"4","author":"FE Koehn","year":"2005","unstructured":"Koehn FE, Carter GT. The evolving role of natural products in drug discovery. Nat Rev Drug Discov. 2005; 4(3):206\u201320.","journal-title":"Nat Rev Drug Discov"},{"issue":"4","key":"1249_CR8","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1093\/bib\/bbp063","volume":"11","author":"J Zhao","year":"2010","unstructured":"Zhao J, Jiang P, Zhang W. Molecular networks for the study of tcm pharmacology. Brief Bioinform. 2010; 11(4):417\u201330.","journal-title":"Brief Bioinform"},{"issue":"12","key":"1249_CR9","doi-asserted-by":"publisher","first-page":"4826","DOI":"10.1073\/pnas.0712365105","volume":"105","author":"L Wang","year":"2008","unstructured":"Wang L, Zhou GB, Liu P, Song JH, Liang Y, Yan XJ, Xu F, Wang BS, Mao JH, Shen ZX, Chen SJ, Chen Z. Dissection of mechanisms of chinese medicinal formula realgar-indigo naturalis as an effective treatment for promyelocytic leukemia. Proc Natl Acad Sci. 2008; 105(12):4826\u2013831.","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"1249_CR10","doi-asserted-by":"publisher","first-page":"15939","DOI":"10.1371\/journal.pone.0015939","volume":"6","author":"CYC Chen","year":"2011","unstructured":"Chen CYC. Tcm database@taiwan: the world\u2019s largest traditional chinese medicine database for drug screening in silico. PloS ONE. 2011; 6(1):15939.","journal-title":"PloS ONE"},{"issue":"D1","key":"1249_CR11","doi-asserted-by":"publisher","first-page":"D1089","DOI":"10.1093\/nar\/gks1100","volume":"41","author":"R Xue","year":"2013","unstructured":"Xue R, Fang Z, Zhang M, Yi Z, Wen C, Shi T. Tcmid: traditional chinese medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2013; 41(D1):D1089-95.","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"1249_CR12","doi-asserted-by":"publisher","first-page":"1092","DOI":"10.1038\/sj.bjp.0706945","volume":"149","author":"X Chen","year":"2006","unstructured":"Chen X, Zhou H, Liu YB, Wang JF, Li H, Ung CY, Han LY, Cao ZW, Chen YZ. Database of traditional chinese medicine and its application to studies of mechanism and to prescription validation. Br J Pharmacol. 2006; 149(8):1092\u20131103.","journal-title":"Br J Pharmacol"},{"issue":"suppl 1","key":"1249_CR13","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1093\/nar\/gkq1165","volume":"39","author":"H Ye","year":"2011","unstructured":"Ye H, Ye L, Kang H, Zhang D, Tao L, Tang K, Liu X, Zhu R, Liu Q, Chen YZ, Li Y, Cao Z. Hit: linking herbal active ingredients to targets. Nucleic Acids Res. 2011; 39(suppl 1):1055\u20131059.","journal-title":"Nucleic Acids Res"},{"issue":"suppl 1","key":"1249_CR14","first-page":"684","volume":"36","author":"M Kuhn","year":"2008","unstructured":"Kuhn M, von Mering C, Campillos M, Jensen L, Bork P. Stitch: interaction networks of chemicals and proteins. Nucleic Acids Res. 2008; 36(suppl 1):684\u20138.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1249_CR15","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1002\/(SICI)1098-1004(200001)15:1<57::AID-HUMU12>3.0.CO;2-G","volume":"15","author":"A Hamosh","year":"2000","unstructured":"Hamosh A, Scott AF, Amberger J, Valle D, McKusick VA. Online mendelian inheritance in man (omim). Hum Mutat. 2000; 15(1):57\u201361.","journal-title":"Hum Mutat"},{"key":"1249_CR16","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1093\/nar\/gkj067","volume":"34","author":"DS Wishart","year":"2006","unstructured":"Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. Drugbank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006; 34:668\u201372.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"1249_CR17","doi-asserted-by":"publisher","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","volume":"40","author":"S Federhen","year":"2012","unstructured":"Federhen S. The NCBI Taxonomy database. Nucleic Acids Res. 2012; 40(Database issue):D136\u201343.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1249_CR18","doi-asserted-by":"publisher","first-page":"1003432","DOI":"10.1371\/journal.pcbi.1003432","volume":"10","author":"K Jenson","year":"2014","unstructured":"Jenson K, Panagiotou G, Kouskoumvekaki I. Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level. PLoS Comput Biol. 2014; 10(1):1003432.","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"1249_CR19","first-page":"313","volume":"19","author":"M Marcus","year":"1993","unstructured":"Marcus M, Santorini S, Marcinkiewicz M. Building a large annotated corpus of english: the penn treebank. Comput Linguist. 1993; 19(2):313\u201330.","journal-title":"Comput Linguist"},{"key":"1249_CR20","doi-asserted-by":"publisher","first-page":"bat064","DOI":"10.1093\/database\/bat064","volume":"2013","author":"DC Comeau","year":"2013","unstructured":"Comeau DC, Dogan RI, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. Bioc: a minimalist approach to interoperability for biomedical text processing. Database. 2013; 2013:bat064.","journal-title":"Database"},{"issue":"1","key":"1249_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-11-85","volume":"11","author":"M Gerner","year":"2010","unstructured":"Gerner M, Nenadic G, Bergman CM. Linnaeus: a species name identification system for biomedical literature. BMC Bioinforma. 2010; 11(1):1.","journal-title":"BMC Bioinforma"},{"issue":"6","key":"1249_CR22","doi-asserted-by":"publisher","first-page":"65390","DOI":"10.1371\/journal.pone.0065390","volume":"8","author":"E Pafilis","year":"2013","unstructured":"Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, Arvanitidis C, Jensen LJ. The species and organisms resources for fast and accurate identification of taxonomic names in text. PLoS ONE. 2013; 8(6):65390.","journal-title":"PLoS ONE"},{"issue":"1","key":"1249_CR23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1758-2946-7-S1-S1","volume":"7","author":"M Krallinger","year":"2015","unstructured":"Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, Leaman R, Lu Y, Ji D, Lowe DM, Sayle RA, Batista-Navarro RT, Rak R, Huber T, Rocktaschel T, Matos S, Campos D, Tang B, Xu H, Munkhdalai T, Ryu KH, Ramanan SV, Nathan S, Zitnik S, Bajec M, Weber L, Irmer M, Akhondi SA, Kors JA, Xu S, An X, Sikdar UK, Ekbal A, Yoshioka M, Dieb TM, Choi M, Verspoor K, Khabsa M, Giles CL, Liu H, Ravikumar KE, Lamurias A, Couto FM, Dai H, Tsai RT, Ata C, Can T, Usie A, Alves R, Segura-Bedmar I, Martinez P, Oryzabal J, Valencia A. The chemdner corpus of chemicals and drugs and its annotation principles. J Cheminformatics. 2015; 7(1):1.","journal-title":"J Cheminformatics"},{"key":"1249_CR24","unstructured":"Li J, Sun Y, Jonhnson R, Sciaky D, Wei C, Leaman R, Davis AP, Mattingly C, Wiegers T, Lu Z. Annotating chemicals, diseases and their interactions in biomedical literature. In: Proceedings of the fifth BioCreative challenge evaluation workshop, BioCreative Organizing Committee. Sevilla: 2015. p. 173\u2013182."},{"issue":"Web Server issu","key":"1249_CR25","doi-asserted-by":"publisher","first-page":"W518","DOI":"10.1093\/nar\/gkt441","volume":"41","author":"CH Wei","year":"2013","unstructured":"Wei CH, Kao HY, Lu Z. Pubtator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 2013; 41(Web Server issue):W518\u201322.","journal-title":"Nucleic Acids Res"},{"issue":"22","key":"1249_CR26","doi-asserted-by":"publisher","first-page":"2909","DOI":"10.1093\/bioinformatics\/btt474","volume":"29","author":"R Leaman","year":"2013","unstructured":"Leaman R, Dogan RI, Lu Z. Dnorm: disease name normalization with pairwise learning to rank. Bioinformatics. 2013; 29(22):2909\u201317.","journal-title":"Bioinformatics"},{"issue":"1","key":"1249_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13321-014-0049-z","volume":"7","author":"R Leaman","year":"2015","unstructured":"Leaman R, Wei CH, Lu Z. tmchem: a high performance approach for chemical named entity recognition and normalization. J Cheminformatics. 2015; 7(1):1.","journal-title":"J Cheminformatics"},{"issue":"1","key":"1249_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-10-326","volume":"10","author":"T Wiegers","year":"2009","unstructured":"Wiegers T, Davis A, Cohen KB, Hischman L, Mattingly C. Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (ctd). BMC Bioinforma. 2009; 10(1):1.","journal-title":"BMC Bioinforma"},{"issue":"2","key":"1249_CR29","first-page":"1","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 Bioinforma. 2009; 10(2):1.","journal-title":"BMC Bioinforma"},{"key":"1249_CR30","unstructured":"Baldwin B, Carpenter B. LingPipe. http:\/\/www.alias-i.com\/lingpipe. Accessed 19 Jan 2015."},{"key":"1249_CR31","doi-asserted-by":"publisher","first-page":"1633","DOI":"10.1093\/bioinformatics\/bts183","volume":"28","author":"T Rocktaschel","year":"2012","unstructured":"Rocktaschel T, Weidlich M, Leser U. Chemspot: a hybrid system for chemical named entity recognition. Bioinformatics. 2012; 28:1633\u20131640.","journal-title":"Bioinformatics"},{"key":"1249_CR32","first-page":"360","volume":"37","author":"AJ Viera","year":"2005","unstructured":"Viera AJ, Garrett JM. Understanding interobserver agreement: the kappa statistic. Fam Med J. 2005; 37:360\u20133.","journal-title":"Fam Med J"},{"issue":"4","key":"1249_CR33","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1111\/j.1467-8640.2011.00405.x","volume":"27","author":"KB Cohen","year":"2011","unstructured":"Cohen KB, Verspoor K, Johnson HL, Roeder C, Ogren PV, Jr WAB, White E, Tipney H, Hunter L. High-precision biological event extraction: Effects of system and of data. Comput Intell. 2011; 27(4):681\u2013701.","journal-title":"Comput Intell"},{"key":"1249_CR34","first-page":"827","volume":"October","author":"L Chiticariu","year":"2013","unstructured":"Chiticariu L, Li Y, Frederick FR. Rule-based information extraction is dead! long live rule-based information extraction systems!. In EMNLP. 2013; October:827\u201332.","journal-title":"In EMNLP"},{"key":"1249_CR35","unstructured":"Bj\u00f6rne J, Salakoski T. Tees 2.1: Automated annotation scheme learning in the bionlp 2013 shared task. In: Proceedings of the BioNLP Shared Task 2013 Workshop, Association for Computational Linguistics (ACL); Sofia: 2013. p. 16\u201325."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1249-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-1249-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1249-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:16:51Z","timestamp":1706811411000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1249-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,20]]},"references-count":35,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["1249"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1249-5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,20]]},"assertion":[{"value":"19 January 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 September 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 September 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"386"}}