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2017 | OriginalPaper | Buchkapitel

Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature: A Use Case in Biomedical Software Identification

verfasst von : Muhammad Amith, Yaoyun Zhang, Hua Xu, Cui Tao

Erschienen in: Advances in Artificial Intelligence: From Theory to Practice

Verlag: Springer International Publishing

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Abstract

Statistical and machine learning approaches to named entity recognition have risen to prominence in the field of natural language processing. Certain named entities, specifically biomedical software, is a challenge to identify as a named entity. One direction is investigating the use of contextual semantic information to assist in this task as alluded to by previous researchers. We introduce an ontology-driven method that experiments with both information extraction and inherited features of ontologies (e.g., embedded semantic relationships and links to entities) to automatically identify familiar and unfamiliar software names. We evaluated this method with a set of biomedical research abstracts containing software entities. Our proposed approach could be used to further augment other named entity recognition methods.

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https://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/.

http://www.w3.org/TR/owl2-overview/.

https://bd2k.nih.gov/.

http://bioportal.bioontology.org/ontologies/SWO.

http://owlapi.sourceforge.net/.

https://code.google.com/p/ws4j/.

Hirst and St-Onge (1988), Leacock and Chodorow (1988), Banerjee and Pedersen (2002), Wu and Palmer (1994), Resnik (1995), Jiang and Conrath (1997), Lin (1998), and ws4J’s PATH.

http://commons.apache.org/.

https://github.com/google/guava.

http://eclipse.org.

Brazas, M.D., Yim, D.S., Yamada, J.T., Ouellette, B.F.F.: The 2011 bioinformatics links directory update: more resources, tools and databases and features to empower the bioinformatics community. Nucl. Acids Res. 39(suppl), W3–W7 (2011). http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkr514 CrossRef

Brooks, F.P.: The Mythical Man-Month, vol. 1995. Addison-Wesley, Reading (1975)

Budgen, D.: Software Design. Pearson Education, Harlow (2003)MATH

de la Calle, G., Garca-Remesal, M., Chiesa, S., de la Iglesia, D., Maojo, V.: BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature. BMC Bioinform. 10(1), 320 (2009). http://www.biomedcentral.com/1471-2105/10/320 CrossRef

Cannata, N., Merelli, E., Altman, R.B.: Time to organize the bioinformatics resourceome. PLoS Comput. Biol. 1(7), e76 (2005)CrossRef

Chiang, J.H., Yu, H.C.: MeKE: discovering the functions of gene products from biomedical literature via sentence alignment. Bioinformatics 19(11), 1417–1422 (2003)CrossRef

Cimiano, P., Vlker, J.: Towards large-scale, open-domain and ontology-based named entity classification. In: Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP) (2005)

Cohen, W., Ravikumar, P., Fienberg, S.: A comparison of string metrics for matching names and records. In: KDD Workshop on Data Cleaning and Object Consolidation, vol. 3, pp. 73–78 (2003). https://www.cs.cmu.edu/afs/cs/Web/People/wcohen/postscript/kdd-2003-match-ws.pdf

Del Corro, L., Gemulla, R.: ClausIE: clause-based open information extraction. In: Proceedings of the 22nd International Conference on World Wide Web, pp. 355–366. International World Wide Web Conferences Steering Committee (2013). http://dl.acm.org/citation.cfm?id=2488420

10.

Duck, G., Nenadic, G., Brass, A., Robertson, D.L., Stevens, R.: Extracting patterns of database and software usage from the bioinformatics literature. Bioinformatics 30(17), i601–i608 (2014). http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btu471 CrossRef

11.

Duck, G., Kovacevic, A., Robertson, D.L., Stevens, R., Nenadic, G.: Ambiguity and variability of database and software names in bioinformatics. J. Biomed. Semant. 6(1), 29 (2015). http://www.jbiomedsem.com/content/6/1/29 CrossRef

12.

Duck, G., Nenadic, G., Brass, A., Robertson, D.L., Stevens, R.: bioNerDS: exploring bioinformatics database and software use through literature mining. BMC Bioinform. 14(1), 194 (2013). http://www.biomedcentral.com/1471-2105/14/194 CrossRef

13.

Finlayson, M.A.: Java libraries for accessing the princeton wordnet: comparison and evaluation. In: Proceedings of the 7th Global Wordnet Conference, pp. 78–85 (2014)

14.

Grannis, S.J., Overhage, J.M., McDonald, C.: Real world performance of approximate string comparators for use in patient matching. Medinfo 11, 43–47 (2004)

15.

Gruber, T.R.: Toward principles for the design of ontologies used for knowledge sharing? Int. J. Hum. Comput. Stud. 43(56), 907–928 (1995). http://www.sciencedirect.com/science/article/pii/S1071581985710816 CrossRef

16.

Hassell, J., Aleman-Meza, B., Arpinar, I.B.: Ontology-driven automatic entity disambiguation in unstructured text. In: Cruz, I., et al. (eds.) ISWC 2006. LNCS, vol. 4273, pp. 44–57. Springer, Heidelberg (2006). doi:10.1007/11926078_4 CrossRef

17.

Hirschman, L., Yeh, A., Blaschke, C., Valencia, A.: Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinform. 6(Suppl 1), S1 (2005). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1869002/ CrossRef

18.

Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J., Ananiadou, S.: Using workflows to explore and optimise named entity recognition for chemistry. PLoS ONE 6(5), e20181 (2011). http://dx.doi.org/10.1371/journal.pone.0020181 CrossRef

19.

Lei, J., Tang, B., Lu, X., Gao, K., Jiang, M., Xu, H.: A comprehensive study of named entity recognition in Chinese clinical text. J. Am. Med. Inform. Assoc. 21(5), 808–814 (2014). http://jamia.oxfordjournals.org/content/21/5/808 CrossRef

20.

Malone, J., Brown, A., Lister, A.L., Ison, J., Hull, D., Parkinson, H., Stevens, R.: The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. J. Biomed. Semant. 5(1), 25 (2014). http://www.jbiomedsem.com/content/5/1/25/abstract CrossRef

21.

Mendes, P.N., Jakob, M., Garca-Silva, A., Bizer, C.: DBpedia spotlight: shedding light on the web of documents. In: Proceedings of the 7th International Conference on Semantic Systems, pp. 1–8. ACM (2011). http://dl.acm.org/citation.cfm?id=2063519

22.

Mukherjea, S., Subramaniam, L.V., Chanda, G., Sankararaman, S., Kothari, R., Batra, V., Bhardwaj, D., Srivastava, B.: Enhancing a biomedical information extraction system with dictionary mining and context disambiguation. IBM J. Res. Dev. 48(5.6), 693–701 (2004)CrossRef

23.

Nadeau, D., Sekine, S.: A survey of named entity recognition and classification. Lingvisticae Investigationes 30(1), 3–26 (2007). http://www.ingentaconnect.com/content/jbp/li/2007/00000030/00000001/art00002 CrossRef

24.

Sekine, S.: Extended named entity ontology with attribute information. In: LREC, pp. 52–57 (2008). http://nlp.cs.nyu.edu/sekine/papers/lrec08.pdf

25.

Settles, B.: ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics 21(14), 3191–3192 (2005). http://bioinformatics.oxfordjournals.org/content/21/14/3191 CrossRef

26.

Spasic, I., Ananiadou, S., McNaught, J., Kumar, A.: Text mining and ontologies in biomedicine: making sense of raw text. Brief. Bioinform. 6(3), 239–251 (2005). http://bib.oxfordjournals.org/content/6/3/239.short CrossRef

27.

Tsuruoka, Y., Tsujii, J.: Improving the performance of dictionary-based approaches in protein name recognition. J. Biomed. Inform. 37(6), 461–470 (2004). http://linkinghub.elsevier.com/retrieve/pii/S1532046404000814 CrossRef

28.

Yamamoto, Y., Takagi, T.: OReFiL: an online resource finder for life sciences. BMC Bioinform. 8(1), 287 (2007). http://www.biomedcentral.com/1471-2105/8/287 CrossRef

Titel: Knowledge-Based Approach for Named Entity Recognition in Biomedical Literature: A Use Case in Biomedical Software Identification
verfasst von: Muhammad Amith
Yaoyun Zhang
Hua Xu
Cui Tao
Verlag: Springer International Publishing
Buch: Advances in Artificial Intelligence: From Theory to Practice
Print ISBN: 978-3-319-60044-4

Electronic ISBN: 978-3-319-60045-1

Copyright-Jahr: 2017
DOI: https://doi.org/10.1007/978-3-319-60045-1_40

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