Top

Published in:

2019 | OriginalPaper | Chapter

Concept Bag: A New Method for Computing Concept Similarity in Biomedical Data

Authors : Richard L. Bradshaw, Ramkiran Gouripeddi, Julio C. Facelli

Published in: Bioinformatics and Biomedical Engineering

Publisher: Springer International Publishing

Activate our intelligent search to find suitable subject content or patents.

search-config

AI-assisted search

Off

Abstract

Biomedical data are a rich source of information and knowledge, not only for direct patient care, but also for secondary use in population health, clinical research, and translational research. Biomedical data are typically scattered across multiple systems and syntactic and semantic data integration is necessary to fully utilize the data’s potential. This paper introduces new algorithms that were devised to support automatic and semi-automatic integration of semantically heterogeneous biomedical data. The new algorithms incorporate both data mining and biomedical informatics methods to create “concept bags” in the same way that “word bags” are used in data mining and text retrieval. The methods are highly configurable and were tested in five different ways on different types of biomedical data. The new methods performed well in computing similarity between medical terms and data elements - both critical for semi/automatic data integration operations.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

previous chapter Developing a DEVS-JAVA Model to Simulate and Pre-test Changes to Emergency Care Delivery in a Safe and Efficient Manner

next chapter A Reliable Method to Remove Batch Effects Maintaining Group Differences in Lymphoma Methylation Case Study

Gouripeddi, R., Warner, P., Mo, P.: Federating clinical data from six pediatric hospitals: process and initial results for microbiology from the PHIS+ Consortium. In: AMIA Annual Symposium Proceedings (2012)

Narus, S.P., Srivastava, R., Gouripeddi, R., Livne, O.E., Mo, P., Bickel, J.P., et al.: Federating clinical data from six pediatric hospitals: process and initial results from the PHIS+ Consortium. In: AMIA Annual Symposium Proceedings, pp. 994–1003 (2011). PubMed PMID: 22195159; PubMed Central PMCID: PMCPMC3243196

Pedersen, T., Pakhomov, S.V.S., Patwardhan, S., Chute, C.G.: Measures of semantic similarity and relatedness in the biomedical domain. J. Biomed. Inform. 40(3), 288–299 (2007). https://doi.org/10.1016/j.jbi.2006.06.004CrossRef

Lasalle, B., Varner, M., Botkin, J., Jackson, M., Stark, L., Cessna, M., et al.: Biobanking informatics infrastructure to support clinical and translational research. AMIA Jt. Summits Transl. Sci. Proc. 132–5 (2013). PubMed PMID: 24303252; PubMed Central PMCID: PMC3845745

Murphy, S.N., Weber, G., Mendis, M., Gainer, V., Chueh, H.C., Churchill, S., et al.: Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J. Am. Med. Inform. Assoc. (JAMIA) 17(2), 124–130 (2010). https://doi.org/10.1136/jamia.2009.000893. PubMed PMID: 20190053; PubMed Central PMCID: PMC3000779CrossRef

Chute, C.G., Beck, S.A., Fisk, T.B., Mohr, D.N.: The enterprise data trust at Mayo clinic: a semantically integrated warehouse of biomedical data. J. Am. Med. Inform. Assoc. (JAMIA) 17(2), 131–135 (2010). https://doi.org/10.1136/jamia.2009.002691. PubMed PMID: 20190054; PubMed Central PMCID: PMC3000789CrossRef

Fan, J.W., Friedman, C.: Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies. J Biomed. Inform. 44(5), 805–814 (2011). https://doi.org/10.1016/j.jbi.2011.04.006. PubMed PMID: 21549857; PubMed Central PMCID: PMC3172402CrossRef

Jezek, P., Moucek, R.: Semantic framework for mapping object-oriented model to semantic web languages. Front Neuroinform. 9, 3 (2015). https://doi.org/10.3389/fninf.2015.00003. PubMed PMID: 25762923; PubMed Central PMCID: PMC4340193

Price, S.J., Stapley, S.A., Shephard, E., Barraclough, K., Hamilton, W.T.: Is omission of free text records a possible source of data loss and bias in clinical practice research datalink studies? A case–control study. BMJ open 6(5) (2016). https://bmjopen.bmj.com/content/6/5/e011664CrossRef

10.

Dhombres, F., Charlet, J.: As ontologies reach maturity, artificial intelligence starts being fully efficient: findings from the section on knowledge representation and management for the yearbook 2018. Yearb. Med. Inform. 27(1), 140–145 (2018). https://doi.org/10.1055/s-0038-1667078. PubMed PMID: 30157517CrossRef

11.

Baayen, R.H., Hendrix, P., Ramscar, M.: Sidestepping the combinatorial explosion: an explanation of n-gram frequency effects based on naive discriminative learning. Lang. Speech 56(Pt 3), 329–347 (2013). PubMed PMID: 24416960CrossRef

12.

Patrick, J., Li, M.: High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge. J. Am. Med. Inform. Assoc. (JAMIA) 17(5), 524–527 (2010). https://doi.org/10.1136/jamia.2010.003939. PubMed PMID: 20819856; PubMed Central PMCID: PMC2995676CrossRef

13.

Aronson, A.R., Lang, F.M.: An overview of MetaMap: historical perspective and recent advances. J. Am. Med. Inform. Assoc. (JAMIA) 17(3), 229–236 (2010). https://doi.org/10.1136/jamia.2009.002733. PubMed PMID: 20442139; PubMed Central PMCID: PMCPMC2995713CrossRef

14.

Bradshaw, R.: Concept bag: a new method for computing similarity. University of Utah (2015)

15.

Jaccard, P.J.: Similarity and shingling. Data mining (2015). http://www.cs.utah.edu/~jeffp/teaching/cs5955/L4-Jaccard+Shingle.pdf

16.

Harris, P.A., Taylor, R., Thielke, R., Payne, J., Gonzalez, N., Conde, J.G.: Research electronic data capture (REDCap)–a metadata-driven methodology and workflow process for providing translational research informatics support. J. Biomed. Inform. 42(2), 377–381 (2009). https://doi.org/10.1016/j.jbi.2008.08.010. PubMed PMID: 18929686; PubMed Central PMCID: PMC2700030CrossRef

17.

Garla, V.N., Brandt, C.: Semantic similarity in the biomedical domain: an evaluation across knowledge sources. BMC Bioinform. 13, 261 (2012). https://doi.org/10.1186/1471-2105-13-261. PubMed PMID: 23046094; PubMed Central PMCID: PMCPMC3533586CrossRef

18.

Lopez-Raton, M., Rodriguez-Alvarez, M., Cadarso-Suarez, C., Gude-Sampedro, F.: Optimal cutpoints: an R package for selecting optimal cutpoints in diagnostic tests. J. Stat. Softw. 61(8), 1–36 (2015)

19.

Aquire, E., cuadros, M., Rigua, G., Soroa, A. (eds.): Exploring knowledge bases for similarity. In: Proceedings of the Seventh International Conference on Language Resources and Evaluation. European Language Resources Association, Valleta (2010)

20.

Leacock, C., Chodorow, M.: Using corpus statistics and wordnet relations for sense identification. In: Fellbaum, C. (ed.) Wordnet: An Electronic Lexical Database, pp. 265–283. MIT Press, Cambridge (1998)

21.

Wu, Z., Palmer, M.: Verbs semantics and lexical selection. In: Proceedings of the 32nd Annual Meeting on Association for Computational Linguistics. Association for Computational Linguistics, Las Cruces (1994)

Title: Concept Bag: A New Method for Computing Concept Similarity in Biomedical Data
Authors: Richard L. Bradshaw
Ramkiran Gouripeddi
Julio C. Facelli
Publisher: Springer International Publishing
Book: Bioinformatics and Biomedical Engineering
Print ISBN: 978-3-030-17934-2

Electronic ISBN: 978-3-030-17935-9

Copyright Year: 2019
DOI: https://doi.org/10.1007/978-3-030-17935-9_2

Springer Professional

Abstract

Please log in to get access to your license.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Premium Partner