Topological Analysis of Large-scale Biomedical Terminology Structures Export

@article{Bales2007, abstract = {OBJECTIVE: To characterize global structural features of large-scale biomedical terminologies using currently emerging statistical approaches. DESIGN: Given rapid growth of terminologies, this research was designed to address scalability. We selected 16 terminologies covering a variety of domains from the UMLS Metathesaurus, a collection of terminological systems. Each was modeled as a network in which nodes were atomic concepts and links were relationships asserted by the source vocabulary. For comparison against each terminology we created three random networks of equivalent size and density. MEASUREMENTS: Average node degree, node degree distribution, clustering coefficient, average path length. RESULTS: Eight of 16 terminologies exhibited the small-world characteristics of a short average path length and strong local clustering. An overlapping subset of nine exhibited a power law distribution in node degrees, indicative of a scale-free architecture. We attribute these features to specific design constraints. Constraints on node connectivity, common in more synthetic classification systems, localize the effects of changes and deletions. In contrast, small-world and scale-free features, common in comprehensive medical terminologies, promote flexible navigation and less restrictive organic-like growth. CONCLUSION: While thought of as synthetic, grid-like structures, some controlled terminologies are structurally indistinguishable from natural language networks. This paradoxical result suggests that terminology structure is shaped not only by formal logic-based semantics, but by rules analogous to those that govern social networks and biological systems. Graph theoretic modeling shows early promise as a framework for describing terminology structure. Deeper understanding of these techniques may inform the development of scalable terminologies and ontologies.}, address = {∗Correspondence: Stephen Johnson, Department of Biomedical Informatics, Columbia University, Vanderbilt Clinic, 5 Floor, 622 West 168th Street, New York, NY 10032 (Email: stephen.johnson@dbmi.columbia.edu).}, author = {Bales, M. E. and Lussier, Y. A. and Johnson, S. B.}, citeulike-article-id = {1957977}, citeulike-linkout-0 = {http://dx.doi.org/10.1197/jamia.M2080}, citeulike-linkout-1 = {http://www.jamia.org/cgi/content/abstract/14/6/788}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17712094}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17712094}, comment = {http://vkwn.com/blog/2009/09/biomedical-terminologies-might-not-be-so-formal/}, day = {21}, doi = {10.1197/jamia.M2080}, issn = {1067-5027}, journal = {Journal of the American Medical Informatics Association}, keywords = {analysis, classification, ontology, taxonomy}, month = {August}, number = {6}, pages = {788--797}, posted-at = {2009-09-01 09:22:15}, priority = {0}, title = {Topological Analysis of Large-scale Biomedical Terminology Structures}, url = {http://dx.doi.org/10.1197/jamia.M2080}, volume = {14}, year = {2007} }

TY - JOUR ID - Bales2007 L3 - citeulike-article-id:1957977 N2 - OBJECTIVE: To characterize global structural features of large-scale biomedical terminologies using currently emerging statistical approaches. DESIGN: Given rapid growth of terminologies, this research was designed to address scalability. We selected 16 terminologies covering a variety of domains from the UMLS Metathesaurus, a collection of terminological systems. Each was modeled as a network in which nodes were atomic concepts and links were relationships asserted by the source vocabulary. For comparison against each terminology we created three random networks of equivalent size and density. MEASUREMENTS: Average node degree, node degree distribution, clustering coefficient, average path length. RESULTS: Eight of 16 terminologies exhibited the small-world characteristics of a short average path length and strong local clustering. An overlapping subset of nine exhibited a power law distribution in node degrees, indicative of a scale-free architecture. We attribute these features to specific design constraints. Constraints on node connectivity, common in more synthetic classification systems, localize the effects of changes and deletions. In contrast, small-world and scale-free features, common in comprehensive medical terminologies, promote flexible navigation and less restrictive organic-like growth. CONCLUSION: While thought of as synthetic, grid-like structures, some controlled terminologies are structurally indistinguishable from natural language networks. This paradoxical result suggests that terminology structure is shaped not only by formal logic-based semantics, but by rules analogous to those that govern social networks and biological systems. Graph theoretic modeling shows early promise as a framework for describing terminology structure. Deeper understanding of these techniques may inform the development of scalable terminologies and ontologies. IS - 6 JF - Journal of the American Medical Informatics Association SN - 1067-5027 AD - ∗Correspondence: Stephen Johnson, Department of Biomedical Informatics, Columbia University, Vanderbilt Clinic, 5 Floor, 622 West 168th Street, New York, NY 10032 (Email: stephen.johnson@dbmi.columbia.edu). EP - 797 TI - Topological Analysis of Large-scale Biomedical Terminology Structures VL - 14 SP - 788 KW - analysis KW - classification KW - ontology KW - taxonomy N1 - http://vkwn.com/blog/2009/09/biomedical-terminologies-might-not-be-so-formal/ AU - Bales, ME AU - Lussier, YA AU - Johnson, SB PY - 2007/08/21/c UR - http://dx.doi.org/10.1197/jamia.M2080 ER -