Can SNOMED CT be squeezed without losing its shape?. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: López-García, Pablo; Schulz, Stefan
• Is Part Of: Journal of biomedical semantics. Volume 7:Issue 1(2016)
• Page Start: 1
• Page End: 7
• Publication Date: 2016-12
• Subjects: SNOMED CT -- Ontology modularization -- Biomedical terminology; Semantics -- Periodicals; Medicine -- Research -- Periodicals; Biology -- Research -- Periodicals; Computer systems -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1186/s13326-016-0101-1
• Languages: English
• ISSNs: 2041-1480

Abstract

Abstract Background In biomedical applications where the size and complexity of SNOMED CT become problematic, using a smaller subset that can act as a reasonable substitute is usually preferred. In a special class of use cases—like ontology-based quality assurance, or when performing scaling experiments for real-time performance—it is essential that modules show a similar shape than SNOMED CT in terms of concept distribution per sub-hierarchy. Exactly how to extract such balanced modules remains unclear, as most previous work on ontology modularization has focused on other problems. In this study, we investigate to what extent extracting balanced modules that preserve the original shape of SNOMED CT is possible, by presenting and evaluating an iterative algorithm. Methods We used a graph-traversal modularization approach based on an input signature. To conform to our definition of a balanced module, we implemented an iterative algorithm that carefully bootstraped and dynamically adjusted the signature at each step. We measured the error for each sub-hierarchy and defined convergence as a residual sum of squares <1. Results Using 2000 concepts as an initial signature, our algorithm converged after seven iterations and extracted a module 4.7 % the size of SNOMED CT. Seven sub-hierarhies were either over or under-represented within a range of 1–8 %. Conclusions Our study shows that balanced modules from large terminologies can be extracted using ontology graph-traversal modularization techniques under certain conditions: that the process is repeated a number of times, the input signature is dynamically adjusted in each iteration, and a moderate under/over-representation of some hierarchies is tolerated. In the case of SNOMED CT, our results conclusively show that it can be squeezed to less than 5 % of its size without any sub-hierarchy losing its shape more than 8 %, which is likely sufficient in most use cases.