Revising the UMLS Semantic Network

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration

Using data-driven sublanguage pattern mining to induce knowledge models: application in medical image reports knowledge representation

Background: The use of knowledge models facilitates information retrieval, knowledge base development, and therefore supports new knowledge discovery that ultimately enables decision support applications. Most existing works have employed machine learning techniques to construct a knowledge base. However, they often suffer from low precision in extracting entity and relationships. In this paper, we described a data-driven sublanguage pattern mining method that can be used to create a knowledge model. We combined natural language processing (NLP) and semantic network analysis in our model generation pipeline. Methods: As a use case of our pipeline, we utilized data from an open source imaging case repository, Radiopaedia.org, to generate a knowledge model that represents the contents of medical imaging reports. We extracted entities and relationships using the Stanford part-of-speech parser and the “Subject:Relationship:Object” syntactic data schema. The identified noun phrases were tagged with the Unified Medical Language System (UMLS) semantic types. An evaluation was done on a dataset comprised of 83 image notes from four data sources. Results: A semantic type network was built based on the co-occurrence of 135 UMLS semantic types in 23,410 medical image reports. By regrouping the semantic types and generalizing the semantic network, we created a knowledge model that contains 14 semantic categories. Our knowledge model was able to cover 98% of the content in the evaluation corpus and revealed 97% of the relationships. Machine annotation achieved a precision of 87%, recall of 79%, and F-score of 82%. Conclusion: The results indicated that our pipeline was able to produce a comprehensive content-based knowledge model that could represent context from various sources in the same domain

Handgrip pattern recognition

There are numerous tragic gun deaths each year. Making handguns safer by personalizing them could prevent most such tragedies. Personalized handguns, also called smart guns, are handguns that can only be fired by the authorized user. Handgrip pattern recognition holds great promise in the development of the smart gun. Two algorithms, static analysis algorithm and dynamic analysis algorithm, were developed to find the patterns of a person about how to grasp a handgun. The static analysis algorithm measured 160 subjects\u27 fingertip placements on the replica gun handle. The cluster analysis and discriminant analysis were applied to these fingertip placements, and a classification tree was built to find the fingertip pattern for each subject. The dynamic analysis algorithm collected and measured 24 subjects\u27 handgrip pressure waveforms during the trigger pulling stage. A handgrip recognition algorithm was developed to find the correct pattern. A DSP box was built to make the handgrip pattern recognition to be done in real time. A real gun was used to evaluate the handgrip recognition algorithm. The result was shown and it proves that such a handgrip recognition system works well as a prototype

Structural auditing methodologies for controlled terminologies

Several auditing methodologies for large controlled terminologies are developed. These are applied to the Unified Medical Language System XXXX and the National Cancer Institute Thesaurus (NCIT). Structural auditing methodologies are based on the structural aspects such as IS-A hierarchy relationships groups of concepts assigned to semantic types and groups of relationships defined for concepts. Structurally uniform groups of concepts tend to be semantically uniform. Structural auditing methodologies focus on concepts with unlikely or rare configuration. These concepts have a high likelihood for errors. One of the methodologies is based on comparing hierarchical relationships between the META and SN, two major knowledge sources of the UMLS. In general, a correspondence between them is expected since the SN hierarchical relationships should abstract the META hierarchical relationships. It may indicate an error when a mismatch occurs. The UMLS SN has 135 categories called semantic types. However, in spite of its medium size, the SN has limited use for comprehension purposes because it cannot be easily represented in a pictorial form, it has many (about 7,000) relationships. Therefore, a higher-level abstraction for the SN called a metaschema, is constructed. Its nodes are meta-semantic types, each representing a connected group of semantic types of the SN. One of the auditing methodologies is based on a kind of metaschema called a cohesive metaschema. The focus is placed on concepts of intersections of meta-semantic types. As is shown, such concepts have high likelihood for errors. Another auditing methodology is based on dividing the NCIT into areas according to the roles of its concepts. Moreover, each multi-rooted area is further divided into pareas that are singly rooted. Each p-area contains a group of structurally and semantically uniform concepts. These groups, as well as two derived abstraction networks called taxonomies, help in focusing on concepts with potential errors. With genomic research being at the forefront of bioscience, this auditing methodology is applied to the Gene hierarchy as well as the Biological Process hierarchy of the NCIT, since processes are very important for gene information. The results support the hypothesis that the occurrence of errors is related to the size of p-areas. Errors are more frequent for small p-areas

Partitioning the UMLS semantic network

The unified medical language system (UMLS) integrates many well-established biomedical terminologies. The UMLS semantic network (SN) can help orient users to the vast knowledge content of the UMLS Metathesaurus (META) via its abstract conceptual view. However, the SN itself is large and complex and may still be difficult to comprehend. Our technique partitions the SN into smaller meaningful units amenable to display on limited-sized computer screens. The basis for the partitioning is the distribution of the relationships within the SN. Three rules are applied to transform the original partition into a second more cohesive partition