Extended Analysis of Topological-Pattern-Based Ontology Enrichment

He, Zhe; Keloth, Vipina Kuttichi; Chen, Yan; Geller, James

doi:10.1109/bibm.2018.8621564

Cited by 6 publications

(4 citation statements)

References 24 publications

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“…89 The formula was extended to the cases where cross-ontology synonyms are possible. 90 These methods leveraged the vertical density differences between 2 ontologies. Keloth et al 91 considered the horizontal density differences (number of siblings) in 2 ontologies.…”

Section: Resultsmentioning

confidence: 99%

A review of auditing techniques for the Unified Medical Language System

Zheng

Wei

et al. 2020

Journal of the American Medical Informatics Association

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Objective The study sought to describe the literature related to the development of methods for auditing the Unified Medical Language System (UMLS), with particular attention to identifying errors and inconsistencies of attributes of the concepts in the UMLS Metathesaurus. Materials and Methods We applied the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) approach by searching the MEDLINE database and Google Scholar for studies referencing the UMLS and any of several terms related to auditing, error detection, and quality assurance. A qualitative analysis and summarization of articles that met inclusion criteria were performed. Results Eighty-three studies were reviewed in detail. We first categorized techniques based on various aspects including concepts, concept names, and synonymy (n = 37), semantic type assignments (n = 36), hierarchical relationships (n = 24), lateral relationships (n = 12), ontology enrichment (n = 8), and ontology alignment (n = 18). We also categorized the methods according to their level of automation (ie, automated systematic, automated heuristic, or manual) and the type of knowledge used (ie, intrinsic or extrinsic knowledge). Conclusions This study is a comprehensive review of the published methods for auditing the various conceptual aspects of the UMLS. Categorizing the auditing techniques according to the various aspects will enable the curators of the UMLS as well as researchers comprehensive easy access to this wealth of knowledge (eg, for auditing lateral relationships in the UMLS). We also reviewed ontology enrichment and alignment techniques due to their critical use of and impact on the UMLS.

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Section: Resultsmentioning

confidence: 99%

A review of auditing techniques for the Unified Medical Language System

Zheng

Wei

et al. 2020

Journal of the American Medical Informatics Association

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“…In (28) , UMLS and SNOMED CT are used in the development of semantic annotations for medical data, aiming to provide uniform codes. In (33) cancer phenotypes are modeled with terms from the NCI Thesaurus, while (32) describes a cross-ontology topological standard, using UMLS and NCIt. In (27) , the authors use ICD9 in a care flow algorithm based on the tumor's clinical and histopathological characteristics.…”

Section: Discussionmentioning

confidence: 99%

Semântica em prontuários eletrônicos para oncologia pediátrica: uma revisão integrativa

Figueiredo,

Rosa,

Zanetti

et al. 2023

J Health Inform

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Objetivo: Este estudo tem como objetivo analisar o uso de Sistemas de Organização do Conhecimento (SOC) como meio de enriquecimento do Prontuário Eletrônico do Paciente (PEP) para o domínio da oncologia pediátrica. Métodos: Foi aplicado um método de revisão integrativa da literatura. Foram realizadas três revisões de literatura, com busca de artigos de 2016 até Julho/2023 em PubMed, Scopus, IEEE Xplore e ACM Digital Library escritos em Inglês ou Português. Resultados: Foram analisados 52 artigos. Os resultados apontam os padrões adotados para a especificação de PEP e descrevem os SOC mais frequentemente usados com PEP na oncologia e também no domínio da oncologia pediátrica. Conclusão: Embora existam esforços para adotar padrões internacionais para PEP, vários projetos não fazem uso desses padrões. Os sistemas de PEPs para oncologia, em geral, fazem uso mais amplo de SOCs, enquanto na oncologia pediátrica o foco está nos relacionados à genética. Há necessidade de mais pesquisas para integrar PEP com padrões internacionais.

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“…This idea was later extended to identify topological patterns called trapezoids or diamonds arising from the vertical density differences, to import missing concepts into the SNOMED CT and National Cancer Institute Thesaurus (NCIt) [6,7,13]. A quantitative analysis of the difficulty in importing the pattern-based concepts was also performed [10,14]. We subsequently proposed a metric for identifying likely cases of alternative classifications using horizontal density differences [15].…”

Section: Related Work Density Differencesmentioning

confidence: 99%

“…We use the term "density" following Rector et al [9]. The resulting topological pattern was referred to as a diamond [10]. A horizontal density difference arises out of the fact that the same concept in two different terminologies may have different sets of children in each terminology (Fig.…”

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confidence: 99%

Extending import detection algorithms for concept import from two to three biomedical terminologies

Keloth

Geller

Chen

et al. 2020

BMC Med Inform Decis Mak

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Background While enrichment of terminologies can be achieved in different ways, filling gaps in the IS-A hierarchy backbone of a terminology appears especially promising. To avoid difficult manual inspection, we started a research program in 2014, investigating terminology densities, where the comparison of terminologies leads to the algorithmic discovery of potentially missing concepts in a target terminology. While candidate concepts have to be approved for import by an expert, the human effort is greatly reduced by algorithmic generation of candidates. In previous studies, a single source terminology was used with one target terminology. Methods In this paper, we are extending the algorithmic detection of “candidate concepts for import” from one source terminology to two source terminologies used in tandem. We show that the combination of two source terminologies relative to one target terminology leads to the discovery of candidate concepts for import that could not be found with the same “reliability” when comparing one source terminology alone to the target terminology. We investigate which triples of UMLS terminologies can be gainfully used for the described purpose and how many candidate concepts can be found for each individual triple of terminologies. Results The analysis revealed a specific configuration of concepts, overlapping two source and one target terminology, for which we coined the name “fire ladder” pattern. The three terminologies in this pattern are tied together by a kind of “transitivity.” We provide a quantitative analysis of the discovered fire ladder patterns and we report on the inter-rater agreement concerning the decision of importing candidate concepts from source terminologies into the target terminology. We algorithmically identified 55 instances of the fire ladder pattern and two domain experts agreed on import for 39 instances. In total, 48 concepts were approved by at least one expert. In addition, 105 import candidate concepts from a single source terminology into the target terminology were also detected, as a “beneficial side-effect” of this method, increasing the cardinality of the result. Conclusion We showed that pairs of biomedical source terminologies can be transitively chained to suggest possible imports of concepts into a target terminology.

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Extended Analysis of Topological-Pattern-Based Ontology Enrichment

Cited by 6 publications

References 24 publications

A review of auditing techniques for the Unified Medical Language System

A review of auditing techniques for the Unified Medical Language System

Semântica em prontuários eletrônicos para oncologia pediátrica: uma revisão integrativa

Extending import detection algorithms for concept import from two to three biomedical terminologies

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