OntoCR: A CEN/ISO-13606 clinical repository based on ontologies

Objective: To design a new semantically interoperable clinical repository, based on ontologies, conforming to CEN/ISO 13606 standard. Materials and Methods: The approach followed is to extend OntoCRF, a framework for the development of clinical repositories based on ontologies. The meta-model of OntoCRF has been extended by incorporating an OWL model integrating CEN/ISO 13606, ISO 21090 and SNOMED CT structure. Results: This approach has demonstrated a complete evaluation cycle involving the creation of the meta-model in OWL format, the creation of a simple test application, and the communication of standardized extracts to another organization. Discussion: Using a CEN/ISO 13606 based system, an indefinite number of archetypes can be merged (and reused) to build new applications. Our approach, based on the use of ontologies, maintains data storage independent of content specification. With this approach, relational technology can be used for storage, maintaining extensibility capabilities. Conclusions: The present work demonstrates that it is possible to build a native CEN/ISO 13606 repository for the storage of clinical data. We have demonstrated semantic interoperability of clinical information using CEN/ISO 13606 extracts

Complexities, variations, and errors of numbering within clinical notes: the potential impact on information extraction and cohort-identification

Abstract Background Numbers and numerical concepts appear frequently in free text clinical notes from electronic health records. Knowledge of the frequent lexical variations of these numerical concepts, and their accurate identification, is important for many information extraction tasks. This paper describes an analysis of the variation in how numbers and numerical concepts are represented in clinical notes. Methods We used an inverted index of approximately 100 million notes to obtain the frequency of various permutations of numbers and numerical concepts, including the use of Roman numerals, numbers spelled as English words, and invalid dates, among others. Overall, twelve types of lexical variants were analyzed. Results We found substantial variation in how these concepts were represented in the notes, including multiple data quality issues. We also demonstrate that not considering these variations could have substantial real-world implications for cohort identification tasks, with one case missing > 80% of potential patients. Conclusions Numbering within clinical notes can be variable, and not taking these variations into account could result in missing or inaccurate information for natural language processing and information retrieval tasks.https://deepblue.lib.umich.edu/bitstream/2027.42/148519/1/12911_2019_Article_784.pd

Interoperabilidade semântica: uma análise das perspectivas teóricas dos estudos desenvolvidos na área de Ciência da Informação

It analyzes the theoretical perspectives of the studies on semantic interoperability of Information Science in order to identify their approach with ontological and/or epistemological approaches. It is a bibliographic and exploratory research that uses the technique of content analysis and bibliometric analysis. From the analysis of 54 articles on semantic interoperability indexed in the Web of Science and classified in the Information Science Library Science categoryit was identified that research on semantic interoperability in the LIS area is mostly applied and, often, are limited to describing the development of processes and products without worrying about presenting the fundamentals behind them. Most research has little or no theoretical foundation on language or on what is meant by objectivity.Esse estudo analisa as perspectivas teóricas dos estudos sobre interoperabilidade semântica da Ciência da Informação e identifica a aproximação destas com as abordagens ontológica e/ou epistemológica. É uma pesquisa bibliográfica e exploratória que emprega a técnica de análise de conteúdo e análise bibliométrica. A partir da análise de 54 artigos sobre interoperabilidade semântica indexados na Web of Science e classificados na categoria Information Science Library Science, identificou-seque as pesquisas sobre interoperabilidade semântica na área de CI são majoritariamente aplicadas e, muitas vezes, limitam-se a descrever o desenvolvimento de processos e produtos sem se preocupar em apresentar os fundamentos que estão por trás dos mesmos. A maior parte das pesquisas apresenta pouca ou nenhuma fundamentação teórica sobre a linguagem ou sobre o que se entende por objetividade

Semantic enrichment of clinical models towards semantic interoperability : the heart failure summary use case

Objective: To improve semantic interoperability of electronic health records (EHRs) by ontology-based mediation across syntactically heterogeneous representations of the same or similar clinical information. Materials and Methods: Our approach is based on a semantic layer that consists of: (1) a set of ontologies supported by (2) a set of semantic patterns. The first aspect of the semantic layer helps standardize the clinical information modeling task and the second shields modelers from the complexity of ontology modeling. We applied this approach to heterogeneous representations of an excerpt of a heart failure summary. Results: Using a set of finite top-level patterns to derive semantic patterns, we demonstrate that those patterns, or compositions thereof, can be used to represent information from clinical models. Homogeneous querying of the same or similar information, when represented according to heterogeneous clinical models, is feasible. Discussion: Our approach focuses on the meaning embedded in EHRs, regardless of their structure. This complex task requires a clear ontological commitment (ie, agreement to consistently use the shared vocabulary within some context), together with formalization rules. These requirements are supported by semantic patterns. Other potential uses of this approach, such as clinical models validation, require further investigation. Conclusion: We show how an ontology-based representation of a clinical summary, guided by semantic patterns, allows homogeneous querying of heterogeneous information structures. Whether there are a finite number of top-level patterns is an open question

Interoperabilidade semântica: uma análise sob a perspectiva da abordagem ontológica de Willard van Orman Quine

Tese (doutorado) - Universidade Federal de Santa Catarina, Centro de Ciências da Educação, Programa de Pós-Graduação em Ciência da Informação, Florianópolis, 2019.O cenário contemporâneo apresenta um crescimento exponencial do volume e da diversidade informacional, o que torna a busca e a recuperação da informação cada vez mais complexa e a integração entre diferentes fontes de informacionais cada vez mais necessária. A interoperabilidade corresponde à capacidade de dois ou mais sistemas trocarem informações e usarem as informações que foram trocadas, o que pode envolver diversos níveis operacionais. O nível de conteúdo remete à interoperabilidade semântica, na qual a representação e organização do conhecimento são áreas-chave a serem estudadas. A organização do conhecimento é um dos principais temas de pesquisa na área de Ciência da Informação, tais pesquisas são desenvolvidas com base em diferentes abordagens e posturas epistêmicas, dentre as quais se destacam as abordagens ontológica e epistemológica e as posturas pragmática e positivista. Willard van Orman Quine é considerado um dos mais importantes filósofos contemporâneos por ter renovado o pragmatismo e libertado a filosofia analítica do positivismo lógico. Ele deu contribuições valorosas aos estudos de ontologia no escopo da filosofia analítica e enfrenta a questão ontológica de modo muito peculiar, o que dificulta enquadrá-lo em uma corrente filosófica. Em vista disso, o objetivo geral da tese é analisar as perspectivas ontológicas dos estudos sobre interoperabilidade semântica da Ciência da Informação à luz das noções propostas na abordagem ontológica de Willard Van Orman Quine. Os objetivos específicos são: a) sintetizar a abordagem ontológica de Quine; b) caracterizar a pesquisa sobre interoperabilidade semântica; c) descrever a pesquisa sobre interoperabilidade semântica da área de Ciência da Informação; d) relacionar as perspectivas ontológicas presentes nas pesquisas sobre interoperabilidade semântica da área de Ciência da Informação com a abordagem ontológica de Quine. Quanto aos seus objetivos, caracteriza-se como uma pesquisa exploratória que adota uma abordagem de pesquisa qualitativa. Quanto aos procedimentos metodológicos, configura-se em uma pesquisa bibliográfica que se utiliza da Análise de Conteúdo e da análise bibliométrica. Apresenta os resultados divididos de forma a atender os quatro objetivos específicos. A abordagem ontológica de Quine compreende sete noções, as quais são teórica e filosoficamente vinculadas e integram o sistema filosófico geral de Quine. Para Quine qualquer debate sobre ontologia exige a estipulação de um conceito de existência, ele rejeita a doutrina que relaciona o ser, ou a existência, à significância e defende a que relaciona o ser à referência, que para ele pode ser uma entidade concreta ou abstrata. Para Quine não cabe aos filósofos dizerem se há ou não classes ou qualquer outro tipo de entidade abstrata, mas sim aos pesquisadores e cientistas dizerem o que há, o que existe. As pesquisas sobre interoperabilidade semântica são desenvolvidas em diversas áreas, como por exemplo, em Ciência da Computação, Informática Médica e Ciência da Informação. A partir da análise de indicadores bibliométricos foi possível identificar o desenvolvimento progressivo na quantidade de pesquisas ao longo dos últimos anos, as principais temáticas de interesse, dentre as quais se destaca o estudo de ontologias, e os trabalhos e autores mais citados, dentre os quais se destacam Gruber(1993) e Dolin, et al. (2006), que tratam, respectivamente, sobre ontologias e normas internacionais para a representação e a transferência de dados entre sistemas de informação em saúde. No âmbito da Ciência da Informação, as pesquisas sobre interoperabilidade semântica são majoritariamente aplicadas e se destinam ao desenvolvimento de processos e produtos que visam a interoperabilidade semântica de modo geral ou em domínios específicos, dentre os quais se destacam os domínios de saúde, Geociências e cultura ou linguagem chinesa. Muitas pesquisas se limitam a desenvolver processos e produtos que visam a interoperabilidade semântica sem se preocupar em apresentar os fundamentos que estão por trás dos mesmos. A identificação das perspectivas ontológicas e a comparação com a abordagem ontológica de Quine foi possível principalmente a partir das pesquisas teóricas sobre interoperabilidade semântica. Considera-se que a interoperabilidade semântica diz respeito à comunicação, que de um modo geral parece ser vista como algo relativamente simples. O que é considerado complexo é a linguagem. Desse modo busca-se desenvolver linguagens simplificadas e/ou objetivas (livres de interpretações subjetivas) para permitir a interoperabilidade semântica. Contudo, o que se percebe é que diferente da comunicação humana, a interoperabilidade semântica entre sistemas de informação automatizados é altamente complexa e ainda não foi plenamente atingida. O que mostra que talvez seja a complexidade e adaptabilidade da linguagem natural que proporcione a simplicidade na comunicação humana, ao mesmo tempo em que uma linguagem demasiadamente simplista, como a almejada para a interoperabilidade semântica, torne a comunicação inviável. Desse modo, a simplicidade e objetividade das linguagens artificias ou formais, que de um modo geral é considerada necessária para a interoperabilidade semântica, a nosso ver é algo questionável. Além disso, ainda que do ponto de vista da abordagem ontológica de Quine a objetividade da referência seja colocada em xeque (com o caso artificial de gavagai, por exemplo), se a simplicidade e objetividade da linguagem são a chave para a interoperabilidade semântica, tal objetividade parece não ser possível por meio da mera especulação lógica e filosófica (ou dos cientistas da computação e da informação), pois para Quine os filósofos não possuem um ponto de vista privilegiado que possa responder à pergunta o que há e resolver as discussões ontológicas que dela suscitam.Abstract : The contemporary scenario presents an exponential growth of information volume and diversity, which makes information retrieval and search increasingly complex and the integration between different sources of information increasingly necessary. Interoperability refers to the ability of two or more systems to exchange information and to use the information that has been exchanged, which may involve several operational levels. The level of content refers to semantic interoperability, in which knowledge organization and representation are key areas to be studied. Knowledge organization is one of the main research topics in the field of Information Science. Such research is developed based on different approaches and epistemic postures, among which are the ontological and epistemological approaches and the pragmatic and positivist postures. Willard van Orman Quine is considered one of the most important contemporary philosophers for having renewed pragmatism and having liberated the analytic philosophy of logical positivism. He has made valuable contributions to ontology studies within the scope of analytical philosophy and faces the ontological question in a very peculiar way, which makes it difficult to fit him in a philosophical current. Therefore, the general objective of the thesis is to analyze the ontological perspectives of the studies on semantic interoperability of Information Science, in light of the notions proposed in the ontological approach by Willard Van Orman Quine. The specific objectives are: a) To synthesize Quine s ontological approach; b) to characterize the research on semantic interoperability; c) to describe the research on the semantic interoperability of the Information Science; d) to relate the ontological approaches present in the researches on semantic interoperability of the Information Science area with Quine s ontological approach. Regarding its objectives, it is characterized as an exploratory research that adopts a qualitative research approach. As for the methodological procedures, it is configured in a bibliographic research that uses Content Analysis and bibliometric analysis. It displays the results divided to meet the four specific objectives. Quine's ontological approach comprises seven notions, which are theoretically and philosophically linked and they integrate Quine's general philosophical system. For Quine, any debate about ontology requires the stipulation of a concept of existence; he rejects the doctrine that relates the being, or the existence, to meaning and defends the one that relates the being to the reference, which for him can be a concrete or abstract entity. For Quine, it is not for philosophers to say whether there are or not classes or any other type of abstract entity, but for researchers and scientists to tell what is there, what exists. Researches on semantic interoperability are developed in several areas, such as in Computer Science, Medical Informatics and Information Science. From the analysis of bibliometric indicators, it was possible to identify the progressive development in the quantity of researches over the last years, the main topics of interest, among which the study of ontologies stands out, and the most cited authors and works, among which Gruber (1993) and Dolin, et al. (2006) stand out, which deal, respectively, on ontologies and international norms for the representation and transfer of data between health information systems. In the Information Science area, research on semantic interoperability is mostly applied and intended to develop processes and products that aim at semantic interoperability in general or in specific domains, among which, the areas of health, geosciences and culture or Chinese language stand out. Many researches are limited to developing processes and products that aim at semantic interoperability without worrying about presenting the fundamentals that are behind them. The identification of the ontological approaches and the comparison with Quine s ontological approach was possible mainly from the theoretical investigations on semantic interoperability. Semantic interoperability is considered to be about communication, which in general seems to be seen as relatively simple. What is considered complex is the language, in this way it seeks to develop simplified languages (objective, free of subjective interpretations) to allow semantic interoperability. However, what is perceived is that, unlike human communication, semantic interoperability between automated information systems is highly complex and it has not yet been fully achieved. What shows that, it may be the complexity and adaptability of natural language that provides simplicity in human communication, at the same time too simplistic language, such as that the one intended for semantic interoperability, makes communication unfeasible. Thus, the simplicity and objectivity of the artificial or formal languages, which are generally considered necessary for semantic interoperability, in our view is somewhat questionable. Moreover, although from the point of view of Quine's ontological approach, the objectivity of the reference is checked (with the artificial case of gavagai, for example), if language simplicity and objectivity are the key to semantic interoperability, such objectivity seems not to be possible by mere logical and philosophical speculation (or by computer and information scientists),but for to Quine, the philosophers do not have a privileged point of view that can answer the question \"what is there\" and solve the ontological discussions that give rise to it

An experimental study and evaluation of a new architecture for clinical decision support - integrating the openEHR specifications for the Electronic Health Record with Bayesian Networks

Healthcare informatics still lacks wide-scale adoption of intelligent decision support methods, despite continuous increases in computing power and methodological advances in scalable computation and machine learning, over recent decades. The potential has long been recognised, as evidenced in the literature of the domain, which is extensively reviewed. The thesis identifies and explores key barriers to adoption of clinical decision support, through computational experiments encompassing a number of technical platforms. Building on previous research, it implements and tests a novel platform architecture capable of processing and reasoning with clinical data. The key components of this platform are the now widely implemented openEHR electronic health record specifications and Bayesian Belief Networks. Substantial software implementations are used to explore the integration of these components, guided and supplemented by input from clinician experts and using clinical data models derived in hospital settings at Moorfields Eye Hospital. Data quality and quantity issues are highlighted. Insights thus gained are used to design and build a novel graph-based representation and processing model for the clinical data, based on the openEHR specifications. The approach can be implemented using diverse modern database and platform technologies. Computational experiments with the platform, using data from two clinical domains – a preliminary study with published thyroid metabolism data and a substantial study of cataract surgery – explore fundamental barriers that must be overcome in intelligent healthcare systems developments for clinical settings. These have often been neglected, or misunderstood as implementation procedures of secondary importance. The results confirm that the methods developed have the potential to overcome a number of these barriers. The findings lead to proposals for improvements to the openEHR specifications, in the context of machine learning applications, and in particular for integrating them with Bayesian Networks. The thesis concludes with a roadmap for future research, building on progress and findings to date

Front-Line Physicians' Satisfaction with Information Systems in Hospitals

Day-to-day operations management in hospital units is difficult due to continuously varying situations, several actors involved and a vast number of information systems in use. The aim of this study was to describe front-line physicians' satisfaction with existing information systems needed to support the day-to-day operations management in hospitals. A cross-sectional survey was used and data chosen with stratified random sampling were collected in nine hospitals. Data were analyzed with descriptive and inferential statistical methods. The response rate was 65 % (n = 111). The physicians reported that information systems support their decision making to some extent, but they do not improve access to information nor are they tailored for physicians. The respondents also reported that they need to use several information systems to support decision making and that they would prefer one information system to access important information. Improved information access would better support physicians' decision making and has the potential to improve the quality of decisions and speed up the decision making process.Peer reviewe