This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.
The openEHR specifications are designed to support implementation of flexible and interoperable Electronic Health Record (EHR) systems. Despite the increasing number of solutions based on the openEHR specifications, it is difficult to find publicly available healthcare datasets in the openEHR format that can be used to test, compare and validate different data persistence mechanisms for openEHR. To foster research on openEHR servers, we present the openEHR Benchmark Dataset, ORBDA, a very large healthcare benchmark dataset encoded using the openEHR formalism. To construct ORBDA, we extracted and cleaned a de-identified dataset from the Brazilian National Healthcare System (SUS) containing hospitalisation and high complexity procedures information and formalised it using a set of openEHR archetypes and templates. Then, we implemented a tool to enrich the raw relational data and convert it into the openEHR model using the openEHR Java reference model library. The ORBDA dataset is available in composition, versioned composition and EHR openEHR representations in XML and JSON formats. In total, the dataset contains more than 150 million composition records. We describe the dataset and provide means to access it. Additionally, we demonstrate the usage of ORBDA for evaluating inserting throughput and query latency performances of some NoSQL database management systems. We believe that ORBDA is a valuable asset for assessing storage models for openEHR-based information systems during the software engineering process. It may also be a suitable component in future standardised benchmarking of available openEHR storage platforms.
This paper aims at to present the integration of the files of the Brazilian Cervical Cancer Information System (SISCOLO) in order to identify all women in the system. SISCOLO has the exam as the unit of observation and the women are not uniquely identified. It has two main tables: histology and cytology, containing the histological and cytological examinations of women, respectively. In this study, data from June 2006 to December 2009 were used. Each table was linked with itself and with the other through record linkage methods. The integration identified 6236 women in the histology table and 1,678,993 in the cytology table. 5324 women from the histology table had records in the cytology table. The sensitivities were above 90% and the specificities and precisions near 100%. This study showed that it is possible to integrate SISCOLO to produce indicators for the evaluation of the cervical cancer screening programme taking the woman as the unit of observation.
RESUMO -Objetivo: Avaliar a relação do índice de resistência (IR) obtido pela ultra-sonografia Doppler transfontanela com o neurodesenvolvimento até um ano de idade, em recém-nascidos (RN) a termo com encefalopatia hipóxica-isquêmica (EHI) leve a moderada, secundária à asfixia intra-parto. Método: Estudo prospectivo em 20 RN com EHI leve a moderada, IR elevado no primeiro exame de Doppler, e sem doenças associadas ou anormalidades morfológicas cerebrais. Foram realizados exames seriados bimensais de Doppler transfontanela a partir do sétimo dia de vida, e avaliações clínicas mensais do neurodesenvolvimento no primeiro ano de vida. Resultados: Houve normalização progressiva dos valores de IR até o último exame realizado. Cinco pacientes apresentaram normalização clínico-neurológica no período neonatal, após o primeiro exame de Doppler. Quinze lactentes apresentaram alterações neurológicas com resolução a partir do segundo trimestre de vida. Conclusão: Houve relação entre os períodos em que ocorreu a normalização dos valores de IR e a melhora clínica-neurológica. PALAVRAS-CHAVE: encefalopatia hipóxica-isquêmica, ultra-sonografia Doppler, recém-nascido, neurodesenvolvimento.Relation between the resistance index obtained by the transfontanellar Doppler ultrasonography and the neurological development until the first year of life in term infants with mild or moderate hypoxic-ischaemic encephalopathy ABSTRACT -Objective: To evaluate the relation between the resistance index (RI) obtained by transfontanellar Doppler ultrasonography, and the neurodevelopment until one year of life, at term newborns with mild or moderate hypoxic-ischaemic encephalopathy due to intrapartum asphyxia. Method: 20 term newborns, with mild or moderate hypoxic-ischemic encephalopathy, high values of resistance index in the first exam, and without cerebral morfologic abnormalities or other diseases. They were submitted to serial bimonthly transfontanellar Doppler ultrasonography, from the seventh day of life on, and monthly clinical neurodevelopment assessment until one year of life. Results: There was a progressive normalization of RI values until the last examination. In five cases there were clinical neurologic normalization in the neonatal period after the first Doppler exam. Fifteen infants presented neurologic abnormalities, with normalization after the second trimester of life. Conclusion: There was a relation between the normal RI values with the normalization of the clinical assessment.
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