Dataset Information

On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data.

ABSTRACT: Informatics for Integrating Biology and the Bedside (i2b2) is a database system to facilitate sharing and reuse of clinical patients' data collected in individual hospitals. The i2b2 provides an ontology based object-oriented database system with highly simple and flexible database schema which enables us to integrate clinical patients' data from different laboratories and different hospitals. 392 patients' data including carcinoma and non-carcinoma specimens from cancer patients are transported from the Integrated Clinical Omics Database (iCOD) to the i2b2 database for a feasibility study to check applicability of i2b2 ontology and database schema on Japanese clinical patients' data. No modification is required for the i2b2 data model to deal with Japanese characters. Some modification of ontology is required to integrate biomedical information extracted from the cancer patients' data. We believe that the i2b2 system will be practical infrastructure to integrate Japanese clinical databases if appropriate disease ontology for Japanese patients is provided.

SUBMITTER: Takai-Igarashi T

PROVIDER: S-EPMC3082863 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

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On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data.

Takai-Igarashi Takako T Akasaka Ryo R Suzuki Kenji K Furukawa Takahisa T Yoshida Makiko M Inoue Keisuke K Maruyama Tomohisa T Maejima Toshimasa T Bando Masahiro M Takasaki Masakazu M Sakota Miki M Eguchi Maki M Konagaya Akihiko A Matsuura Hiroya H Suzumura Toyotaro T Tanaka Hiroshi H

Bioinformation 20110326 2

Informatics for Integrating Biology and the Bedside (i2b2) is a database system to facilitate sharing and reuse of clinical patients' data collected in individual hospitals. The i2b2 provides an ontology based object-oriented database system with highly simple and flexible database schema which enables us to integrate clinical patients' data from different laboratories and different hospitals. 392 patients' data including carcinoma and non-carcinoma specimens from cancer patients are transported ...[more]

PMID: 21544172

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Project description:BackgroundSelecting patient cohorts is a critical, iterative, and often time-consuming aspect of studies involving human subjects; informatics tools for helping streamline the process have been identified as important infrastructure components for enabling clinical and translational research. We describe the evaluation of a free and open source cohort selection tool from the Informatics for Integrating Biology and the Bedside (i2b2) group: the i2b2 hive.MethodsOur evaluation included the usability and functionality of the i2b2 hive using several real world examples of research data requests received electronically at the University of Utah Health Sciences Center between 2006 - 2008. The hive server component and the visual query tool application were evaluated for their suitability as a cohort selection tool on the basis of the types of data elements requested, as well as the effort required to fulfill each research data request using the i2b2 hive alone.ResultsWe found the i2b2 hive to be suitable for obtaining estimates of cohort sizes and generating research cohorts based on simple inclusion/exclusion criteria, which consisted of about 44% of the clinical research data requests sampled at our institution. Data requests that relied on post-coordinated clinical concepts, aggregate values of clinical findings, or temporal conditions in their inclusion/exclusion criteria could not be fulfilled using the i2b2 hive alone, and required one or more intermediate data steps in the form of pre- or post-processing, modifications to the hive metadata, etc.ConclusionThe i2b2 hive was found to be a useful cohort-selection tool for fulfilling common types of requests for research data, and especially in the estimation of initial cohort sizes. For another institution that might want to use the i2b2 hive for clinical research, we recommend that the institution would need to have structured, coded clinical data and metadata available that can be transformed to fit the logical data models of the i2b2 hive, strategies for extracting relevant clinical data from source systems, and the ability to perform substantial pre- and post-processing of these data.

Dataset Information

On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data.

Publications

On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data.

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