Dataset Information

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

ABSTRACT:

Summary

InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages.

Availability

Freely available from http://www.intermine.org under the LGPL license.

Contact

g.micklem@gen.cam.ac.uk

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Smith RN

PROVIDER: S-EPMC3516146 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

Smith Richard N RN Aleksic Jelena J Butano Daniela D Carr Adrian A Contrino Sergio S Hu Fengyuan F Lyne Mike M Lyne Rachel R Kalderimis Alex A Rutherford Kim K Stepan Radek R Sullivan Julie J Wakeling Matthew M Watkins Xavier X Micklem Gos G

Bioinformatics (Oxford, England) 20120927 23

<h4>Summary</h4>InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing vari ...[more]

PMID: 23023984

Similar Datasets

Project description:BackgroundThe American Society for Clinical Oncology recently launched the minimal common oncology data elements project to facilitate cancer data interoperability. However, clinical data are often unrecorded in an organized way, and converting them into a structured format can be time-consuming. Clinical Data Warehouse (CDW) is a database that consolidates data from different clinical sources. However, the clinical data extracted from this database include not only structured data but also natural language generated during clinical practice. Therefore, applying these data to a clinical study is challenging because they are unstructured, and unformatted to allow essential content to be found. This study determined how best to organize a huge amount of clinical data to evaluate the upper aerodigestive tract cancers' clinical features and outcomes, including cancer of the head and neck, esophagus, lung, thymus, and mesothelioma.MethodsThe Real-time autOmatically updated data warehOuse in healThcare (ROOT) uses six main regions to describe the journey of cancer patients. This study, developed an algorithm optimized for each disease category using natural language processing of unstructured data and data capture of structured data. Data from patients diagnosed at the Samsung Medical Center from 2008-2020 were used.ResultsComprehensive clinical data for 67,617 patients across six tumor types: 28,954 with non-small-cell lung cancer, 2,540 with small-cell lung cancer, 30,035 with head and neck cancer, 4,950 with esophageal cancer, 966 with thymic cancer, and 172 with mesothelioma were collected. Additionally, the results of a longitudinal molecular study, including epidermal growth factor receptor (EGFR) mutations, anaplastic lymphoma kinase (ALK) tests, and next-generation sequencing (NGS), were included. Scattered information was integrated and automatically built up to match the cohort, allowing users to capture the most updated test results and treatment outcomes.ConclusionsThis landmark study documented the successful construction of a real-time updating system for medical big data, based on the CDW program.

Dataset Information

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

Summary

Availability

Contact

Supplementary information

Publications

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets