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To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have implemented an extension of Chado - the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different \u201comics\u201d technologies with patient\u2019s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/dcm.ffclrp.usp.br\/caib\/pg=iptrans\" ext-link-type=\"uri\">http:\/\/dcm.ffclrp.usp.br\/caib\/pg=iptrans<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-180","type":"journal-article","created":{"date-parts":[[2013,6,6]],"date-time":"2013-06-06T12:16:50Z","timestamp":1370521010000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Computational framework to support integration of biomolecular and clinical data within a translational approach"],"prefix":"10.1186","volume":"14","author":[{"given":"Newton Shydeo Brand\u00e3o","family":"Miyoshi","sequence":"first","affiliation":[]},{"given":"Daniel Guariz","family":"Pinheiro","sequence":"additional","affiliation":[]},{"suffix":"Jr","given":"Wilson Ara\u00fajo","family":"Silva","sequence":"additional","affiliation":[]},{"given":"Joaquim Cezar","family":"Felipe","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,6,6]]},"reference":[{"key":"5931_CR1","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1001\/jama.2007.26","volume":"299","author":"SH Woolf","year":"2008","unstructured":"Woolf SH: The meaning of translational research and why it matters. 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