Ontology-based, Tissue MicroArray oriented, image centered tissue bank

<p>Abstract</p> <p>Background</p> <p>Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly managed, if possible with an infrastructure able to support tissue sharing between institutes. Moreover, the available frameworks oriented to Tissue MicroArray provide good storage for clinical patient, sample treatment and block construction information, but their utility is limited by the lack of data integration with biomolecular information.</p> <p>Results</p> <p>In this work we propose a Tissue MicroArray web oriented system to support researchers in managing bio-samples and, through the use of ontologies, enables tissue sharing aimed at the design of Tissue MicroArray experiments and results evaluation. Indeed, our system provides ontological description both for pre-analysis tissue images and for post-process analysis image results, which is crucial for information exchange. Moreover, working on well-defined terms it is then possible to query web resources for literature articles to integrate both pathology and bioinformatics data.</p> <p>Conclusions</p> <p>Using this system, users associate an ontology-based description to each image uploaded into the database and also integrate results with the ontological description of biosequences identified in every tissue. Moreover, it is possible to integrate the ontological description provided by the user with a full compliant gene ontology definition, enabling statistical studies about correlation between the analyzed pathology and the most commonly related biological processes.</p

A metadata-aware application for remote scoring and exchange of tissue microarray images.

BACKGROUND: The use of tissue microarrays (TMA) and advances in digital scanning microscopy has enabled the collection of thousands of tissue images. There is a need for software tools to annotate, query and share this data amongst researchers in different physical locations. RESULTS: We have developed an open source web-based application for remote scoring of TMA images, which exploits the value of Microsoft Silverlight Deep Zoom to provide a intuitive interface for zooming and panning around digital images. We use and extend existing XML-based standards to ensure that the data collected can be archived and that our system is interoperable with other standards-compliant systems. CONCLUSION: The application has been used for multi-centre scoring of TMA slides composed of tissues from several Phase III breast cancer trials and ten different studies participating in the International Breast Cancer Association Consortium (BCAC). The system has enabled researchers to simultaneously score large collections of TMA and export the standardised data to integrate with pathological and clinical outcome data, thereby facilitating biomarker discovery.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Ontology-based, Tissue MicroArray oriented, image centered tissue bank-0

Access the ontology term handler (based on MESH and GO ontologies) and the underlying RDBMS which contains sample and array data. The ontology terms allow users to perform a semantic web search to link litarature to the described concepts.<p><b>Copyright information:</b></p><p>Taken from "Ontology-based, Tissue MicroArray oriented, image centered tissue bank"</p><p>http://www.biomedcentral.com/1471-2105/9/S4/S4</p><p>BMC Bioinformatics 2008;9(Suppl 4):S4-S4.</p><p>Published online 25 Apr 2008</p><p>PMCID:PMC2367631.</p><p></p

Highlights CNR 2008-2009

Selezione ragionata degli oltre 14.000 articoli scientifici che i ricercatori del CNR hanno pubblicato nel corso del biennio 2008-2009 sulle principali riviste o volumi di riferimento della propria attività. I temi sono divisi per comodità in 4 grandi settori: Habitat e Vita, Materia e Energia, Informazione e Comunicazione, Cultura e Societ