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

BACKGROUND: 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 betwee...

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Autores principales: Viti, Federica, Merelli, Ivan, Caprera, Andrea, Lazzari, Barbara, Stella, Alessandra, Milanesi, Luciano
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367631/
https://www.ncbi.nlm.nih.gov/pubmed/18460177
http://dx.doi.org/10.1186/1471-2105-9-S4-S4
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author Viti, Federica
Merelli, Ivan
Caprera, Andrea
Lazzari, Barbara
Stella, Alessandra
Milanesi, Luciano
author_facet Viti, Federica
Merelli, Ivan
Caprera, Andrea
Lazzari, Barbara
Stella, Alessandra
Milanesi, Luciano
author_sort Viti, Federica
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
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spelling pubmed-23676312008-05-07 Ontology-based, Tissue MicroArray oriented, image centered tissue bank Viti, Federica Merelli, Ivan Caprera, Andrea Lazzari, Barbara Stella, Alessandra Milanesi, Luciano BMC Bioinformatics Research BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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. BioMed Central 2008-04-25 /pmc/articles/PMC2367631/ /pubmed/18460177 http://dx.doi.org/10.1186/1471-2105-9-S4-S4 Text en Copyright © 2008 Viti et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Viti, Federica
Merelli, Ivan
Caprera, Andrea
Lazzari, Barbara
Stella, Alessandra
Milanesi, Luciano
Ontology-based, Tissue MicroArray oriented, image centered tissue bank
title Ontology-based, Tissue MicroArray oriented, image centered tissue bank
title_full Ontology-based, Tissue MicroArray oriented, image centered tissue bank
title_fullStr Ontology-based, Tissue MicroArray oriented, image centered tissue bank
title_full_unstemmed Ontology-based, Tissue MicroArray oriented, image centered tissue bank
title_short Ontology-based, Tissue MicroArray oriented, image centered tissue bank
title_sort ontology-based, tissue microarray oriented, image centered tissue bank
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367631/
https://www.ncbi.nlm.nih.gov/pubmed/18460177
http://dx.doi.org/10.1186/1471-2105-9-S4-S4
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