7,566 research outputs found

    In Silico Approaches and the Role of Ontologies in Aging Research

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    The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin

    Pairwise gene GO-based measures for biclustering of high-dimensional expression data

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    Background: Biclustering algorithms search for groups of genes that share the same behavior under a subset of samples in gene expression data. Nowadays, the biological knowledge available in public repositories can be used to drive these algorithms to find biclusters composed of groups of genes functionally coherent. On the other hand, a distance among genes can be defined according to their information stored in Gene Ontology (GO). Gene pairwise GO semantic similarity measures report a value for each pair of genes which establishes their functional similarity. A scatter search-based algorithm that optimizes a merit function that integrates GO information is studied in this paper. This merit function uses a term that addresses the information through a GO measure. Results: The effect of two possible different gene pairwise GO measures on the performance of the algorithm is analyzed. Firstly, three well known yeast datasets with approximately one thousand of genes are studied. Secondly, a group of human datasets related to clinical data of cancer is also explored by the algorithm. Most of these data are high-dimensional datasets composed of a huge number of genes. The resultant biclusters reveal groups of genes linked by a same functionality when the search procedure is driven by one of the proposed GO measures. Furthermore, a qualitative biological study of a group of biclusters show their relevance from a cancer disease perspective. Conclusions: It can be concluded that the integration of biological information improves the performance of the biclustering process. The two different GO measures studied show an improvement in the results obtained for the yeast dataset. However, if datasets are composed of a huge number of genes, only one of them really improves the algorithm performance. This second case constitutes a clear option to explore interesting datasets from a clinical point of view.Ministerio de Economía y Competitividad TIN2014-55894-C2-

    Creating hospital-specific customized clinical pathways by applying semantic reasoning to clinical data

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    AbstractObjectiveClinical pathways (CPs) are widely studied methods to standardize clinical intervention and improve medical quality. However, standard care plans defined in current CPs are too general to execute in a practical healthcare environment. The purpose of this study was to create hospital-specific personalized CPs by explicitly expressing and replenishing the general knowledge of CPs by applying semantic analysis and reasoning to historical clinical data.MethodsA semantic data model was constructed to semantically store clinical data. After querying semantic clinical data, treatment procedures were extracted. Four properties were self-defined for local ontology construction and semantic transformation, and three Jena rules were proposed to achieve error correction and pathway order recognition. Semantic reasoning was utilized to establish the relationship between data orders and pathway orders.ResultsA clinical pathway for deviated nasal septum was used as an example to illustrate how to combine standard care plans and practical treatment procedures. A group of 224 patients with 11,473 orders was transformed to a semantic data model, which was stored in RDF format. Long term order processing and error correction made the treatment procedures more consistent with clinical practice. The percentage of each pathway order with different probabilities was calculated to declare the commonality between the standard care plans and practical treatment procedures. Detailed treatment procedures with pathway orders, deduced pathway orders, and orders with probability greater than 80% were provided to efficiently customize the CPs.ConclusionsThis study contributes to the practical application of pathway specifications recommended by the Ministry of Health of China and provides a generic framework for the hospital-specific customization of standard care plans defined by CPs or clinical guidelines

    Neurocognitive Informatics Manifesto.

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    Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given
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