ecoBalade: Towards a workflow for Citizen Science Nature Trails

In the context of Citizen Science, where potential users may not be familiar with traditional keys and criteria, it seems necessary to provide a simplified interface in order to guide the users through the complexity of natural biodiversity. Tacit knowledge [1] necessary for citizen science projects; is well known to be difficult to transfer to another person by means of writing it down or verbalizing it. The ecoBalade solves that constraint by putting the user in a problem solving situation in the context of determination, observation, and recording of field data. In order to be successful the workflow must include three stages; a filter of the potential taxa by an expert naturalist, support thoughtout the first identification process and a finally visualization of the field observations by the subject. In a typical ecoBalade scenario, an expert naturalist will survey the potential species beforehand, and will generate a list of potential taxa criteria and pictures. This is then formalized in a XML semantic structure used by a PDA software Pocket eReleve [2] to guide the users thought the identification process. This concept has been successfully tested on the field in Saint Mandrier with approximately twenty novice users and three PDAs, it has generated in the course of two hours 32 observations [3]. The experience will be generalized to other locations in the months to come

A transversal approach to predict gene product networks from ontology-based similarity

<p>Abstract</p> <p>Background</p> <p>Interpretation of transcriptomic data is usually made through a "standard" approach which consists in clustering the genes according to their expression patterns and exploiting Gene Ontology (GO) annotations within each expression cluster. This approach makes it difficult to underline functional relationships between gene products that belong to different expression clusters. To address this issue, we propose a transversal analysis that aims to predict functional networks based on a combination of GO processes and data expression.</p> <p>Results</p> <p>The transversal approach presented in this paper consists in computing the semantic similarity between gene products in a Vector Space Model. Through a weighting scheme over the annotations, we take into account the representativity of the terms that annotate a gene product. Comparing annotation vectors results in a matrix of gene product similarities. Combined with expression data, the matrix is displayed as a set of functional gene networks. The transversal approach was applied to 186 genes related to the enterocyte differentiation stages. This approach resulted in 18 functional networks proved to be biologically relevant. These results were compared with those obtained through a standard approach and with an approach based on information content similarity.</p> <p>Conclusion</p> <p>Complementary to the standard approach, the transversal approach offers new insight into the cellular mechanisms and reveals new research hypotheses by combining gene product networks based on semantic similarity, and data expression.</p

Acquisition incrémentale et représentation des systèmes intégrés bactériens par une approche orienté-objet

Dans le cadre de l'étude des interactions entre les objets biologiques, nous avons développé ISYMOD, un environnement informatique de représentation, d'acquisition, et d'exploitation des connaissances sur les systèmes intégrés bactériens. Une base de connaissances de domaine modélise les systèmes biologiques, par un ensemble de classes et d'associations, organisées hiérarchiquement. Pour assurer la cohérence globale de la base, nous avons intégré dans le système de représentation, un algorithme de propagation de la classification. L'analyse des systèmes intégrés est représentée au sein d'une base de connaissances méthodologiques extensible, à travers des problèmes décrits et hiérarchisés, des méthodes exécutables, et des stratégies de résolution associant problèmes et méthodes. La co-existence des deux bases dans un même environnement permet un contrôle du flux de données entre les étapes incrémentales d'analyse et de stockage, même en cas d'évolution du schéma des bases.AIX-MARSEILLE1-BU Sci.St Charles (130552104) / SudocSudocFranceF

ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems

Motivation: Complex biological functions emerge from interactions between proteins in stable supra-molecular assemblies and/or through transitory contacts. Most of the time protein partners of the assemblies are composed of one or several domains which exhibit different biochemical functions. Thus the study of cellular process requires the identification of different functional units and their integration in an interaction network; such complexes are referred to as integrated systems. In order to exploit with optimum efficiency the increased release of data, automated bioinformatics strategies are needed to identify, reconstruct and model such systems. For that purpose, we have developed a knowledge warehouse dedicated to the representation and acquisition of bacterial integrate

A transversal approach to predict gene product networks from ontology-based similarity-1

<p><b>Copyright information:</b></p><p>Taken from "A transversal approach to predict gene product networks from ontology-based similarity"</p><p>http://www.biomedcentral.com/1471-2105/8/235</p><p>BMC Bioinformatics 2007;8():235-235.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1940024.</p><p></p>ow curve represents the number of gene products that is weighted by the normalized number of terms. This curve reaches its maximum for the fifth level interval which corresponds then to the

A transversal approach to predict gene product networks from ontology-based similarity-3

<p><b>Copyright information:</b></p><p>Taken from "A transversal approach to predict gene product networks from ontology-based similarity"</p><p>http://www.biomedcentral.com/1471-2105/8/235</p><p>BMC Bioinformatics 2007;8():235-235.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1940024.</p><p></p>rness, only the highest similarity links are represented. (b) Amine metabolism network. (c) Lipid metabolism and Catabolism. Up-regulated, Down-regulated and invariant genes are represented respectively as red hexagons, green boxes and yellow ellipses