Category Archives: Projects

wikiMap

Posted on January 26, 2011 by sgtp

wikiMap is a very, very simple project. It is a tiny bit of the Phibase project, and it is basically a beginner exercise in Javascript. Said that, it does something nice, it shows on a map which countries related to … Continue reading →

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BioPAX

Posted on December 5, 2010 by sgtp

I’ve been involved since 2005 with BioPAX, which I first approached in search a suitable knowledge base to develop pathway analysis methods. I have been mostly focused on “consuming” BioPAX, which has meant debugging of the specification and some tools … Continue reading →

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DC-RESEARCH.EU

Posted on November 23, 2010 by sgtp

DC-RESEARCH.EU is a system that aims at representing the communication and know-how proper of a research networks. DC-RESEARCH.EU has been developed in the context of the network DC-THERA by Leaf Bioscience s.r.l., in collaboration with other participants in the network. DC-RESEARCH.EU stores synthetic … Continue reading →

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Ontology based Data Analysis

Posted on November 23, 2010 by sgtp

More information coming (hopefully) soon!

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PHI-Base

Posted on November 23, 2010 by sgtp

I am involved in the re-design of the Host Pathogen Interaction database PHI-BASE, where I have devised a new information model and a new database schema. Rather than focusing on “storing” the data, the new information model makes explicit the … Continue reading →

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Ondex

Posted on November 23, 2010 by sgtp

I’m currently working on Ondex, in the context of the Ondex SABR project. Ondex is a data integration software aimed at the molecular biology domain. It provides tools to map databases to the Ondex data structure, tools for the integration, … Continue reading →

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The Genopolis Microarray Database

Posted on November 13, 2010 by sgtp

The Genopolis Microarray Database originated as custom microarray database project for Affymetrix GeneChip data, supporting an homogeneous community studying dendritic cells differentiation. It is based on an object model MAGEcompliant, and provides support for MIAME annotation, export to ArrayExpress as … Continue reading →

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Beat

Posted on November 13, 2007 by sgtp

Beat is platform for the matching and enrichment of ontologies, which was first implemented in the context of the Bootstrep project. It was aimed at providing a platform where several tasks related to ontology alignment/enrichment can be modularly composed. I … Continue reading →

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RDFScape

Posted on November 13, 2007 by sgtp

RDFScape originated as an attempt to “merge” Cytoscape, a popular network analysis software,  with Semantic Web technologies. In its original design, RDFScape was including a variety of experimental features: Cytoscape-based interactive visual interface for RDF-based knowledge bases Interactive visual SPARQL … Continue reading →

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