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With the explosion of online accessible bioinformatics data and tools, systems integration has become very important for further progress. Currently, bioinformatics relies heavily on the Web. But the Web is geared towards human interaction rather than automated processing. The vision of a Semantic Web facilitates this automation by annotating web content and by providing adequate reasoning languages.
GoPubMed classifies abstracts resulting from a PubMed search using Gene Ontology and Medical Subject Headings (MeSH). A screencast is available
(Note: For viewing you need the Microsoft MPEG-4 version 2 codec available with Windows Media Player or in the Codec Installation Package for Windows Media Player.)More: http://www.gopubmed.org
Uses the MeSH Ontology to perform a semantic search on millions of PubMed articles.
More: http://www.meshpubmed.org
GoProteins allows users to browse the GeneOntology and retrieve protein structure data from the web. It uses ontologies, deduction rules, reaction rules, databases and XML.
More: http://rewerse.net/deliverables/m24/a2-d4.pdf
More: http://www.prova.ws
A Language for Rule Based Java Scripting, Information Integration, and Agent Programming.
EarthFeed reads RSS feeds on the web, extracts locations and maps them onto a map of the world. The demonstrator uses XML and reactivity. EarthFeed can be configured to display general news and biotec news from any RSS feed available. EarthFeed can also be used to interact with the world. You can visit all places on the world and see the current news.
More: http://rewerse.net/deliverables/m24/a2-d4.pdf and http://www.transinsight.com/index.php?site=lab
Download:http://labs.transinsight.com/earthfeed/earthfeed.jnlp
EagleVista is a plug-in for the visualisation software Cytoscape, which identifies modules in networks and unravels the hidden structures of these networks.
The BioRevise system is built on REVISE a nonmonotonic reasoning system that revises extended logic programms. It is based on logic programming with explicit negation and integrity constraints and provides two-valued revision assumptions to remove contradictions from the knowledge base. This Belief revision system is used to model inhibition of reactions in metabolic and biosynthesis pathways to explain the alternation on the concentration levels of metabolites after being exposed to external factors like toxins. The system will process the data related to the Pathways which are extracted from the KEGG pathways database.
More: http://rewerse.net/deliverables/m24/a2-d4.pdf
Sambo integrates bio-ontologies such as the GeneOntology and Mesh. It deploys novel algorithms for concept mapping.
More: http://www.ida.liu.se/~iislab/projects/SAMBO/
Tool for evaluating and comparing ontology alignment algorithms.
More: http://www.ida.liu.se/~iislab/projects/KitAMO/
Environment for comparing and evaluating different grouping algorithms.
More: http://www.ida.liu.se/~iislab/projects/KitEGA/
BIOCHAM is a programming environment for modeling biochemical systems, making simulations and querying the model in temporal logic.
Type checking and type inference are important concepts and methods of programming languages and software engineering. In this demonstration, we illustrate the application of these concepts to systems biology. More specifically, we consider the Systems Biology Markup Language SBML and the Biochemical Abstract Machine BIOCHAM with their repositories of models of biochemical systems. We study three type systems: one for checking or inferring the functions of proteins in a reaction model, one for checking or inferring the activation and inhibition effects of proteins in a reaction model, and another one for checking or inferring the topology of compartments or locations. Through some examples, we show that the analysis of biochemical models by type inference provides accurate and useful information. In particular, we are currently developing an interface between SBML/BIOCHAM objects and the ontologies on the web, that uses the protein function types.
The demo has been developed in co-operation with the REWERSE workpackage I3.
More: http://contraintes.inria.fr/BIOCHAM/
Chemera is a molecular graphics and modeling program, primarily intended for studying protein structures and interactions.
More: http://www.cqfb.fct.unl.pt/bioin/chemera/Chemera/Intro.html
Further Information on A2 website
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