NeuroRDF: Semantic Data Integration Strategies for Modeling Neurodegenerative Diseases

NeuroRDF is a RDF based framework designed to build and to explore a heterogenous neurodegenerative disease knowledgebase 
through a semantic modelling approach.

This webpage hosts the supplementary materials referred in the following publication:
Iyappan A, Bagewadi S, Page M, Hofmann-Apitius M, and Senger P. In Proceedings of the 6th International 
Symposium on Semantic Mining in Biomedicine (SMBM2014). Aveiro, Portugal, 2014:[page numbers yet to be published].

Files made available through work are:

1. Namespaces used for building the RDF schemas
2. Generated RDF Schemas
3. Literature evidences supporting proposed subnetworks
4. List of brain regions in healthy PPI network
5. Visualization of RDF sub-graph in Cytoscape

The detailed description of each file is given below.

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Namespaces Used for Building the RDF Schemas

Url_Namespaces.xlsx

The file consists of the ontological namespaces used for generation of the different RDF schemas. 
The first column provides the name of the resources 
from which the namespaces are extracted. The second column describes the Resources and Properties 
used for each of the schema. The third column represents the exact 2014
namespace (URIs) used for these Resources and Properties.
             
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Generated RDF Schemas

RDF Schemas for the five data resources  used for building NeuroRDF are provided here:

1. Alzheimer Disease PPI network schema	: DiseasePPI_RDF_Schema.pdf
2. Healthy PPI network schema			: HealthyPPI_RDF_Schema.pdf
3. MiRNA-target interaction schema		: MiRNA-target-interaction_RDF_Schema.pdf
4. Gene-Pathway interaction schema		: Reactome_Pathway_RDF_Schema.pdf
5. Microarray schema					: Microarray_RDF_Schema.pdf

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Literature Evidences Supporting Proposed Subnetworks

Subnetwork_evidences.xls

For the two derived sub-networks (in Use-case Analysis), associated PMIDs retrieved during the literature 
survey are provided in this file.
Evidences from human studies are provided in a separate column.

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List of Brain Regions in Healthy PPI Network

List of brain regions that are linked to PPIs in Healthy PPI network can be found here: BrainRegions.txt

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Visualization of RDF Sub-Graph in Cytoscape

Visualization of an RDF sub-network generated using sample SPARQl query in Cytoscape is provided here.
The sample query used for generating the graph (along with detailed explaination of the query) 
can be found in QueryForVisualization.txt. 


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How to Cite: Iyappan & Bagewadi et al. NeuroRDF: Semantic Data Integration 
Strategies for Modeling Neurodegenerative Diseases. In Proceedings of the 6th International 
Symposium on Semantic Mining in Biomedicine (SMBM2014). Aveiro, Portugal, 2014:[page numbers yet to be published].