NeuroRDF

This webpage hosts the supplementary files for two publications associated with NeuroRDF work.

Publication 2016:

Iyappan & Kawalia et al. NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. Journal of Biomedical Semantics 2016. Accepted

Download neuroRDFModels_Queries.zip:

Single File Download:

• NeuroRDFQueries.txt
• AlzheimersPPI_NeuroRDF.rdf
• Brain_PPI_Interactome_NeuroRDF.rdf
• Microarray_NeuroRDF.rdf
• MiRNA_NeuroRDF.rdf

Publication 2014:

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.

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.

Namespaces Used for Building the RDF Schemas

Url_Namespaces, XLSX 11 KB

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 namespace (URIs) used for these Resources and Properties.

Generated RDF Schemas

RDF Schemas for the five data resources are additionally provided. Below are the schemas and their respective file names:

• DiseasePPI_RDF_Schema, PDF 59KB
• HealthyPPI_RDF_Schema, PDF 124 KB
• MiRNA-target-interaction_RDF_Schema, PDF 97 KB
• Reactome_Pathway_RDF_Schema, PDF 93 KB
• Microarray_RDF_Schema.pdf

Literature Evidences Supporting Proposed Subnetworks

Subnetwork_evidences, XLS 5 KB

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

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

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 explanation of the query)  can be found in QueryForVisualization.txt.

All descriptions of this page can be found in README.TXT.

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.