semnext

Related Research

Current Research Applications


SemNExT is already being used to explore relationships between gene expression and brain formation, particularly in the presence of structural disorders such as Microcephaly. Semantically-informed and interactive visualizations (such as the one below, available at the SemNExT project demo page) are used to aid researchers in the medical community as they explore the causes of these conditions.

Features

Semantics + Numerics


The ability to model and inform analyses of numerical datasets using semantics poses significant advantages over traditional programming methods, which are typically unaware of the interactions of the various components that constitute the methodology. This means that data provenance is also lost, as there is no record of the type of analysis performed.

Features

Semantics + Numerics


Services as Containers


True Data-Driven Analysis


Developer's Guide

Top-Level Overview


SemNExT is built on top of Docker and Docker Compose, meaning it must be run on either OS X or Linux. When built, SemNExT and each of its constituent services are constructed as a Docker container, linked to each other through the configuration in the .yml file Docker Compose is executed against. Three core services will underlie every SemNExT-based application: the SemNExT service, a SPARQL endpoint and Redis. The SPARQL endpoint is used to handle internal knowledge representation, especially the application's ontology.

Dependencies


Before running SemNExT, you'll need the following installed:

Seriously, that's basically it. Everything else is installed in the Docker image at run time.

Architecture

Components

SemNExT Component Flow Chart

The block diagram above shows a typical flow in a SemNExT application between components. The webservice API acts as an interface for clients to communicate with the application, abstracting interaction for both ease of use and security.

Documentation

Documentation is handled using Sphinx, which allows the documentation to be embedded in the source code as comments.

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