In BioGateway, these edges are also called relation types, because they represent a type of relation between two entities. Subjects and objects are always nodes, while predicates are edges. We construct a query by step-wise specifying the nodes we want, and the relationships / type of edges between them.Įach new line represents an additional part of the query, consisting of a subject, predicate and object. The BioGateway database is powered by Virtuoso, and queryable through SPARQL, a graph query language based on the same principle as above. Note that even though “Mouse” is not an animal satisfying all the conditions of the query, it is included because it is part of the relevant network for the query. And by further constraining the results to those pets that also are “Chasing” mice, we end up with a final query that results in the network shown in the last part of the animation. The second line in the query restricts the pets to those that are “Walking”, eliminating the Parrot from the results. This returns a subset of the network containing the nodes representing “Pet”, and the animals with edges of the type “Kept as” pointing to the “Pet” node.īy adding more question parts to the query, we can further specify the search. The first question (part of a final query) selects for the animals that have the property of being “kept as” a “Pet”. In the animation to the right, we see a representation of a mock network in a (very small) graph database of animals and some of their properties. In this context, the “graph” is a network of nodes – shown as circles – and edges – the arrows connecting the nodes (see Example Graph Database, animation, to the right). In the image below, we represent the SQL schema of the DisGeNET sqlite database.BioGateway is an RDF Graph Database or ‘triple store’, and can be searched by building a query consisting of a set of questions that together specify what you are looking for. Please login to download the results of your search.ĭon't have an account? Signup for a free account here In case you encounter problems downloading the DisGeNET 7.0 SQLite database use this link to download the database and unpack it on the desired directory. Note: You need to have Java 1.8 or higher installed to use the app. The DisGeNET Cytoscape App (version 7.0.0) is available at theįor more information about how to install it and use it. Which allows users to create workflows executed entirely within Cytoscape or by external tools (such as RStudio or Jupyter) The DisGeNET app includes an automation module with a set of REST endpoints These networks can be filtered by source, disease class, or built Nodes are connected if they share a neighbor in the specific diseases, genes, or variants, and lists and combinations of themĪdditionally, gene-gene, and disease-disease networks can be generated.Using the DisGeNET Cytoscape App, gene-disease and variant-disease networks are easily generated. Genetic basis of human complex diseases by a variety of built-in functions. It assists the user in the interpretation and exploration of the The DisGeNET Cytoscape App is designed to visualize, query and analyse a network representation ofĭisGeNET data (version 7.0). If you find any problems, please contact us at support(at)disgenet(dot)org