SmartBioGraph

About

SmartBioGraph is a graph database mainly based on data retrieved from CROssBAR database. SmartBioGraph is designed to query complicated biological networks easier than traditional relational databases. We provide access to almost 2,5 million nodes and above 10 million relationships retrieved from more than 10 biological databases included in CROssBAR. Moreover, we provide user-friendly and scalable network queries, as well as filtering mechanisms to access the most valuable information and many visualization options in SmartBioSearch interface. Check out SmartBioSearch interface for user-friendly queries and filtering options or access directly to the database via Neo4J Browser if you are comfortable with cypher query language (CQL).

SmartBioGraph Database

SmartBioGraph Database (SmartBioGraphDB) is a graph database mainly based on the data retrieved from CROssBAR database, which is a document-oriented database. Currently, SmartBioGraphDB has over 2.5 million nodes with 16 labels and over 11 million relationships with 17 types. Our node types that come from CROssBAR are proteins (UniProt), genes (UniProt and HPO gene symbols), compounds (CHEMBL and DrugBank), pathways (Reactome), diseases (EFO), phenotypes (HPO), Gene Ontology and Interpro nodes. In addition to nodes coming from CROssBAR database, we also provide disease and pathway nodes which come from KEGG. There are also cross-references for nodes to other databases such as PubChem, OMIM and PubMed.

SmartBioSearch Interface

SmartBioSearch is a web application designed to provide a user-friendly querying, visualization and filtering interface for SmartBioGraph database. The application has a basic search functionality which automatically generates a cyper query to retrieve a node and its immediate neighbors, provided with the node label and search field. It has a visualization module based on Cytoscape with a custom concentric layout and other standard layout options. The interface can also support custom user queries written in CQL, provided that the resulting data from query is a graph. Click here to start your search.

SmartBioSearch Interface Graph Search

Perhaps, the most exciting feature of SmartBioSearch interface is Graph Search, where users can search for a customized network topology with a easy-to-use network creator tool. Then, enrichment analysis is performed on the resulting graph from the query and nodes with less statistical significance are filtered out. This functionality enables users to obtain a statistically valuable biological network very easily, which would otherwise require a very detailed process. Check out our demo videos to see how this functionality can be used.

Neo4j Browser

Neo4J browser is a third party software that provides direct access to SmartBioGraph database. It is a great tool for visualization in small scale and for advanced custom user queries written in CQL. Neo4J Browser also has its own API to support software development on top of SmartBioGraph database.