Welcome to the KnetMiner wiki!
This wiki contains detailed information about the installation and development of KnetMiner, and how to set up a knowledge network using Ondex.
Ondex is a software application that allows users to use (biological) data from various sources to create graph-based knowledge networks. The data used is mostly in the form of gene-protein networks and additional information (such as GO-terms or homologies) for these proteins. Ondex represents genes or proteins in as concepts (aka nodes) that are connected by relations (aka edges) such as "encodes for", "cooccurs_with" and so on.
Ondex itself is a GUI-based application but also has a terminal-based application called ondex-mini, which should be used for working with larger datasets.
KnetMiner is a web application that represents Ondex-networks in a webpage for easier searching and browsing. KnetMiner consists of a client deployed using any web server. Users enter their search terms into the web page's search engine. The client then takes these search-terms and sends them to the KnetMiner server, which searches the Ondex network for any concepts/nodes relating to these terms. The search results are aggregated and scored using Lucene search. The server then sends the results back to the client, after which the client parses and represents them visually to the user.