Previous | 
Home
Section: New Software and Platforms
KDD systems in Biology
IntelliGO Online
Functional Description.
The IntelliGO measure computes semantic similarity between terms from a structured vocabulary (Gene Ontology: GO) and uses these values for computing functional similarity between genes annotated by sets of GO terms [82] . The IntelliGO measure is available on line (http://plateforme-mbi.loria.fr/intelligo/ ) to be used for evaluation purposes. It is possible to compute the functional similarity between two genes, the intra-set similarity value in a given set of genes, and the inter-set similarity value for two given sets of genes.
WAFOBI: KNIME Nodes for Relational Mining of Biological Data
Functional Description.
KNIME (for “Konstanz Information Miner”) is an open-source visual programming environment for data integration, processing, and analysis. The KNIME platform aims at facilitating the data mining experiment settings as many tests are required for tuning the mining algorithms. Various KNIME nodes were developed for supporting relational data mining using the ALEPH program (http://www.comlab.ox.ac.uk/oucl/research/areas/machlearn/Aleph/aleph.pl ). These nodes include a data preparation node for defining a set of first-order predicates from a set of relation schemes and then a set of facts from the corresponding data tables (learning set). A specific node allows to configure and run the ALEPH program to build a set of rules. Subsequent nodes allow to test the first-order rules on a test set and to perform configurable cross validations.
MODIM: MOdel-driven Data Integration for Mining
Functional Description.
The MODIM software (MOdel-driven Data Integration for Mining) is a user-friendly data integration tool which can be summarized along three functions: (i) building a data model taking into account mining requirements and existing resources; (ii) specifying a workflow for collecting data, leading to the specification of wrappers for populating a target database; (iii) defining views on the data model for identified mining scenarios.
Although MODIM is domain independent, it was used so far for biological data integration in various internal research studies and for organizing data about non ribosomal peptide syntheses.