BIANA

BIANA: Biologic Interaction and Network Analysis

Biana: a software framework for compiling biological interactions and analyzing networks
Javier Garcia-Garcia, Emre Guney, Ramon Aragues, Joan Planas-Iglesias and Baldo Oliva.
BMC Bioinformatics 2010, 11:56. 27 January 2010

SBI BIANA Datasets

BIANA offers the possibity to integrate different biologic databases. However, probably you are interested in integrating other databases or your own data with other databases. If you are interested in it, you can check which available parsers there exist for BIANA or create your own parsers (Parsers). Also, if you thing your parser can be useful for other people, you can submit it to us and we will add them to the list of available parsers! In our lab, Structural Bioinformatics Lab, we have created different datasets as a result of different projects. In this section you can find our datasets and their parsers to integrate them in BIANA:

SBI Datasets

Dataset Name	Dataset Description	Author	Dataset file	Parser file
Metabolic Network	This dataset corresponds to a metabolical network reconstruction that gives an score to each pair of possible chained enzymatic reactions. These chained reactions are possible when there is at least one chemical compound acting at the same time as product of enzyme A and substrate of enzyme B, a shared compound. The score is based in the plausability of oberving such chemical compounds, according to their own frequency and the frequency of other products of enzyme A and other substrates of enzyme B wich do not take part in chaining reactions. Most of existing methods for reconstructing metabolic networks disregard relationships in which enzymes only share very frequent compounds. The method from which this dataset is derived tries to discern wether these relationships can be taken into consideraction or not. Hence, cases in which a relationship between two enzymes can only be stablished due to the presence of shared common compounds are tagged as “special”. Often, a given enzyme, described by an EC code, can perform a given reaction bidirectionally (from substrates to products and viceversa) and/or can perform more than a single reaction. The provided score is specific for the reaction each enzyme is performing in the relationship and their directions. It is recomended to use high reliability scores ( pValue <= 0.05 ).	Joan Planas	Download	inferredMetabolicNetworkParser.py
Transcription Factors	This dataset contains 2 files giving information on: 1- transcription factors and the genes they are regulating and 2- transcription factors that are working cooperatively.	Daniel Aguilar	Download	Use "generic" parser (GenericParser.py) deployed with BIANA
PPI Predictions	(2005) "Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships" Bioinformatics 21(16):3360-8	Espadaler J., O. Romero-Isart, et al	Download	Use "generic" parser (GenericParser.py) deployed with BIANA