ArticleBMC bioinformatics2010
Biana: a software framework for compiling biological interactions and analyzing networks.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- APV-Sankey: a k-mer persistence visualization tool for HT-SELEX data analysis to identify aptamer candidates.Analytical and bioanalytical chemistry · 2026Article
- Oxidative stress-driven transcriptomic remodeling in human astrocytes reveals network signatures associated with neurodegenerative and cardiovascular processes.Computational and structural biotechnology journal · 2026Article
- Article
- Shared Proteins and Pathways of Cardiovascular and Cognitive Diseases: Relation to Vascular Cognitive Impairment.Journal of proteome research · 2024Article
- Recent developments of sequence-based prediction of protein-protein interactions.Biophysical reviews · 2022Review
- Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning.Frontiers in bioinformatics · 2022Article
- A random forest classifier for protein-protein docking models.Bioinformatics advances · 2022Article
- Construction and contextualization approaches for protein-protein interaction networks.Computational and structural biotechnology journal · 2022Review
- Characterization and comparison of gene-centered human interactomes.Briefings in bioinformatics · 2021Article
- SamPler - a novel method for selecting parameters for gene functional annotation routines.BMC bioinformatics · 2019Article
- Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology.Pharmaceuticals (Basel, Switzerland) · 2018Article
- Network spectra for drug-target identification in complex diseases: new guns against old foes.Applied network science · 2018Review
- Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury.Frontiers in genetics · 2018Article
- Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins.Scientific reports · 2017Article
- Genetic and functional characterization of disease associations explains comorbidity.Scientific reports · 2017Article
- PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology.PloS one · 2017Article
- Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing.Scientific reports · 2016Article
- CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction.BMC bioinformatics · 2016Article
- FN14 and GRP94 expression are prognostic/predictive biomarkers of brain metastasis outcome that open up new therapeutic strategies.Oncotarget · 2015Article
- PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction.International journal of genomics · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.
resultsWe introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.
conclusionsBIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.