BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways.

Algorithms Signal Transduction Software

Journal

Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944

Informations de publication

Date de publication:
01 08 2020
Historique:
received: 07 10 2019
revised: 08 05 2020
accepted: 15 05 2020
pubmed: 22 5 2020
medline: 2 2 2021
entrez: 22 5 2020
Statut: ppublish

Résumé

Biological pathways are fundamental for learning about healthy and disease states. Many existing formats support automatic software analysis of biological pathways, e.g. BioPAX (Biological Pathway Exchange). Although some algorithms are available as web application or stand-alone tools, no general graphical application for the parsing of BioPAX pathway data exists. Also, very few tools can perform pathway enrichment analysis (PEA) using pathway encoded in the BioPAX format. To fill this gap, we introduce BiP (BioPAX-Parser), an automatic and graphical software tool aimed at performing the parsing and accessing of BioPAX pathway data, along with PEA by using information coming from pathways encoded in BioPAX. BiP is freely available for academic and non-profit organizations at https://gitlab.com/giuseppeagapito/bip under the LGPL 2.1, the GNU Lesser General Public License. Supplementary data are available at Bioinformatics online.

Identifiants

DOI: 10.1093/bioinformatics/btaa529 PMID: 32437515
pubmed: 32437515
pii: 5841664
doi: 10.1093/bioinformatics/btaa529
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

4377-4378

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Auteurs

Giuseppe Agapito (G)

Department of Legal, Economic and Social Sciences.
Data Analytics Research Center, Magna Graecia University of Catanzaro, Catanzaro, Italy.

Chiara Pastrello (C)

Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.

Pietro Hiram Guzzi (PH)

Data Analytics Research Center, Magna Graecia University of Catanzaro, Catanzaro, Italy.
Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy.

Igor Jurisica (I)

Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
Department of Computer Science, University of Toronto, Toronto, ON, Canada.

Mario Cannataro (M)

Data Analytics Research Center, Magna Graecia University of Catanzaro, Catanzaro, Italy.
Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › BioPAX-Parser: parsing and enrichment analysis...
questionsmedicales.fr › Phénomènes physiologiques cellulaires › Transduction du signal › BioPAX-Parser: parsing and enrichment analysis...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › BioPAX-Parser: parsing and enrichment analysis...