Building pathway graphs from BioPAX data in R
- Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. One can retrieve the information in this data model in the scripting language R using the package rBiopaxParser, which converts the BioPAX format to one readable in R. It also has a function to build a regulatory network from the pathway information. Here we describe an extension of this function. The new function allows the user to build graphs of entire pathways, including regulated as well as non-regulated elements, and therefore provides a maximum of information. This function is available as part of the rBiopaxParser distribution from Bioconductor.
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| Author: | Nirupama Benis, Dirkjan Schokker, Frank KramerORCiDGND, Mari A. Smits, Maria Suarez-Diez |
|---|---|
| URN: | urn:nbn:de:bvb:384-opus4-1140379 |
| Frontdoor URL | https://opus.bibliothek.uni-augsburg.de/opus4/114037 |
| ISSN: | 2046-1402OPAC |
| Parent Title (English): | F1000Research |
| Publisher: | F1000 Research Ltd |
| Type: | Article |
| Language: | English |
| Year of first Publication: | 2016 |
| Publishing Institution: | Universität Augsburg |
| Release Date: | 2024/07/15 |
| Volume: | 5 |
| First Page: | 2414 |
| DOI: | https://doi.org/10.12688/f1000research.9582.2 |
| Institutes: | Fakultät für Angewandte Informatik |
| Fakultät für Angewandte Informatik / Institut für Informatik | |
| Fakultät für Angewandte Informatik / Institut für Informatik / Lehrstuhl für IT-Infrastrukturen für die Translationale Medizinische Forschung | |
| Dewey Decimal Classification: | 0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 004 Datenverarbeitung; Informatik |
| Licence (German): |  CC-BY 4.0: Creative Commons: Namensnennung (mit Print on Demand) |
