Editing, validating and translating of SBGN maps

Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life...

Descripción completa

Detalles Bibliográficos
Autores principales: Czauderna, Tobias, Klukas, Christian, Schreiber, Falk
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935428/
https://www.ncbi.nlm.nih.gov/pubmed/20628075
http://dx.doi.org/10.1093/bioinformatics/btq407
_version_ 1782186400756531200
author Czauderna, Tobias
Klukas, Christian
Schreiber, Falk
author_facet Czauderna, Tobias
Klukas, Christian
Schreiber, Falk
author_sort Czauderna, Tobias
collection PubMed
description Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable. Results: We present SBGN-ED, a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases into SBGN and the export of SBGN maps into several file and image formats. Availability: SBGN-ED is freely available from http://vanted.ipk-gatersleben.de/addons/sbgn-ed. The web site contains also tutorials and example files. Contact: schreibe@ipk-gatersleben.de
format Text
id pubmed-2935428
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-29354282010-09-08 Editing, validating and translating of SBGN maps Czauderna, Tobias Klukas, Christian Schreiber, Falk Bioinformatics Applications Note Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable. Results: We present SBGN-ED, a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases into SBGN and the export of SBGN maps into several file and image formats. Availability: SBGN-ED is freely available from http://vanted.ipk-gatersleben.de/addons/sbgn-ed. The web site contains also tutorials and example files. Contact: schreibe@ipk-gatersleben.de Oxford University Press 2010-09-15 2010-07-13 /pmc/articles/PMC2935428/ /pubmed/20628075 http://dx.doi.org/10.1093/bioinformatics/btq407 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Czauderna, Tobias
Klukas, Christian
Schreiber, Falk
Editing, validating and translating of SBGN maps
title Editing, validating and translating of SBGN maps
title_full Editing, validating and translating of SBGN maps
title_fullStr Editing, validating and translating of SBGN maps
title_full_unstemmed Editing, validating and translating of SBGN maps
title_short Editing, validating and translating of SBGN maps
title_sort editing, validating and translating of sbgn maps
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935428/
https://www.ncbi.nlm.nih.gov/pubmed/20628075
http://dx.doi.org/10.1093/bioinformatics/btq407
work_keys_str_mv AT czaudernatobias editingvalidatingandtranslatingofsbgnmaps
AT klukaschristian editingvalidatingandtranslatingofsbgnmaps
AT schreiberfalk editingvalidatingandtranslatingofsbgnmaps

Ejemplares similares