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A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

BACKGROUND: The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the nota...

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Autores principales: Luna, Augustin, Karac, Evrim I, Sunshine, Margot, Chang, Lucas, Nussinov, Ruth, Aladjem, Mirit I, Kohn, Kurt W
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118169/
https://www.ncbi.nlm.nih.gov/pubmed/21586134
http://dx.doi.org/10.1186/1471-2105-12-167
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author Luna, Augustin
Karac, Evrim I
Sunshine, Margot
Chang, Lucas
Nussinov, Ruth
Aladjem, Mirit I
Kohn, Kurt W
author_facet Luna, Augustin
Karac, Evrim I
Sunshine, Margot
Chang, Lucas
Nussinov, Ruth
Aladjem, Mirit I
Kohn, Kurt W
author_sort Luna, Augustin
collection PubMed
description BACKGROUND: The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. RESULTS: A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. CONCLUSIONS: The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim.
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spelling pubmed-31181692011-06-19 A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method Luna, Augustin Karac, Evrim I Sunshine, Margot Chang, Lucas Nussinov, Ruth Aladjem, Mirit I Kohn, Kurt W BMC Bioinformatics Research Article BACKGROUND: The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. RESULTS: A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. CONCLUSIONS: The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim. BioMed Central 2011-05-17 /pmc/articles/PMC3118169/ /pubmed/21586134 http://dx.doi.org/10.1186/1471-2105-12-167 Text en Copyright ©2011 Luna et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Luna, Augustin
Karac, Evrim I
Sunshine, Margot
Chang, Lucas
Nussinov, Ruth
Aladjem, Mirit I
Kohn, Kurt W
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
title A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
title_full A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
title_fullStr A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
title_full_unstemmed A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
title_short A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
title_sort formal mim specification and tools for the common exchange of mim diagrams: an xml-based format, an api, and a validation method
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118169/
https://www.ncbi.nlm.nih.gov/pubmed/21586134
http://dx.doi.org/10.1186/1471-2105-12-167
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