Paper Info
Title
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.
Abstract
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.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.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.
Year
DOI
Venue
2011
10.1186/1471-2105-12-167
BMC Bioinformatics
Keywords
Field
DocType
algorithms,programming languages,software development,signal transduction,source code,software requirements,bioinformatics,microarrays,application program interface
Notation,XML,Computer science,Formal specification,B-Method,Software,Document Object Model,Application programming interface,Bioinformatics,Software requirements
Journal
Volume
Issue
ISSN
12
1
1471-2105
Citations 
PageRank 
References 
15
0.84
11
Authors
7
Name
Order
Citations
PageRank
Augustin Luna1577.87
Evrim I Karac2150.84
Margot Sunshine3856.09
Lucas Chang4150.84
Ruth Nussinov5845113.97
Mirit I. Aladjem6504.65
Kurt W Kohn7283.07