TY - JOUR
AU - Kohn, Kurt
AB - 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 
TI - A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method
JF - BMC Bioinformatics
DO - 10.1186/1471-2105-12-167
DA - 2011-05-17
UR - https://www.deepdyve.com/lp/springer-journals/a-formal-mim-specification-and-tools-for-the-common-exchange-of-mim-LEZzd0cw5d
SP - 1
EP - 13
VL - 12
IS - 1
DP - DeepDyve
ER -