BioPNMLBioPNMLBiology Petri Net Markup Language (BioPNML) is an Extensible Markup Language (XML) based tag set designed help standardize how metabolic network and its Petri net model data is stored and transferred between different Petri net tools and biology analysis systems and databases. The goal is to provide a standard method of exchanging metabolic network data along with the associated Petri net model. The BioPNML data file format has the following advantages:
Standardization for storing and transferring data between different Petri net tools and biology analysis systems and databases
Is XML-based
Keeps track of which data collection methodology was used, enabling normalization, integration, and comparison of data across methodologies
Extensible through the ability to specify additional metabolic networks
Independent of any particular database schema.
BioPNML is a language for exchange of biology Petri net
modeling data. It is not a software environment for developing Petri net
model and executing them. By exchange language, BioPNML is inteded to be
used as an intermediate language for transferring biology Petri net modeling
data among different database systems and application programs.
BioPNML is designed to provide a mechanism for encoding ontologies within a flat file that may be easily published on the WWW for exchange among a set of application developers. It is designed to be readable by humans, and to be easily parasable by programs of modest complexity. It is designed to be easily understandable by people who do not have a complete understanding of XML. It is also designed to be expressive, so that it may capture a rich variety of ontologies.
Understanding BioPNML requires both an understanding of Petri net, metabolism modeling and XML.
The diagram below shows how information is converted to BioPNML format and then used for analysis:
