PML: Toward a High-Level Formal Language for Biological Systems

Bor-Yuh Evan Chang, Manu Sridharan
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="" style="color: black;">Electronical Notes in Theoretical Computer Science</a> </i> &nbsp;
Documentation of knowledge about biological pathways is often informal and vague, making it difficult to efficiently synthesize the work of others into a holistic understanding of a system. Several researchers have proposed solving this problem by modeling pathways using formal languages, which have a precise and consistent semantics. While precise, many of these languages may be too low-level to model feasibly complex pathways. We have developed the Pathway Modeling Language (PML), a
more &raquo; ... language for modeling pathways. PML is based on a biological metaphor of molecules with binding sites and has special constructs for handling compartment changes in pathways. Our preliminary work has shown that PML's language constructs serve as a promising basis for modeling complex pathways in a readable and composable manner.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="">doi:10.1016/j.entcs.2004.01.039</a> <a target="_blank" rel="external noopener" href="">fatcat:cff3j7h3xfcdpbgzugo524ssmq</a> </span>
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