The BioPAX community standard for pathway data sharing

Abstract

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

Figure 1

BioPAX is a shared language for biological pathways. BioPAX reduces the effort required to efficiently communicate between pathway users, databases and software tools. Without a shared language, each system must speak the language of all other systems in the worst case (black lines). With a shared language, each system only needs to speak that language (central red box).

Figure 2

BioPAX enables computational data gathering, publication and use of information about biological processes. Traditional pathway information processing: Observations considering prior models published as text and figures. Computable pathway information processing: Scientist’s description represented using formal, computable framework (ontology) published in a computer software readable format for analysis by scientists.

Figure 3

The AKT pathway as represented by a traditional method (top left, from http://www.biocarta.com), a formalized SBGN diagram (http://www.sbgn.org 84) (left), and using the BioPAX language (right). An important advantage of the BioPAX representation is that it can be interpreted by computer software and used in multiple ways, including automatic diagram creation, information retrieval and analysis. Online documentation at http://www.biopax.org contains more details about how to represent diverse types of biological pathways. Actual samples of pathway data in BioPAX OWL XML format are available in Supplementary Tables S2 and S3.

Figure 4

High-level view of the BioPAX ontology. Classes are shown as boxes and arrows represent inheritance relationships. The three main types of classes in BioPAX are colored, Pathway (red), Interaction (green) and PhysicalEntity and Gene (blue). For brevity, only the properties of the Protein class are shown as an example at the top right. Refer to BioPAX documentation at http://www.biopax.org for full details of all classes and properties.

Figure 5

Example uses of pathway information in BioPAX format. Red colored boxes or lines indicate use of BioPAX.

Figure 6

The relationship among popular standard formats for pathway information. BioPAX and PSI-MI are designed for data exchange to and from databases and pathway and network data integration. SBML and CellML are designed to support mathematical simulations of biological systems and SBGN represents pathway diagrams.