A Python implementation of the BioPAX object model, and parts of PaxTools.
PyBioPAX: A python implementation of the BioPAX object model
PyBioPAX implements the BioPAX level 3 object model ( http://www.biopax.org/release/biopax-level3-documentation.pdf) as a set of Python classes. It exposes API functions to read OWL files into this object model, and to dump OWL files from this object model. This allows for the processing and creation of BioPAX models natively in Python.
PyBioPAX can be installed from PyPI as a package:
$ pip install pybiopax
Reading an OWL file into a BioPaxModel object:
import pybiopax model = pybiopax.model_from_owl_file('test.owl')
Writing a BioPaxModel into an OWL file:
import pybiopax pybiopax.model_to_owl_file(model, 'test.owl')
Querying Pathway Commons to get a BioPaxModel object:
import pybiopax model = pybiopax.model_from_pc_query('pathsfromto', ['MAP2K1'], ['MAPK1'])
Working with the elements of the Python object model:
import pybiopax model = pybiopax.model_from_pc_query('pathsfromto', ['MAP2K1'], ['MAPK1']) # Each BioPaxModel instance has an objects attribute which is a dict # whose keys are object URIs (strings) and values are BioPaxObject instances. assert isinstance(model.objects, dict) assert all(isinstance(obj, pybiopax.biopax.BioPaxObject) for obj in model.objects.values()) # Let's look at a specific object bcr = model.objects['BiochemicalReaction_4f689747397d98089c551022a3ae2d88'] # This is a BiochemicalReaction which has a left and a right side. All list/set # types per the BioPAX specification are represented as lists in the Python # object model # Both left and right consist of a single protein left = bcr.left assert isinstance(left, pybiopax.biopax.Protein) assert left.display_name == 'ERK1-2' right = bcr.right assert isinstance(right, pybiopax.biopax.Protein) assert right.display_name == 'ERK1-2-active'
Each BioPaxObject has attributes that are consistent with the BioPAX level 3 specification.
The development of PyBioPAX is funded under the DARPA Communicating with Computers program (ARO grant W911NF-15-1-0544).
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