BioPAX对象模型的Python实现，以及PaxTools的一部分。
pybiopax的Python项目详细描述
PyBioPAX：BioPAX对象模型的python实现
PyBioPAX实现BioPAX级别3对象模型( http://www.biopax.org/release/biopax-level3-documentation.pdf）作为一组 Python类。它公开API函数来将OWL文件读入 对象模型，并从该对象模型转储OWL文件。 这允许在本机中处理和创建BioPAX模型 Python。在
安装
PyBioPAX可以从PyPI安装为一个包：
$ pip install pybiopax
使用
将OWL文件读入BioPaxModel对象：
^{pr2}$将BioPaxModel写入OWL文件：
importpybiopaxpybiopax.model_to_owl_file(model,'test.owl')
查询Pathway Commons以获取BioPaxModel对象：
importpybiopaxmodel=pybiopax.model_from_pc_query('pathsfromto',['MAP2K1'],['MAPK1'])
使用Python对象模型的元素：
importpybiopaxmodel=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.assertisinstance(model.objects,dict)assertall(isinstance(obj,pybiopax.biopax.BioPaxObject)forobjinmodel.objects.values())# Let's look at a specific objectbcr=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 proteinleft=bcr.left[0]assertisinstance(left,pybiopax.biopax.Protein)assertleft.display_name=='ERK1-2'right=bcr.right[0]assertisinstance(right,pybiopax.biopax.Protein)assertright.display_name=='ERK1-2-active'
每个bioAxObject都具有与 BioPAX 3级规范。在
资金
PyBioPAX的开发由DARPA资助，与 计算机程序（ARO grant W911NF-15-1-0544）。在
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