PyBioPAX API

pybiopax.api.model_from_biocyc(identifier)[source]

Return a BioPAX model from a BioCyc entry.

BioCyc contains pathways for model eukaryotes and microbes.

Parameters: identifier (str) – The BioCyc identifier for a pathway (e.g., P105-PWY for TCA cycle IV (2-oxoglutarate decarboxylase))
Return type: BioPaxModel
Returns: A BioPAX model obtained from the BioCyc pathway.

pybiopax.api.model_from_ecocyc(identifier)[source]

Return a BioPAX model from a EcoCyc entry.

EcoCyc contains pathways for Escherichia coli K-12 MG1655.

Parameters: identifier (str) – The EcoCyc identifier for a pathway (e.g., TCA for TCA cycle I (prokaryotic))
Return type: BioPaxModel
Returns: A BioPAX model obtained from the EcoCyc pathway.

pybiopax.api.model_from_humancyc(identifier)[source]

Return a BioPAX model from a HumanCyc entry.

Parameters: identifier (str) – The HumanCyc identifier for a pathway (e.g., PWY66-398 for TCA cycle)
Return type: BioPaxModel
Returns: A BioPAX model obtained from the HumanCyc pathway.

pybiopax.api.model_from_metacyc(identifier)[source]

Return a BioPAX model from a MetaCyc entry.

MetaCyc contains pathways for all organisms

Parameters

identifier (str) –

The MetaCyc identifier for a pathway (e.g., TCA for TCA cycle I (prokaryotic))

Return type

BioPaxModel

Returns

A BioPAX model obtained from the MetaCyc pathway.

pybiopax.api.model_from_netpath(identifier)[source]

Return a BioPAX model from a NetPath entry.

Parameters: identifier (str) – The NetPath identifier for a pathway (e.g., 22 for the leptin signaling pathway
Return type: BioPaxModel
Returns: A BioPAX model obtained from the NetPath resource.

pybiopax.api.model_from_owl_file(fname, encoding=None)[source]

Return a BioPAX Model from an OWL string.

Parameters

fname (Union[str, Path, PathLike]) – A path to an OWL file of BioPAX content.
encoding (Optional[str]) – The encoding type to be passed to open().

Return type

BioPaxModel

Returns

A BioPAX Model deserialized from the OWL file.

pybiopax.api.model_from_owl_gz(path, encoding=None)[source]

Return a BioPAX Model from an OWL file (gzipped).

Parameters

path (Union[str, Path, PathLike]) – A path to a gzipped OWL file of BioPAX content.
encoding (Optional[str]) – The encoding to read the file with. Defaults to the system default. Sometimes, windows users will need to explicitly set this to utf-8.

Return type

BioPaxModel

Returns

A BioPAX Model deserialized from the OWL file.

pybiopax.api.model_from_owl_str(owl_str)[source]

Return a BioPAX Model from an OWL string.

Parameters: owl_str (str) – A OWL string of BioPAX content.
Returns: A BioPAX Model deserialized from the OWL string.
Return type: pybiopax.biopax.BioPaxModel

pybiopax.api.model_from_owl_url(url, request_params=None)[source]

Return a BioPAX Model from an URL pointing to an OWL file.

Parameters

url (str) – A OWL URL with BioPAX content.
request_params (Optional[Mapping[str, Any]]) – Additional keyword arguments to pass to requests.get()

Return type

BioPaxModel

Returns

A BioPAX Model deserialized from the OWL file.

pybiopax.api.model_from_pc_query(kind, source, target=None, **query_params)[source]

Return a BioPAX Model from a Pathway Commons query.

For more information on these queries, see http://www.pathwaycommons.org/pc2/#graph

Parameters

kind (str) – The kind of graph query to perform. Currently 3 options are implemented, ‘neighborhood’, ‘pathsbetween’ and ‘pathsfromto’.
source (list[str]) – A single gene name or a list of gene names which are the source set for the graph query.
target (Optional[list[str]]) – A single gene name or a list of gene names which are the target set for the graph query. Only needed for ‘pathsfromto’ queries.
limit (Optional[int]) – This limits the length of the longest path considered in the graph query. Default: 1
organism (Optional[str]) – The organism used for the query. Default: ‘9606’ corresponding to human.
datasource (Optional[list[str]]) – A list of database sources that the query results should include. Example: [‘pid’, ‘panther’]. By default, all databases are considered.

Returns

A BioPAX Model obtained from the results of the Pathway Commons query.

Return type

pybiopax.biopax.BioPaxModel

pybiopax.api.model_from_reactome(identifier)[source]

Return a BioPAX model from a Reactome entry (pathway, event, etc.).

Parameters: identifier (str) – The Reactome identifier for a pathway (e.g., 177929 for Signaling by EGFR) or reaction (e.g., 177946 for Pro-EGF is cleaved to form mature EGF). For human pathways, the identifier for the BioPAX download is the same as the part that comes after R-HSA-. For non-human pathways, this is not so clear.
Return type: BioPaxModel
Returns: A BioPAX model obtained from the Reactome resource.

pybiopax.api.model_to_owl_file(model, fname)[source]

Write an OWL string serialized from a BioPaxModel object into a file.

Parameters

model (BioPaxModel) – The BioPaxModel to serialize into an OWL file.
fname (Union[str, Path, PathLike]) – The path to the target OWL file.

pybiopax.api.model_to_owl_str(model)[source]

Return an OWL string serialized from a BioPaxModel object.

Parameters: model (BioPaxModel) – The BioPaxModel to serialize into an OWL string.
Return type: str
Returns: The OWL string for the model.