pypath.core.evidence.Evidences

class pypath.core.evidence.Evidences(evidences=())

Bases: object

A collection of evidences. All evidences supporting a relationship such as molecular interaction, molecular complex, enzyme-PTM interaction, annotation, etc should be collected in one Evidences object. This way the set of evidences can be queried a comprehensive way.

Parameters:

evidences (tuple,list,set,Evidences) – An iterable providing Evidence instances. It is possible to create an empty evidence collection and populate it later or to show this way that certain relationship has no supporting evidences.

__init__(evidences=())

Methods

__init__([evidences])
asdict()	Evidence set as a list of dictionaries.
contains_database(database, **kwargs)
contains_reference(reference, **kwargs)
count_curation_effort(**kwargs)
count_references(**kwargs)
count_resources(**kwargs)
filter([resource, data_model, ...])
get_curation_effort(**kwargs)
get_data_models(**kwargs)
get_datasets(**kwargs)
get_interaction_types(**kwargs)
get_references(**kwargs)
get_resource_names(**kwargs)
get_resource_names_via(**kwargs)
get_resources(**kwargs)
get_resources_via(**kwargs)
has_data_model(data_model, **kwargs)
has_database_via(database, via, **kwargs)
has_dataset(dataset, **kwargs)	Contains evidence(s) from a given dataset meeting the criteria.
has_interaction_type(interaction_type[, ...])	If via is False then it will be ignored, otherwise if None only primary resources are considered.
intersection(other)
items()	Returns
keys()	Returns
match([resource, data_model, ...])
reload()	Reloads the object from the module level.
remove([resource, interaction_type, via])
serialize_attrs([top_key_prefix])	Serialize the extra attributes of the evidences as a JSON string.

Attributes

evidences
attrs	Combines the custom attributes from all evidences within this set.
datasets	Datasets in this evidence set.
simple_dict	Returns Keys are resource labels, values are Evidence objects.

asdict() → list[dict]

Evidence set as a list of dictionaries.

property attrs: dict

Combines the custom attributes from all evidences within this set.

property datasets: set

Datasets in this evidence set.

has_dataset(dataset: str, **kwargs) → bool

Contains evidence(s) from a given dataset meeting the criteria.

Parameters:

• dataset – Name of the dataset.

• kwargs – Filtering criteria for evidences.

has_interaction_type(interaction_type, database=None, via=False)

If via is False then it will be ignored, otherwise if None only primary resources are considered.

items()

Returns

(dict_items): The evidences as a mapping, with

pypath.internals.resource.NetworkResourceKey objects as keys and pypath.core.evidence.Evidence objects as values.

keys()

Returns

(dict_keys): The keys of this dictionary are

pypath.internals.resource.NetworkResourceKey objects.

reload()

Reloads the object from the module level.

serialize_attrs(top_key_prefix: bool = True) → str

Serialize the extra attributes of the evidences as a JSON string.

Returns

A JSON serialized string with the evidences from each resource.

property simple_dict: dict[str, evidence.Evidence]

Returns Keys are resource labels, values are Evidence objects.