pypath.core.evidence.Evidence

class pypath.core.evidence.Evidence(resource, references=None, attrs=None)

Bases: AttributeHandler

Represents an evidence supporting a relationship such as molecular interaction, molecular complex, enzyme-PTM interaction, annotation, etc.

The evidence consists of two main parts: the database and the literature references. If a relationship is supported by multiple databases, for each one Evidence object should be created and

Parameters:

• resource (pypath.resource.ResourceAttributes) – An object derived from pypath.resource.ResourceAttributes.

• references (str,list,set,NoneType) – Optional, one or more literature references (preferably PubMed IDs).

__init__(resource, references=None, attrs=None)

Methods

__init__(resource[, references, attrs])
asdict()	Dictionary representation of the evidence.
contains_database(database)
contains_reference(reference)
has_data_model(data_model)
has_database_via(database, via)
has_interaction_type(interaction_type[, ...])	If via is False then it will be ignored, otherwise if None only primary resources are considered.
match([resource, data_model, ...])
merge(other)	Merges two evidences.
reload()	Reloads the object from the module level.
serialize(**kwargs)	Generates a JSON string with the full contents of the attributes, without any whitespace or line break.
update_attrs([attrs])	Updates the attributes stored here.

Attributes

resource
references
dataset
attrs
key
pubmeds	PubMed IDs of the references supporting this evidence.

asdict() → dict

Dictionary representation of the evidence.

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.

merge(other)

Merges two evidences. Returns set of either one or two evidences depending on whether the two evidences are from the same resource.

property pubmeds: list[str]

PubMed IDs of the references supporting this evidence.

reload()

Reloads the object from the module level.

serialize(**kwargs)

Generates a JSON string with the full contents of the attributes, without any whitespace or line break.

Returns

(str): The attributes JSON serialized.

update_attrs(attrs=None, **kwargs)

Updates the attributes stored here. The attributes with identical keys are merged using the pypath.share.common.combine_attrs() function.

The new attributes can be provided three ways: an object with an attribute called attrs; a dictionary of attributes; or the attributes as keyword arguments.