core

Metadata for entities that are used in multiple contexts (e.g. in both electrophysiology and in simulation).

class fairgraph.core.Subject(name, species, age=None, sex=None, handedness=None, strain=None, genotype=None, death_date=None, group=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

The individual organism that is the subject of an experimental study.

Parameters:

• name (str) –
• species (Species) –
• strain (Strain) –
• genotype (Genotype) –
• sex (Sex) –
• handedness (Handedness) –
• age (Age) –
• death_date (date) –
• group (Group) –

class fairgraph.core.Organization(name, address=None, parent=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

An organization associated with research data or models, e.g. a university, lab or department.

Parameters:

• name (str) –
• address (Address) –
• parent (Organization) –

class fairgraph.core.Person(family_name, given_name, email=None, affiliation=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

A person associated with research data or models, for example as an experimentalist,

or a data analyst.

Parameters:

• family_name (str) – Family name / surname
• given_name (str) – Given name
• email (str) – e-mail address
• affiliation (Organization) – Organization to which person belongs

classmethod list(client, size=100, api='query', scope='released', resolved=False, **filters)

List all objects of this type in the Knowledge Graph

resolve(client, api='query', use_cache=True)

To avoid having to check if a child attribute is a proxy or a real object, a real object resolves to itself.

classmethod me(client, api='query', allow_multiple=False)

Return the Person who is currently logged-in.

(the user associated with the token stored in the client).

If the Person node does not exist in the KG, it will be created.

class fairgraph.core.Identifier(id=None, instance=None, **properties)

Bases: fairgraph.base.KGObject

class fairgraph.core.Material(name, molar_weight=None, formula=None, stock_keeping_unit=None, reagent_distribution=None, vendor=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Metadata about a chemical product or other material used in an experimental protocol.

Parameters:

• name (str) –
• molar_weight (QuantitativeValue) –
• formula (str) –
• stock_keeping_unit (str) –
• reagent_distribution (Distribution) –
• vendor (Organization) –

class fairgraph.core.Step(name, previous_step_name=None, sequence_number=None, identifier=None, version=None, distribution=None, description=None, materials=None, author=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

A step in an experimental protocol.

Parameters:

• name (str, int) –
• previous_step_name (str, int) –
• sequence_number (int) –
• identifier (str) –
• version (str, int) –
• distribution (Distribution) –
• description (str) –
• materials (Material) –
• author (Person) –

class fairgraph.core.Protocol(name, version=None, identifier=None, doi=None, distribution=None, number_of_steps=None, steps=None, materials=None, author=None, date_published=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

An experimental protocol.

Parameters:

• name (str) –
• version (str, int) –
• identifier (str) –
• distribution (Distribution) –
• number_of_steps (int) –
• steps (Step) –
• materials (Material) –
• author (Person) –
• date_published (date) –

class fairgraph.core.Collection(name, members, id=None, instance=None)

Bases: fairgraph.base.KGObject

A collection of other metadata objects

Parameters:

• name (str) –
• members (KGObject) –

fairgraph.core.list_kg_classes()

List all KG classes defined in this module

fairgraph.core.use_namespace(namespace)

Set the namespace for all classes in this module.