minds

“Minimal Information for Neuroscience DataSets” - metadata common to all neuroscience datasets independent of the type of investigation

class fairgraph.minds.Person(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

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

or a data analyst.

Parameters:

• identifier (str) –
• name (str) –
• shortname (str) –

class fairgraph.minds.Activity(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A research activity.

Parameters:

• identifier (str) –
• name (str) –
• ethics_approval (EthicsApproval) –
• ethics_authority (EthicsAuthority) –
• methods (Method) –
• preparation (Preparation) –
• protocols (Protocol) –

class fairgraph.minds.AgeCategory(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

An age category, e.g. “adult”, “juvenile”

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.EthicsApproval(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

Record of an ethics approval.

Parameters:

• identifier (str) –
• name (str) –
• generated_by (EthicsAuthority) –

class fairgraph.minds.EthicsAuthority(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A entity legally authorised to approve or deny permission to conduct an experiment on ethical grounds.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.Dataset(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A collection of related data files.

Parameters:

• activity (Activity) –
• container_url_as_ZIP (bool) –
• container_url (str) –
• datalink (str) –
• dataset_doi (str) –
• description (str) –
• external_datalink (str) –
• identifier (str) –
• name (str) –
• release_date (datetime) –
• component (PLAComponent) –
• contributors (Person) –
• doireference (str) –
• embargo_status (EmbargoStatus) –
• formats (Format) –
• license (License) –
• modality (Modality) –
• owners (Person) –
• parcellation_atlas (ParcellationAtlas) –
• parcellation_region (ParcellationRegion) –
• part_of (str) –
• publications (Publication) –
• reference_space (ReferenceSpace) –
• specimen_group (SpecimenGroup) –

methods(client, api='query', scope='released')

Return a list of experimental methods associated with the dataset

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)

List all objects of this type in the Knowledge Graph

class fairgraph.minds.EmbargoStatus(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

Information about the embargo period during which a given dataset cannot be publicly shared.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.File(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

Metadata about a single file.

Parameters:

• absolute_path (str) –
• byte_size (int) –
• content_type (str) –
• hash (str) –
• identifier (str) –
• last_modified (datetime) –
• name (str) –
• relative_path (str) –

class fairgraph.minds.FileAssociation(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A link between a file and a dataset.

Parameters:

• from (File) –
• identifier (str) –
• name (str) –
• to (Dataset) –

class fairgraph.minds.Format(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A file/data format.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.License(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A license governing sharing of a dataset.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.Method(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

An experimental method.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.Modality(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A recording modality.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.ParcellationAtlas(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A brain atlas in which the brain of a given species of animal is divided into regions.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.ParcellationRegion(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A brain region as defined by a brain atlas.

Parameters:

• alias (str) –
• identifier (str) –
• name (str) –
• url (str) –
• species (Species) –

class fairgraph.minds.PLAComponent(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A data or software component, as defined in the HBP “project lifecycle” application.

Parameters:

• description (str) –
• identifier (str) –
• name (str) –
• component (str) –

class fairgraph.minds.Preparation(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

An experimental preparation.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.Protocol(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

An experimental procotol.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.Publication(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A scientific publication.

Parameters:

• cite (str) –
• doi (str) –
• identifier (str) –
• name (str) –
• authors (Person) –

class fairgraph.minds.ReferenceSpace(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A reference space for a brain atlas.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.Role(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

The role of a person within an experiment.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.Sample(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A sample of neural tissue.

Parameters:

• container_url (str) –
• identifier (str) –
• name (str) –
• weight_post_fixation (str) –
• weight_pre_fixation (str) –
• methods (Method) –
• parcellation_atlas (ParcellationAtlas) –
• parcellation_region (ParcellationRegion) –
• reference (str) –

class fairgraph.minds.Sex(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

The sex of an animal or person from whom/which data were obtained.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.SoftwareAgent(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

Software that performed a given activity.

Parameters:

• description (str) –
• identifier (str) –
• name (str) –

class fairgraph.minds.Species(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

The species of an experimental subject, expressed with the binomial nomenclature.

Parameters:

• identifier (str) –
• name (str) –

class fairgraph.minds.SpecimenGroup(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

A group of experimental subjects.

Parameters:

• identifier (str) –
• name (str) –
• subjects (Subject) –

class fairgraph.minds.Subject(id=None, instance=None, **properties)

Bases: fairgraph.minds.MINDSObject

The organism that is the subject of an experimental investigation.

Parameters:

• cause_of_death (str) –
• genotype (str) –
• identifier (str) –
• name (str) –
• strain (str) –
• strains (str) –
• weight (str) –
• age (str) –
• age_category (AgeCategory) –
• samples (Sample) –
• sex (Sex) –
• species (Species) –

fairgraph.minds.list_kg_classes()

List all KG classes defined in this module

fairgraph.minds.Project

alias of fairgraph.minds.PLAComponent