uniminds¶

An updated version of MINDS

class fairgraph.uniminds.UnimindsObject(id=None, instance=None, **properties)[source]¶: Bases: fairgraph.minds.MINDSObject

class fairgraph.uniminds.UnimindsOption(id=None, instance=None, **properties)[source]¶: Bases: fairgraph.minds.MINDSObject

class fairgraph.uniminds.Person(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A person associated with research data or models, for example as an experimentalist,: or a data analyst.

Parameters:	alternatives (KGObject) – email (str) – family_name (str) – given_name (str) – identifier (str) – name (str) – orcid (str) –

class fairgraph.uniminds.AbstractionLevel(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Level of abstraction for a neuroscience model, e.g.rate neurons, spiking neurons

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.AgeCategory(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

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

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.BrainStructure(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

A sub-structure or region with the brain.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.CellularTarget(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

The type of neuron or glial cell that is the focus of the study.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Country(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

A geographical country.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Dataset(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A collection of related data files.

Parameters:

description (str) –
identifier (str) –
intended_release_date (datetime) –
name (str) –
brain_structure (BrainStructure) –
cellular_target (CellularTarget) –
contributor (Person) –
custodian (Person) –
doi (Doi) –
embargo_status (EmbargoStatus) –
ethics_approval (EthicsApproval) –
funding_information (FundingInformation) –
hbp_component (HBPComponent) –
license (License) –
main_contact (Person) –
main_file_bundle (FileBundle) –
method (Method) –
project (Project) –
publication (Publication) –
species (Species) –
study_target (StudyTarget) –
subjectgroup (SubjectGroup) –

class fairgraph.uniminds.Disability(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

A disability or disease.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Doi(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Digital Object Identifier (https://www.doi.org)

Parameters:	citation (str) – identifier (str) – name (str) –

class fairgraph.uniminds.EmbargoStatus(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

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

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.EthicsApproval(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

Record of an ethics approval.

Parameters:	alternatives (KGObject) – hbpethicsapproval (str) – identifier (str) – name (str) – country_of_origin (Country) – ethics_authority (EthicsAuthority) –

class fairgraph.uniminds.EthicsAuthority(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

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

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.ExperimentalPreparation(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

An experimental preparation.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.File(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

Metadata about a single file.

Parameters:	alternatives (KGObject) – description (str) – identifier (str) – name (str) – url (str) – mime_type (MimeType) –

class fairgraph.uniminds.FileAssociation(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A link between a file and a dataset.

Parameters:	from (File) – identifier (str) – name (str) – to (Dataset) –

class fairgraph.uniminds.FileBundle(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A collection of files (e.g. in a folder or directory structure)

Parameters:	alternatives (KGObject) – description (str) – identifier (str) – name (str) – url (str) – usage_notes (str) – file (File) – file_bundle (FileBundle) – mime_type (MimeType) – model_instance (ModelInstance) –

class fairgraph.uniminds.FileBundleGroup(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A collection of file bundles (see FileBundle)

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.FundingInformation(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

Information about the source of funding of a study.

Parameters:	alternatives (KGObject) – grant_id (str) – identifier (str) – name (str) –

class fairgraph.uniminds.Genotype(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Genetic makeup of a study subject, typically a reference to an inbred strain,: with or without mutations.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Handedness(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Preferred hand (left, right, or ambidextrous)

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.HBPComponent(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

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

Parameters:	alternatives (KGObject) – associated_task (str) – identifier (str) – name (str) – component_owner (Person) –

class fairgraph.uniminds.License(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

A license governing sharing of a dataset.

Parameters:	alternatives (KGObject) – fullname (str) – identifier (str) – name (str) – url (str) –

class fairgraph.uniminds.Method(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

An experimental method.

Parameters:

alternatives (KGObject) –
description (str) –
fullname (str) –
identifier (str) –
name (str) –
brain_structure (BrainStructure) –
ethics_approval (EthicsApproval) –
experimental_preparation (ExperimentalPreparation) –
method_category (MethodCategory) –
publication (Publication) –
study_target (StudyTarget) –
submethod (Method) –

class fairgraph.uniminds.MethodCategory(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

A category used for classifying experimental methods (see ExperimentalMethod)

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.MimeType(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Media type of a document

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.ModelFormat(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Programming or markup language used to describe or create a model

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.ModelInstance(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A specific version/parameterization of a neuroscience model.

Parameters:

alternatives (KGObject) –
description (str) –
identifier (str) –
license (License) –
name (str) –
version (str) –
abstraction_level (AbstractionLevel) –
brain_structure (BrainStructure) –
cellular_target (CellularTarget) –
contributor (Person) –
custodian (Person) –
main_contact (Person) –
used_dataset (KGObject) –
produced_dataset (Dataset) –
modelformat (ModelFormat) –
modelscope (ModelScope) –
publication (Publication) –
study_target (StudyTarget) –
embargo_status (EmbargoStatus) –
alternate_of (ModelInstance, MEModel) –

class fairgraph.uniminds.ModelScope(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

‘What is being modelled’: a protein, a single cell, the entire brain, etc.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Organization(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

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

Parameters:	alternatives (KGObject) – identifier (str) – name (str) – created_as (str) –

class fairgraph.uniminds.Project(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A research project, which may have generated one or more datasets (see Dataset)

Parameters:	alternatives (KGObject) – description (str) – identifier (str) – name (str) – coordinator (Person) –

class fairgraph.uniminds.Publication(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A scientific publication.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) – url (str) – brain_structure (BrainStructure) – project (Project) – publication_id (PublicationId) – study_target (StudyTarget) – subjectgroup (SubjectGroup) –

class fairgraph.uniminds.PublicationId(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Identifier for a publication (e.g. a DOI, a PubMed ID)

Parameters:	alternatives (KGObject) – identifier (str) – name (str) – publication (Publication) – publication_id_type (PublicationIdType) –

class fairgraph.uniminds.PublicationIdType(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

A type of publication identifier (e.g. ISBN, DOI)

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Sex(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

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

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Species(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

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

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Strain(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

An inbred sub-population within a species.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.StudyTarget(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

The focus of an experimental or modelling study.

Parameters:	alternatives (KGObject) – fullname (str) – identifier (str) – name (str) – study_target_source (StudyTargetSource) – study_target_type (StudyTargetType) –

class fairgraph.uniminds.StudyTargetSource(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Context of a study target, e.g. if the target is a brain region, the source might be an atlas.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.StudyTargetType(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsOption

Category of study target (see StudyTarget)

Parameters:	alternatives (KGObject) – identifier (str) – name (str) –

class fairgraph.uniminds.Subject(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

The organism that is the subject of an experimental investigation.

Parameters:

age (str, float) –
age_range_max (str, float) –
age_range_min (str, float) –
alternatives (KGObject) –
identifier (str) –
name (str) –
age_category (AgeCategory) –
brain_structure (BrainStructure) –
cellular_target (CellularTarget) –
disability (Disability) –
genotype (Genotype) –
handedness (Handedness) –
publication (Publication) –
sex (Sex) –
species (Species) –
strain (Strain) –
study_target (StudyTarget) –

class fairgraph.uniminds.SubjectGroup(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A group of experimental subjects.

Parameters:

age_range_max (str, float) –
age_range_min (str, float) –
alternatives (KGObject) –
description (str) –
identifier (str) –
name (str) –
num_of_subjects (int) –
age_category (AgeCategory) –
cellular_target (CellularTarget) –
brain_structure (BrainStructure) –
disability (Disability) –
genotype (Genotype) –
handedness (Handedness) –
publication (Publication) –
sex (Sex) –
species (Species) –
strain (Strain) –
study_target (StudyTarget) –
subjects (Subject) –

class fairgraph.uniminds.TissueSample(id=None, instance=None, **properties)[source]¶

Bases: fairgraph.uniminds.UnimindsObject

A sample of brain tissue.

Parameters:	alternatives (KGObject) – identifier (str) – name (str) – subject (Subject) –

fairgraph.uniminds.list_kg_classes()[source]¶: List all KG classes defined in this module

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uniminds¶