fairgraph: a Python API for the EBRAINS Knowledge Graph¶

fairgraph is an experimental Python library for working with metadata in the HBP/EBRAINS Knowledge Graph, with a particular focus on data reuse, although it is also useful in metadata registration/curation. The API is not stable, and is subject to change.

Installation¶

To get the latest release:

pip install fairgraph

To get the development version:

git clone https://github.com/HumanBrainProject/fairgraph.git
pip install -r ./fairgraph/requirements.txt
pip install -U ./fairgraph

About the Knowledge Graph¶

The Human Brain Project/EBRAINS Knowledge Graph is a metadata store for neuroscience.

When sharing neuroscience data, it is essential to also share all of the context and background information needed to interpret and understand the data: the age of the subject, the sampling rate of the recording system, etc. For the HBP/EBRAINS data sharing platform, the actual data files are stored at the Swiss National Supercomputing Center, CSCS. All of the metadata associated with these files (including the precise file locations) is stored in the Knowledge Graph.

There are many ways to access the contents of the Knowledge Graph: through a graphical search interface, with an anatomical search through the EBRAINS brain atlases, through web services, and through Python clients.

fairgraph is an experimental, high-level Python client for the Knowledge Graph, which aims to be convenient, powerful and easy-to-use. Alternative ways to access the Knowledge Graph programmatically are summarized in the section “Alternatives” below.

Structure¶

The HBP/EBRAINS Knowledge Graph is a semantic graph database (in the sense of graph theory). It consists of “nodes”, each of which contains metadata about a specific aspect of a neuroscience experiment. These nodes are connected to each other, and the connections represent the relationships between the different pieces of metadata (for example, a node representing a slice of rat hippocampus will be connected to other nodes representing each of the neurons in that slice that was recorded from with an electrode, or reconstructed from microscopy images. The connections between nodes are of many different types, so that we can represent precisely the meaning of the connection, the type of the relationship (this is why we call it a _semantic_ graph). This graph structure gives great flexibility and ease of evolution compared to a traditional database.

Todo

insert a figure here showing a part of the graph

fairgraph maps the Knowledge Graph onto connected Python objects. For example, a node in the graph containing metadata about a neuron whose activity was recorded using patch-clamp electrophysiology is represented by a Python object PatchedCell whose attributes correspond to the metadata stored in that node _and_ to the semantic connections to other nodes.

Alternatives¶

Todo

write about KG Query API, pyxus, KG Query Python pip

Querying the Knowledge Graph¶

Setting up a connection¶

Communication between fairgraph metadata objects and the Knowledge Graph web service is through a client object, for which an access token associated with an HBP Identity account is needed. To obtain an HBP Identity account, please see https://services.humanbrainproject.eu/oidc/account/request.

If you are working in an HBP Collaboratory Jupyter notebook, you have already logged in with your user name and password, so you can get an access token as follows:

token = clb_oauth.get_token()

If working outside the Collaboratory, we recommend you obtain a token from whichever authentication endpoint is available to you, and save it as an environment variable so the client can find it, e.g. at a shell prompt:

export KG_AUTH_TOKEN=eyJhbGci...nPq

You can then create the client object:

>>> from fairgraph.client_v3 import KGv3Client as KGClient
>>> client = KGClient()

You can also pass the token explicitly to the client:

>>> client = KGClient(token)

Listing the available metadata types¶

Each type of metadata node in the Knowledge Graph is represented by a Python class. These classes are organized into modules according to the openMINDS schemas. For a full list of modules, see Metadata domains.

To get a list of classes in a given module, import the module and then run list_kg_classes(), e.g.:

>>> import fairgraph.openminds.core as omcore

>>> omcore.list_kg_classes()
[fairgraph.openminds.core.research.behavioral_protocol.BehavioralProtocol,
fairgraph.openminds.core.actors.contact_information.ContactInformation,
fairgraph.openminds.core.data.content_type.ContentType,
fairgraph.openminds.core.miscellaneous.doi.DOI,
fairgraph.openminds.core.products.dataset.Dataset,
fairgraph.openminds.core.products.dataset_version.DatasetVersion,
fairgraph.openminds.core.data.file.File,
fairgraph.openminds.core.data.file_bundle.FileBundle,
fairgraph.openminds.core.data.file_repository.FileRepository,
fairgraph.openminds.core.data.file_repository_structure.FileRepositoryStructure,
fairgraph.openminds.core.miscellaneous.funding.Funding,
fairgraph.openminds.core.miscellaneous.gridid.GRIDID,
fairgraph.openminds.core.miscellaneous.isbn.ISBN,
fairgraph.openminds.core.data.license.License,
fairgraph.openminds.core.products.meta_data_model.MetaDataModel,
fairgraph.openminds.core.products.meta_data_model_version.MetaDataModelVersion,
fairgraph.openminds.core.products.model.Model,
fairgraph.openminds.core.products.model_version.ModelVersion,
fairgraph.openminds.core.miscellaneous.orcid.ORCID,
fairgraph.openminds.core.actors.organization.Organization,
fairgraph.openminds.core.actors.person.Person,
fairgraph.openminds.core.products.project.Project,
fairgraph.openminds.core.research.protocol.Protocol,
fairgraph.openminds.core.research.protocol_execution.ProtocolExecution,
fairgraph.openminds.core.miscellaneous.rorid.RORID,
fairgraph.openminds.core.miscellaneous.swhid.SWHID,
fairgraph.openminds.core.data.service_link.ServiceLink,
fairgraph.openminds.core.products.software.Software,
fairgraph.openminds.core.products.software_version.SoftwareVersion,
fairgraph.openminds.core.research.stimulation.Stimulation,
fairgraph.openminds.core.research.subject.Subject,
fairgraph.openminds.core.research.subject_group.SubjectGroup,
fairgraph.openminds.core.research.subject_group_state.SubjectGroupState,
fairgraph.openminds.core.research.subject_state.SubjectState,
fairgraph.openminds.core.research.tissue_sample.TissueSample,
fairgraph.openminds.core.research.tissue_sample_collection.TissueSampleCollection,
fairgraph.openminds.core.research.tissue_sample_collection_state.TissueSampleCollectionState,
fairgraph.openminds.core.research.tissue_sample_state.TissueSampleState,
fairgraph.openminds.core.miscellaneous.url.URL]

Listing all metadata nodes of a given type¶

To obtain a list of all the metadata nodes of a given type, import the associated class and use the list() method, passing the client object you created previously, e.g. to get a list of patched cells:

from fairgraph.openminds.core import License

licenses = License.list(client)

By default, this gives you the first 100 results. You can change the number of results retrieved and the starting point, e.g.

licenses = License.list(client, from_index=15, size=10)

This returns 10 nodes starting with the 15th. To see how many nodes there are in total:

License.count(client)

Note

if you consistently retrieve an empty list, it is probably because you do not yet have the necessary permissions. See Access permissions for more information.

Filtering/searching¶

To obtain only metadata nodes that have certain properties, you can filter the list of nodes. For example, to see only datasets whose name contain the phrase ‘patch-clamp’:

from fairgraph.openminds.core import DatasetVersion

datasets = DatasetVersion.list(client, name="patch-clamp")

Warning

the filtering system is currently primitive, and unaware of hierarchies, e.g. filtering by “hippocampus” will not return cells with the brain region set to “hippocampus CA1”. This is on our list of things to fix soon! To see a list of possible search terms, use the fields() attribute, e.g. DatasetVersion.fields.

Retrieving a specific node based on its name or id¶

If you know the name or unique id of a node in the KnowledgeGraph, you can retrieve it directly:

dataset_of_interest = DatasetVersion.by_name('Whole cell patch-clamp recordings of cerebellar Golgi cells', client)
dataset_of_interest = DatasetVersion.from_id('17196b79-04db-4ea4-bb69-d20aab6f1d62', client)

Viewing metadata and connections¶

Once you have retrieved a node of interest, the associated metadata are available as attributes of the Python object, e.g.:

>>> dataset_of_interest.id
'https://kg.ebrains.eu/api/instances/17196b79-04db-4ea4-bb69-d20aab6f1d62'

>>> dataset_of_interest.uuid
'17196b79-04db-4ea4-bb69-d20aab6f1d62'

>>> dataset_of_interest.description[:100] + "..."
'The Golgi cells, together with granule cells and mossy fibers, form a neuronal microcircuit regulati...'

Connections between graph nodes are also available as attributes:

>>> dataset_of_interest.license
KGProxyV3([<class 'fairgraph.openminds.core.data.license.License'>], 'https://kg.ebrains.eu/api/instances/6ebce971-7f99-4fbc-9621-eeae47a70d85')

By default, for performance reasons, connections are not followed, and instead you will see either a KGQuery or KGProxy object. In both these cases, follow the connection using the resolve() method, e.g.:

>>> license = dataset_of_interest.license.resolve(client)

>>> license.name
'Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International'

Note

It is rather cumbersome to have to follow all these connections manually. In the near future, you will be able to ask fairgraph to resolve the connections for you, although with the risk of poor performance if your node of interest is indirectly connected to many other nodes in the graph.

Strict mode¶

fairgraph is quite strict about which metadata attributes and data types are expected, somewhat stricter than the Knowledge Graph itself. If you find that certain queries produce errors, you can relax this strict checking for a given node type as follows:

DatasetVersion.set_strict_mode(False)

Creating and updating metadata nodes¶

To create a new metadata node, create an instance of the appropriate Python class, then use the save() method, e.g.:

from fairgraph.openminds.core import SoftwareVersion, URL

# By default, fairgraph strictly enforces required fields.
# For demonstration purposes we turn this enforcement off here.
SoftwareVersion.set_strict_mode(False)

sv = SoftwareVersion(
    name="numpy",
    alias="numpy",
    version_identifier="1.14.9"
)
sv.save(client, space="myspace")

To update a node, edit the attributes of the corresponding Python object, then save() again:

from fairgraph.base_v3 import IRI

sv.homepage = URL(url=IRI("https://numpy.org"))
sv.save(client)

(Note that for updating existing objects you don’t need to specify the space.)

How does fairgraph distinguish between creating a new node and modifying an existing one?¶

If a previously-created node has been retrieved from the Knowledge Graph, it will have a unique ID, and therefore calling save() will update the node with this ID.

If a new Python object is created with the same or similar metadata, fairgraph queries for a node with matching metadata for a subset of the fields. If you want to know which fields are included in the match, examine the existence_query_fields attribute, e.g.:

>>> SoftwareVersion.existence_query_fields
('alias', 'version_identifier')

Permissions¶

If you get an error message when trying to create or update a node, it may be because you do not have the necessary permissions. See Access permissions for more information.

Metadata domains¶

KG version 3¶

openminds.core¶

Actors¶

class fairgraph.openminds.core.actors.person.Person(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a person.

Parameters:

digital_identifiers (ORCID) – Digital handle to identify objects or legal persons.
contact_information (ContactInformation) – Any available way used to contact a person or business (e.g., address, phone number, email address, etc.).
family_name (str) – Name borne in common by members of a family.
given_name (str) – Name given to a person, including all potential middle names, but excluding the family name.
affiliations (Affiliation) – Declaration of a person being closely associated to an organization.

class fairgraph.openminds.core.actors.contact_information.ContactInformation(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	email (str) – Address to which or from which an electronic mail can be sent.

class fairgraph.openminds.core.actors.organization.Organization(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on an organization.

Parameters:	digital_identifiers (GRIDID, RORID) – Digital handle to identify objects or legal persons. name (str) – Whole, non-abbreviated name of the organization. has_parent (Organization) – Reference to a parent object or legal person. homepage (URL) – Main website of the organization. alias (str) – Shortened or fully abbreviated name of the organization.

class fairgraph.openminds.core.actors.affiliation.Affiliation(data=None, **properties)[source]¶

Bases: fairgraph.base_v3.EmbeddedMetadata

Parameters:	start_date (date) – Date in the Gregorian calendar at which something begins in time end_date (date) – Date in the Gregorian calendar at which something terminates in time. organization (Organization) – Legally accountable, administrative and functional structure.

class fairgraph.openminds.core.actors.contribution.Contribution(data=None, **properties)[source]¶

Bases: fairgraph.base_v3.EmbeddedMetadata

Structured information on the contribution made to a research product.

Parameters:	contribution_types (ContributionType) – Distinct class of what was given or supplied as a part or share. contributor (Organization, Person) – Legal person that gave or supplied something as a part or share.

Data¶

class fairgraph.openminds.core.data.content_type.ContentType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the content type of a file instance, bundle or repository.

Parameters:

file_extensions (str) – String of characters attached as suffix to the names of files of a particular format.
data_types (DataType) – no description available
description (str) – Longer statement or account giving the characteristics of the content type.
related_media_type (IRI) – Reference to an official two-part identifier for file formats and format contents.
name (str) – Word or phrase that constitutes the distinctive designation of the content type.
specification (IRI) – Detailed and precise presentation of, or proposal for something.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.core.data.file.File(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a file instances.

Parameters:

content (str) – Something that is contained.
file_repository (FileRepository) – no description available
format (ContentType) – Method of digitally organizing and structuring data or information.
hash (Hash) – Term used for the process of converting any data into a single value. Often also directly refers to the resulting single value.
iri (IRI) – Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.
is_part_of (FileBundle) – Reference to the ensemble of multiple things or beings.
name (str) – Word or phrase that constitutes the distinctive designation of the file.
special_usage_role (FileUsageRole) – Particular function of something when it is used.
storage_size (QuantitativeValue) – Quantitative value defining how much disk space is used by an object on a computer system.

class fairgraph.openminds.core.data.file_bundle.FileBundle(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a bundle of file instances.

Parameters:

content (str) – Something that is contained.
descended_from (Technique, BehavioralProtocol, File, FileBundle, SubjectGroupState, SubjectState, TissueSampleCollectionState, TissueSampleState) – no description available
format (ContentType) – Method of digitally organizing and structuring data or information.
grouping_type (FileBundleGrouping) – no description available
hash (Hash) – Term used for the process of converting any data into a single value. Often also directly refers to the resulting single value.
is_part_of (FileBundle, FileRepository) – Reference to the ensemble of multiple things or beings.
name (str) – Word or phrase that constitutes the distinctive designation of the file bundle.
storage_size (QuantitativeValue) – Quantitative value defining how much disk space is used by an object on a computer system.

class fairgraph.openminds.core.data.file_repository.FileRepository(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a file repository.

Parameters:

content_type_patterns (ContentTypePattern) – no description available
format (ContentType) – Method of digitally organizing and structuring data or information.
hash (Hash) – Term used for the process of converting any data into a single value. Often also directly refers to the resulting single value.
hosted_by (Organization) – Reference to an organization that provides facilities and services for something.
iri (IRI) – Stands for Internationalized Resource Identifier which is an internet protocol standard that builds on the URI protocol, extending the set of permitted characters to include Unicode/ISO 10646.
name (str) – Word or phrase that constitutes the distinctive designation of the file repository.
repository_type (FileRepositoryType) – no description available
storage_size (QuantitativeValue) – Quantitative value defining how much disk space is used by an object on a computer system.
structure_pattern (FileRepositoryStructure) – no description available

class fairgraph.openminds.core.data.file_repository_structure.FileRepositoryStructure(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	file_path_patterns (FilePathPattern) – no description available lookup_label (str) – no description available

class fairgraph.openminds.core.data.license.License(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a used license.

Parameters:	name (str) – Whole, non-abbreviated name of the license. legal_code (IRI) – Type of legislation that claims to cover the law system (complete or parts) as it existed at the time the code was enacted. alias (str) – Shortened or fully abbreviated name of the license. webpages (str) – Hypertext document (block of information) found on the World Wide Web.

class fairgraph.openminds.core.data.service_link.ServiceLink(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	data_location (File, FileBundle) – no description available name (str) – Word or phrase that constitutes the distinctive designation of the service link. open_data_in (URL) – no description available service (Service) – no description available

Miscellaneous¶

class fairgraph.openminds.core.miscellaneous.doi.DOI(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	identifier (str) – Term or code used to identify the DOI.

class fairgraph.openminds.core.miscellaneous.funding.Funding(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on used funding.

Parameters:

acknowledgement (str) – Offical declaration or avowal of appreciation of an act or achievement.
award_number (str) – Machine-readable identifier for a benefit that is conferred or bestowed on the basis of merit or need.
award_title (str) – Human-readable identifier for a benefit that is conferred or bestowed on the basis of merit or need.
funder (Organization, Person) – Legal person that provides money for a particular purpose.

class fairgraph.openminds.core.miscellaneous.gridid.GRIDID(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	identifier (str) – Term or code used to identify the GRIDID.

class fairgraph.openminds.core.miscellaneous.isbn.ISBN(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	identifier (str) – Term or code used to identify the ISBN.

class fairgraph.openminds.core.miscellaneous.orcid.ORCID(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	identifier (str) – Term or code used to identify the ORCID.

class fairgraph.openminds.core.miscellaneous.rorid.RORID(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	identifier (str) – Term or code used to identify the RORID.

class fairgraph.openminds.core.miscellaneous.swhid.SWHID(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	identifier (str) – Term or code used to identify the SWHID.

class fairgraph.openminds.core.miscellaneous.url.URL(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	url (IRI) – no description available

Products¶

class fairgraph.openminds.core.products.dataset.Dataset(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on data originating from human/animal studies or simulations (concept level).

Parameters:

authors (Organization, Person) – Creator of a literary or creative work, as well as a dataset publication.
digital_identifier (DOI) – Digital handle to identify objects or legal persons.
versions (DatasetVersion) – Reference to variants of an original.
custodians (Organization, Person) – Legal person entrusted with guarding and maintaining property or records.
description (str) – Longer statement or account giving the characteristics of the dataset.
name (str) – Whole, non-abbreviated name of the dataset.
homepage (URL) – Main website of the dataset.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
alias (str) – Shortened or fully abbreviated name of the dataset.

class fairgraph.openminds.core.products.dataset_version.DatasetVersion(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on data originating from human/animal studies or simulations (version level).

Parameters:

authors (Organization, Person) – Creator of a literary or creative work, as well as a dataset publication.
behavioral_protocols (BehavioralProtocol) – no description available
digital_identifier (DOI) – Digital handle to identify objects or legal persons.
ethics_assessment (EthicsAssessment) – Judgment about the applied principles of conduct governing an individual or a group.
experimental_approachs (ExperimentalApproach) – no description available
input_data (DOI, File, FileBundle) – Data that is put into a process or machine.
is_alternative_version_of (DatasetVersion) – Reference to an original form where the essence was preserved, but presented in an alternative form.
is_new_version_of (DatasetVersion) – Reference to a previous (potentially outdated) particular form of something.
license (License) – Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
preparation_designs (PreparationType) – no description available
studied_specimens (Subject, SubjectGroup, TissueSample, TissueSampleCollection) – no description available
techniques (Technique) – Method of accomplishing a desired aim.
data_types (SemanticDataType) – no description available
study_targets (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.
accessibility (ProductAccessibility) – Level to which something is accessible to the dataset version.
copyright (Copyright) – Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.
custodians (Organization, Person) – Legal person entrusted with guarding and maintaining property or records.
description (str) – Longer statement or account giving the characteristics of the dataset version.
full_documentation (DOI, File, URL) – Non-abridged instructions, comments, and information for using a particular product.
name (str) – Whole, non-abbreviated name of the dataset version.
funding (Funding) – Money provided by a legal person for a particular purpose.
homepage (URL) – Main website of the dataset version.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
keywords (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Significant word or concept that are representative of the dataset version.
other_contributions (Contribution) – Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.
related_publications (DOI, ISBN) – Reference to something that was made available for the general public to see or buy.
release_date (date) – Fixed date on which a product is due to become or was made available for the general public to see or buy
repository (FileRepository) – Place, room, or container where something is deposited or stored.
alias (str) – Shortened or fully abbreviated name of the dataset version.
support_channels (str) – Way of communication used to interact with users or customers.
version_identifier (str) – Term or code used to identify the version of something.
version_innovation (str) – Documentation on what changed in comparison to a previously published form of something.

class fairgraph.openminds.core.products.model.Model(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a computational model (concept level).

Parameters:

abstraction_level (ModelAbstractionLevel) – Extent of simplification of physical, spatial, or temporal details or attributes in the study of objects or systems.
developers (Organization, Person) – Legal person that creates or improves products or services (e.g., software, applications, etc.).
digital_identifier (DOI, SWHID) – Digital handle to identify objects or legal persons.
versions (ModelVersion) – Reference to variants of an original.
model_scope (ModelScope) – Extent of something.
study_targets (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.
custodians (Organization, Person) – Legal person entrusted with guarding and maintaining property or records.
description (str) – Longer statement or account giving the characteristics of the model.
name (str) – Whole, non-abbreviated name of the model.
homepage (URL) – Main website of the model.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
alias (str) – Shortened or fully abbreviated name of the model.

class fairgraph.openminds.core.products.model_version.ModelVersion(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a computational model (version level).

Parameters:

developers (Organization, Person) – Legal person that creates or improves products or services (e.g., software, applications, etc.).
digital_identifier (DOI, SWHID) – Digital handle to identify objects or legal persons.
format (ContentType) – Method of digitally organizing and structuring data or information.
input_data (DOI, File, FileBundle) – Data that is put into a process or machine.
is_alternative_version_of (ModelVersion) – Reference to an original form where the essence was preserved, but presented in an alternative form.
is_new_version_of (ModelVersion) – Reference to a previous (potentially outdated) particular form of something.
licenses (License) – Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
output_data (DOI, File, FileBundle) – Data that comes out of, is delivered or produced by a process or machine.
accessibility (ProductAccessibility) – Level to which something is accessible to the model version.
copyright (Copyright) – Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.
custodians (Organization, Person) – Legal person entrusted with guarding and maintaining property or records.
description (str) – Longer statement or account giving the characteristics of the model version.
full_documentation (DOI, File, URL) – Non-abridged instructions, comments, and information for using a particular product.
name (str) – Whole, non-abbreviated name of the model version.
funding (Funding) – Money provided by a legal person for a particular purpose.
homepage (URL) – Main website of the model version.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
keywords (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Significant word or concept that are representative of the model version.
other_contributions (Contribution) – Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.
related_publications (DOI, ISBN) – Reference to something that was made available for the general public to see or buy.
release_date (date) – Fixed date on which a product is due to become or was made available for the general public to see or buy
repository (FileRepository) – Place, room, or container where something is deposited or stored.
alias (str) – Shortened or fully abbreviated name of the model version.
support_channels (str) – Way of communication used to interact with users or customers.
version_identifier (str) – Term or code used to identify the version of something.
version_innovation (str) – Documentation on what changed in comparison to a previously published form of something.

class fairgraph.openminds.core.products.project.Project(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a research project.

Parameters:

description (str) – Longer statement or account giving the characteristics of the project.
name (str) – Whole, non-abbreviated name of the project.
has_research_products (Dataset, DatasetVersion, MetaDataModel, MetaDataModelVersion, Model, ModelVersion, Software, SoftwareVersion) – Reference to subsidiary research products.
homepage (URL) – Main website of the project.
coordinators (Organization, Person) – Legal person who organizes the collaborative work of people or groups.
alias (str) – Shortened or fully abbreviated name of the project.

class fairgraph.openminds.core.products.software.Software(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a software tool (concept level).

Parameters:

developers (Organization, Person) – Legal person that creates or improves products or services (e.g., software, applications, etc.).
digital_identifier (DOI, SWHID) – Digital handle to identify objects or legal persons.
versions (SoftwareVersion) – Reference to variants of an original.
custodians (Organization, Person) – Legal person entrusted with guarding and maintaining property or records.
description (str) – Longer statement or account giving the characteristics of the software.
name (str) – Whole, non-abbreviated name of the software.
homepage (URL) – Main website of the software.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
alias (str) – Shortened or fully abbreviated name of the software.

class fairgraph.openminds.core.products.software_version.SoftwareVersion(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

application_categories (SoftwareApplicationCategory) – Distinct class that groups software programs which perform a similar task or set of tasks.
developers (Organization, Person) – Legal person that creates or improves products or services (e.g., software, applications, etc.).
devices (OperatingDevice) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.
digital_identifier (DOI, SWHID) – Digital handle to identify objects or legal persons.
has_components (SoftwareVersion) – Reference to an element of a collection.
features (SoftwareFeature) – Structure, form, or appearance that characterizes the software version.
requirements (str) – Something essential to the existence, occurrence or function of something else.
input_formats (ContentType) – Format of data that is put into a process or machine.
is_alternative_version_of (SoftwareVersion) – Reference to an original form where the essence was preserved, but presented in an alternative form.
is_new_version_of (SoftwareVersion) – Reference to a previous (potentially outdated) particular form of something.
languages (Language) – System of communication (words, their pronunciation, and the methods of combining them) used and understood by a particular community.
licenses (License) – Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
operating_systems (OperatingSystem) – Software that controls the operation of a computer and directs the processing of programs.
output_formats (ContentType) – Format of data that comes out of, is delivered or produced by a process or machine.
programming_languages (ProgrammingLanguage) – Distinct set of instructions for computer programs in order to produce various kinds of output.
accessibility (ProductAccessibility) – Level to which something is accessible to the software version.
copyright (Copyright) – Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.
custodians (Organization, Person) – Legal person entrusted with guarding and maintaining property or records.
description (str) – Longer statement or account giving the characteristics of the software version.
full_documentation (DOI, File, URL) – Non-abridged instructions, comments, and information for using a particular product.
name (str) – Whole, non-abbreviated name of the software version.
funding (Funding) – Money provided by a legal person for a particular purpose.
homepage (URL) – Main website of the software version.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
keywords (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Significant word or concept that are representative of the software version.
other_contributions (Contribution) – Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.
related_publications (DOI, ISBN) – Reference to something that was made available for the general public to see or buy.
release_date (date) – Fixed date on which a product is due to become or was made available for the general public to see or buy
repository (FileRepository) – Place, room, or container where something is deposited or stored.
alias (str) – Shortened or fully abbreviated name of the software version.
support_channels (str) – Way of communication used to interact with users or customers.
version_identifier (str) – Term or code used to identify the version of something.
version_innovation (str) – Documentation on what changed in comparison to a previously published form of something.

Research¶

class fairgraph.openminds.core.research.behavioral_protocol.BehavioralProtocol(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

description (str) – Longer statement or account giving the characteristics of the behavioral protocol.
name (str) – Word or phrase that constitutes the distinctive designation of the behavioral protocol.
internal_identifier (str) – Term or code that identifies the behavioral protocol within a particular product.
stimulations (Stimulation) – no description available

class fairgraph.openminds.core.research.protocol.Protocol(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a research project.

Parameters:	description (str) – Longer statement or account giving the characteristics of the protocol. name (str) – Word or phrase that constitutes the distinctive designation of the protocol. stimulations (Stimulation) – no description available techniques (Technique) – Method of accomplishing a desired aim.

class fairgraph.openminds.core.research.protocol_execution.ProtocolExecution(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a protocol execution.

Parameters:

behavioral_protocols (BehavioralProtocol) – no description available
inputs (File, FileBundle, SubjectGroupState, SubjectState, TissueSampleCollectionState, TissueSampleState) – Something or someone that is put into or participates in a process or machine.
is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.
outputs (File, FileBundle, SubjectGroupState, SubjectState, TissueSampleCollectionState, TissueSampleState) – Something or someone that comes out of, is delivered or produced by a process or machine.
preparation_design (PreparationType) – no description available
protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.
description (str) – Longer statement or account giving the characteristics of the protocol execution.
ended_at_time (datetime) – no description available
lookup_label (str) – no description available
parameter_sets (ParameterSet) – Manner, position, or direction in which digital or physical properties are set to determine a particular function, characteristics or behavior of something.
started_at_time (datetime) – no description available
study_targets (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class fairgraph.openminds.core.research.stimulation.Stimulation(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	stimulation_approach (StimulationApproach) – no description available stimulus_type (StimulusType) – no description available

class fairgraph.openminds.core.research.subject.Subject(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a subject.

Parameters:

is_part_of (SubjectGroup) – Reference to the ensemble of multiple things or beings.
studied_states (SubjectState) – Reference to a point in time at which the subject was studied in a particular mode or condition.
biological_sex (BiologicalSex) – Differentiation of individuals of most species (animals and plants) based on the type of gametes they produce.
internal_identifier (str) – Term or code that identifies the subject within a particular product.
lookup_label (str) – no description available
phenotype (Phenotype) – Physical expression of one or more genes of an organism.
species (Species) – Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.
strain (Strain) – Group of presumed common ancestry with physiological but usually not morphological distinctions.

class fairgraph.openminds.core.research.subject_group.SubjectGroup(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

studied_states (SubjectGroupState) – Reference to a point in time at which the subject group was studied in a particular mode or condition.
additional_remarks (str) – Mention of what deserves additional attention or notice.
biological_sex (BiologicalSex) – Differentiation of individuals of most species (animals and plants) based on the type of gametes they produce.
internal_identifier (str) – Term or code that identifies the subject group within a particular product.
lookup_label (str) – no description available
phenotypes (Phenotype) – Physical expression of one or more genes of an organism.
quantity (int) – Total amount or number of things or beings.
species (Species) – Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.
strains (Strain) – Group of presumed common ancestry with physiological but usually not morphological distinctions.

class fairgraph.openminds.core.research.subject_group_state.SubjectGroupState(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

age_categories (AgeCategory) – Distinct life cycle class that is defined by a similar age or age range (developmental stage) within a group of individual beings.
handedness (Handedness) – Degree to which an organism prefers one hand or foot over the other hand or foot during the performance of a task.
additional_remarks (str) – Mention of what deserves additional attention or notice.
age (QuantitativeValue, QuantitativeValueRange) – Time of life or existence at which some particular qualification, capacity or event arises.
lookup_label (str) – no description available
pathologys (Disease, DiseaseModel) – Structural and functional deviation from the normal that constitutes a disease or characterizes a particular disease.
weight (QuantitativeValue, QuantitativeValueRange) – Amount that a thing or being weighs.

class fairgraph.openminds.core.research.subject_state.SubjectState(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a temporary state of a subject.

Parameters:

age_category (AgeCategory) – Distinct life cycle class that is defined by a similar age or age range (developmental stage) within a group of individual beings.
handedness (Handedness) – Degree to which an organism prefers one hand or foot over the other hand or foot during the performance of a task.
additional_remarks (str) – Mention of what deserves additional attention or notice.
age (QuantitativeValue, QuantitativeValueRange) – Time of life or existence at which some particular qualification, capacity or event arises.
lookup_label (str) – no description available
pathologys (Disease, DiseaseModel) – Structural and functional deviation from the normal that constitutes a disease or characterizes a particular disease.
weight (QuantitativeValue, QuantitativeValueRange) – Amount that a thing or being weighs.

class fairgraph.openminds.core.research.tissue_sample.TissueSample(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a tissue sample.

Parameters:

is_part_of (TissueSampleCollection) – Reference to the ensemble of multiple things or beings.
laterality (Laterality) – Differentiation between a pair of lateral homologous parts of the body.
origin (CellType, Organ) – Source at which something begins or rises, or from which something derives.
studied_states (TissueSampleState) – Reference to a point in time at which the tissue sample was studied in a particular mode or condition.
anatomical_locations (UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available
type (TissueSampleType) – Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.
biological_sex (BiologicalSex) – Differentiation of individuals of most species (animals and plants) based on the type of gametes they produce.
internal_identifier (str) – Term or code that identifies the tissue sample within a particular product.
lookup_label (str) – no description available
phenotype (Phenotype) – Physical expression of one or more genes of an organism.
species (Species) – Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.
strain (Strain) – Group of presumed common ancestry with physiological but usually not morphological distinctions.

class fairgraph.openminds.core.research.tissue_sample_collection.TissueSampleCollection(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

anatomical_locations (UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available
laterality (Laterality) – Differentiation between a pair of lateral homologous parts of the body.
origins (CellType, Organ) – Source at which something begins or rises, or from which something derives.
studied_states (TissueSampleCollectionState) – Reference to a point in time at which the tissue sample collection was studied in a particular mode or condition.
types (TissueSampleType) – Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.
additional_remarks (str) – Mention of what deserves additional attention or notice.
biological_sex (BiologicalSex) – Differentiation of individuals of most species (animals and plants) based on the type of gametes they produce.
internal_identifier (str) – Term or code that identifies the tissue sample collection within a particular product.
lookup_label (str) – no description available
phenotypes (Phenotype) – Physical expression of one or more genes of an organism.
quantity (int) – Total amount or number of things or beings.
species (Species) – Category of biological classification comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective.
strains (Strain) – Group of presumed common ancestry with physiological but usually not morphological distinctions.

class fairgraph.openminds.core.research.tissue_sample_collection_state.TissueSampleCollectionState(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

additional_remarks (str) – Mention of what deserves additional attention or notice.
age (QuantitativeValue, QuantitativeValueRange) – Time of life or existence at which some particular qualification, capacity or event arises.
lookup_label (str) – no description available
pathologys (Disease, DiseaseModel) – Structural and functional deviation from the normal that constitutes a disease or characterizes a particular disease.
weight (QuantitativeValue, QuantitativeValueRange) – Amount that a thing or being weighs.

class fairgraph.openminds.core.research.tissue_sample_state.TissueSampleState(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a temporary state of a tissue sample.

Parameters:

additional_remarks (str) – Mention of what deserves additional attention or notice.
age (QuantitativeValue, QuantitativeValueRange) – Time of life or existence at which some particular qualification, capacity or event arises.
lookup_label (str) – no description available
pathologys (Disease, DiseaseModel) – Structural and functional deviation from the normal that constitutes a disease or characterizes a particular disease.
weight (QuantitativeValue, QuantitativeValueRange) – Amount that a thing or being weighs.

openminds.controlledterms¶

class fairgraph.openminds.controlledterms.action_status_type.ActionStatusType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the action status type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the action status type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.age_category.AgeCategory(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the life cycle (semantic term) of a specific age group.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the age category.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the age category.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.anatomical_axes_orientation.AnatomicalAxesOrientation(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the anatomical directions of the X, Y, and Z axis.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the anatomical axes orientation.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the anatomical axes orientation.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.biological_order.BiologicalOrder(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the biological order.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the biological order.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.biological_sex.BiologicalSex(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the biological sex of a subject.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the biological sex.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the biological sex.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.cell_type.CellType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the cell type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the cell type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.contribution_type.ContributionType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the type of contribution a person or organization performed.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the contribution type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the contribution type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.criteria_quality_type.CriteriaQualityType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the quality type of the defined criteria for a measurement.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the criteria quality type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the criteria quality type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.data_type.DataType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the data type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the data type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.device_type.DeviceType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the device type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the device type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.disease.Disease(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a disease.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the disease.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the disease.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.disease_model.DiseaseModel(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the disease model.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the disease model.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.ethics_assessment.EthicsAssessment(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the ethics assessment of a dataset.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the ethics assessment.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the ethics assessment.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.experimental_approach.ExperimentalApproach(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the experimental approach.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the experimental approach.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.file_bundle_grouping.FileBundleGrouping(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the grouping mechanism of a file bundle.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the file bundle grouping.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the file bundle grouping.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.file_repository_type.FileRepositoryType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the file repository type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the file repository type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.file_usage_role.FileUsageRole(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the usage role of a file instance or bundle.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the file usage role.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the file usage role.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.handedness.Handedness(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the handedness.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the handedness.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.language.Language(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the available language setting.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the language.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the language.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.laterality.Laterality(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the lateral direction.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the laterality.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the laterality.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.meta_data_model_type.MetaDataModelType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the meta data model type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the meta data model type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.model_abstraction_level.ModelAbstractionLevel(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on abstraction level of the computational model.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the model abstraction level.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the model abstraction level.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.model_scope.ModelScope(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the scope of the computational model.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the model scope.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the model scope.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.operating_device.OperatingDevice(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the operating device.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the operating device.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the operating device.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.operating_system.OperatingSystem(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the operating system.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the operating system.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the operating system.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.organ.Organ(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the organ.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the organ.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.phenotype.Phenotype(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the phenotype of a subject.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the phenotype.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the phenotype.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.preparation_type.PreparationType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the preparation type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the preparation type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.product_accessibility.ProductAccessibility(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the product accessibility.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the product accessibility.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.programming_language.ProgrammingLanguage(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the programming language.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the programming language.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the programming language.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.qualitative_overlap.QualitativeOverlap(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the qualitative overlap.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the qualitative overlap.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.semantic_data_type.SemanticDataType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the semantic data type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the semantic data type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.service.Service(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the service.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the service.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.software_application_category.SoftwareApplicationCategory(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the category of the software application.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the software application category.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the software application category.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.software_feature.SoftwareFeature(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the software feature.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the software feature.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.species.Species(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the species.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the species.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the species.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.stimulation_approach.StimulationApproach(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the stimulation approach.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the stimulation approach.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.stimulus_type.StimulusType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the stimulus type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the stimulus type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.strain.Strain(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

identifiers (str) – Term or code used to identify the strain.
definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the strain.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the strain.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.technique.Technique(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the technique.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the technique.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the technique.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.term_suggestion.TermSuggestion(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

add_existing_terminology (Terminology) – Reference to an existing terminology (distinct class to group related terms).
suggest_new_terminology (str) – Proposal of a new distinct class to group related terms.
definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the term suggestion.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the term suggestion.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.terminology.Terminology(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the terminology.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the terminology.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.tissue_sample_type.TissueSampleType(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the general type of the tissue sample.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the tissue sample type.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the tissue sample type.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.type_of_uncertainty.TypeOfUncertainty(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the type of uncertainty.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the type of uncertainty.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.uberon_parcellation.UBERONParcellation(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the UBERON parcellation.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the UBERON parcellation.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

class fairgraph.openminds.controlledterms.unit_of_measurement.UnitOfMeasurement(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on the unit of measurement.

Parameters:

definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.
description (str) – Longer statement or account giving the characteristics of the unit of measurement.
interlex_identifier (IRI) – Persistent identifier for a term registered in the InterLex project.
knowledge_space_link (IRI) – Persistent link to an encyclopedia entry in the Knowledge Space project.
name (str) – Word or phrase that constitutes the distinctive designation of the unit of measurement.
preferred_ontology_identifier (IRI) – Persistent identifier of a preferred ontological term.
synonyms (str) – Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.

openminds.sands¶

class fairgraph.openminds.sands.atlas.brain_atlas.BrainAtlas(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a brain atlas (concept level).

Parameters:	authors (Organization, Person) – Creator of a literary or creative work, as well as a dataset publication. digital_identifier (DOI, ISBN) – Digital handle to identify objects or legal persons. has_terminology (ParcellationTerminology) – no description available versions (BrainAtlasVersion) – Reference to variants of an original.

class fairgraph.openminds.sands.atlas.brain_atlas_version.BrainAtlasVersion(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Structured information on a brain atlas (version level).

Parameters:

authors (Organization, Person) – Creator of a literary or creative work, as well as a dataset publication.
coordinate_space (CommonCoordinateSpace) – Two or three dimensional geometric setting.
digital_identifier (DOI, ISBN) – Digital handle to identify objects or legal persons.
has_terminology_version (ParcellationTerminologyVersion) – no description available
is_alternative_version_of (BrainAtlasVersion) – Reference to an original form where the essence was preserved, but presented in an alternative form.
is_new_version_of (BrainAtlasVersion) – Reference to a previous (potentially outdated) particular form of something.
license (License) – Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
ontology_identifier (IRI) – Term or code used to identify the brain atlas version registered within a particular ontology.

class fairgraph.openminds.sands.atlas.common_coordinate_space.CommonCoordinateSpace(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

anatomical_axes_orientation (AnatomicalAxesOrientation) – Relation between reference planes used in anatomy and mathematics.
axes_origins (QuantitativeValue) – Special point in a coordinate system used as a fixed point of reference for the geometry of the surrounding space.
default_images (File) – Two or three dimensional image that particluarly represents a specific coordinate space.
digital_identifier (DOI) – Digital handle to identify objects or legal persons.
name (str) – Whole, non-abbreviated name of the common coordinate space.
homepage (URL) – Main website of the common coordinate space.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
native_unit (UnitOfMeasurement) – Determinate quantity used in the original measurement.
ontology_identifier (IRI) – Term or code used to identify the common coordinate space registered within a particular ontology.
release_date (date) – Fixed date on which a product is due to become or was made available for the general public to see or buy
alias (str) – Shortened or fully abbreviated name of the common coordinate space.
version_identifier (str) – Term or code used to identify the version of something.

class fairgraph.openminds.sands.non_atlas.custom_anatomical_entity.CustomAnatomicalEntity(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	has_annotation (CustomAnnotation) – no description available name (str) – Word or phrase that constitutes the distinctive designation of the custom anatomical entity. related_uberon_term (UBERONParcellation) – no description available relation_assessments (QualitativeRelationAssessment, QuantitativeRelationAssessment) – no description available

class fairgraph.openminds.sands.non_atlas.custom_coordinate_space.CustomCoordinateSpace(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

anatomical_axes_orientation (AnatomicalAxesOrientation) – Relation between reference planes used in anatomy and mathematics.
axes_origins (QuantitativeValue) – Special point in a coordinate system used as a fixed point of reference for the geometry of the surrounding space.
default_images (File) – Two or three dimensional image that particluarly represents a specific coordinate space.
name (str) – Word or phrase that constitutes the distinctive designation of the custom coordinate space.
native_unit (UnitOfMeasurement) – Determinate quantity used in the original measurement.

class fairgraph.openminds.sands.atlas.parcellation_entity.ParcellationEntity(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

has_parents (ParcellationEntity) – Reference to a parent object or legal person.
versions (ParcellationEntityVersion) – Reference to variants of an original.
name (str) – Word or phrase that constitutes the distinctive designation of the parcellation entity.
ontology_identifier (IRI) – Term or code used to identify the parcellation entity registered within a particular ontology.
related_uberon_term (UBERONParcellation) – no description available

class fairgraph.openminds.sands.atlas.parcellation_entity_version.ParcellationEntityVersion(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

has_annotation (AtlasAnnotation) – no description available
has_parents (ParcellationEntity, ParcellationEntityVersion) – Reference to a parent object or legal person.
name (str) – Word or phrase that constitutes the distinctive designation of the parcellation entity version.
ontology_identifier (IRI) – Term or code used to identify the parcellation entity version registered within a particular ontology.
relation_assessments (QualitativeRelationAssessment, QuantitativeRelationAssessment) – no description available
version_identifier (str) – Term or code used to identify the version of something.
version_innovation (str) – Documentation on what changed in comparison to a previously published form of something.

class fairgraph.openminds.sands.atlas.parcellation_terminology_version.ParcellationTerminologyVersion(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

defined_ins (File) – Reference to a file instance in which something is stored.
name (str) – Whole, non-abbreviated name of the parcellation terminology version.
has_entity_versions (ParcellationEntityVersion) – no description available
is_alternative_version_of (ParcellationTerminologyVersion) – Reference to an original form where the essence was preserved, but presented in an alternative form.
is_new_version_of (ParcellationTerminologyVersion) – Reference to a previous (potentially outdated) particular form of something.
ontology_identifier (IRI) – Term or code used to identify the parcellation terminology version registered within a particular ontology.
alias (str) – Shortened or fully abbreviated name of the parcellation terminology version.
version_identifier (str) – Term or code used to identify the version of something.
version_innovation (str) – Documentation on what changed in comparison to a previously published form of something.

openminds.computation¶

class fairgraph.openminds.computation.environment.Environment(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	name (str) – Word or phrase that constitutes the distinctive designation of the environment. hardware (HardwareSystem) – no description available configuration (ParameterSet) – no description available software (SoftwareVersion) – no description available description (str) – Longer statement or account giving the characteristics of the environment.

class fairgraph.openminds.computation.hardware_system.HardwareSystem(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	name (str) – Word or phrase that constitutes the distinctive designation of the hardware system. version (str) – no description available description (str) – Longer statement or account giving the characteristics of the hardware system.

class fairgraph.openminds.computation.launch_configuration.LaunchConfiguration(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

description (str) – Longer statement or account giving the characteristics of the launch configuration.
name (str) – Word or phrase that constitutes the distinctive designation of the launch configuration.
executable (str) – no description available
arguments (str) – no description available
environment_variables (ParameterSet) – no description available

class fairgraph.openminds.computation.data_analysis.DataAnalysis(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

inputs (File, FileBundle, SoftwareVersion) – Something or someone that is put into or participates in a process or machine.
outputs (File, FileBundle) – Something or someone that comes out of, is delivered or produced by a process or machine.
environment (Environment) – no description available
launch_configuration (LaunchConfiguration) – no description available
started_by (SoftwareAgent, Person) – no description available
was_informed_by (DataAnalysis, Simulation, Optimization, Visualization) – no description available
status (ActionStatusType) – no description available
resource_usages (QuantitativeValue, QuantitativeValueRange) – no description available
tags (str) – no description available
description (str) – Longer statement or account giving the characteristics of the data analysis.
ended_at_time (datetime) – no description available
lookup_label (str) – no description available
parameter_sets (ParameterSet) – Manner, position, or direction in which digital or physical properties are set to determine a particular function, characteristics or behavior of something.
started_at_time (datetime) – no description available
study_targets (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class fairgraph.openminds.computation.simulation.Simulation(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

inputs (File, FileBundle, ModelVersion, SoftwareVersion) – Something or someone that is put into or participates in a process or machine.
outputs (File, FileBundle) – Something or someone that comes out of, is delivered or produced by a process or machine.
environment (Environment) – no description available
launch_configuration (LaunchConfiguration) – no description available
started_by (SoftwareAgent, Person) – no description available
was_informed_by (DataAnalysis, Simulation, Optimization, Visualization) – no description available
status (ActionStatusType) – no description available
resource_usages (QuantitativeValue, QuantitativeValueRange) – no description available
tags (str) – no description available
description (str) – Longer statement or account giving the characteristics of the simulation.
ended_at_time (datetime) – no description available
lookup_label (str) – no description available
parameter_sets (ParameterSet) – Manner, position, or direction in which digital or physical properties are set to determine a particular function, characteristics or behavior of something.
started_at_time (datetime) – no description available
study_targets (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class fairgraph.openminds.computation.visualization.Visualization(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

inputs (File, FileBundle, SoftwareVersion) – Something or someone that is put into or participates in a process or machine.
outputs (File, FileBundle) – Something or someone that comes out of, is delivered or produced by a process or machine.
environment (Environment) – no description available
launch_configuration (LaunchConfiguration) – no description available
started_by (SoftwareAgent, Person) – no description available
was_informed_by (DataAnalysis, Simulation, Optimization, Visualization) – no description available
status (ActionStatusType) – no description available
resource_usages (QuantitativeValue, QuantitativeValueRange) – no description available
tags (str) – no description available
description (str) – Longer statement or account giving the characteristics of the visualization.
ended_at_time (datetime) – no description available
lookup_label (str) – no description available
parameter_sets (ParameterSet) – Manner, position, or direction in which digital or physical properties are set to determine a particular function, characteristics or behavior of something.
started_at_time (datetime) – no description available
study_targets (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class fairgraph.openminds.computation.optimization.Optimization(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:

inputs (File, FileBundle, ModelVersion, SoftwareVersion) – Something or someone that is put into or participates in a process or machine.
outputs (File, FileBundle, ModelVersion) – Something or someone that comes out of, is delivered or produced by a process or machine.
environment (Environment) – no description available
launch_configuration (LaunchConfiguration) – no description available
started_by (SoftwareAgent, Person) – no description available
was_informed_by (DataAnalysis, Simulation, Optimization, Visualization) – no description available
status (ActionStatusType) – no description available
resource_usages (QuantitativeValue, QuantitativeValueRange) – no description available
tags (str) – no description available
description (str) – Longer statement or account giving the characteristics of the optimization.
ended_at_time (datetime) – no description available
lookup_label (str) – no description available
parameter_sets (ParameterSet) – Manner, position, or direction in which digital or physical properties are set to determine a particular function, characteristics or behavior of something.
started_at_time (datetime) – no description available
study_targets (BiologicalOrder, BiologicalSex, CellType, Disease, DiseaseModel, Handedness, Organ, Phenotype, Species, Strain, TermSuggestion, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class fairgraph.openminds.computation.software_agent.SoftwareAgent(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	name (str) – Word or phrase that constitutes the distinctive designation of the software agent. software (SoftwareVersion) – no description available environment (Environment) – no description available

class fairgraph.openminds.computation.workflow_execution.WorkflowExecution(id=None, data=None, space=None, **properties)[source]¶

Bases: fairgraph.base_v3.KGObjectV3

Parameters:	stages (DataAnalysis, Optimization, Simulation, Visualization) – no description available started_by (SoftwareAgent, Person) – no description available

fairgraph currently provides the following modules for working with KG v3:

openminds.core: covers general origin, location and content of research products
openminds.sands: covers brain atlases, as well as anatomical locations and relations of non-atlas data.
openminds.controlledterms: covers consistent definition of neuroscience terms
openminds.computation: covers provenance of simulations, data analysis and visualizations in neuroscience

KG version 2¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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')[source]¶: 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)[source]¶: List all objects of this type in the Knowledge Graph

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

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)[source]¶

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)[source]¶

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)[source]¶

Bases: fairgraph.minds.MINDSObject

A file/data format.

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

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

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)[source]¶

Bases: fairgraph.minds.MINDSObject

An experimental method.

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

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

Bases: fairgraph.minds.MINDSObject

A recording modality.

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

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

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)[source]¶

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)[source]¶

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)[source]¶

Bases: fairgraph.minds.MINDSObject

An experimental preparation.

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

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

Bases: fairgraph.minds.MINDSObject

An experimental procotol.

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

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

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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()[source]¶: List all KG classes defined in this module

fairgraph.minds.Project¶: alias of fairgraph.minds.PLAComponent

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

electrophysiology¶

Metadata for electrophysiology experiments.

The following methods are currently supported:

patch clamp recording in brain slices
sharp electrode intracellular recording in brain slices

Coming soon:

patch clamp recordings in cultured neurons
extracellular electrode recording, including tetrodes and multi-electrode arrays

class fairgraph.electrophysiology.Sensor(name, coordinate_system=None, coordinate_units=None, description=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Object specific to sensors used in electrode array experiments

Parameters:	name (str) – coordinate_system (Distribution) – coordinate_units (str) – description (str) –

class fairgraph.electrophysiology.Trace(name, data_location, generated_by, generation_metadata, channel, data_unit, time_step, part_of=None, retrieval_date=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Single time series recorded during an experiment or simulation.

Trace represents a single recording from a single channel. If you have a file containing recordings from multiple channels, or multiple recordings from a single channel, use MultiChannelMultiTrialRecording.

Parameters:	name (str) – data_location (Distribution) – generated_by (PatchClampExperiment) – generation_metadata (QualifiedTraceGeneration) – channel (int) – data_unit (str) – time_step (QuantitativeValue) – part_of (Dataset) – retrieval_date (datetime) –

class fairgraph.electrophysiology.MultiChannelMultiTrialRecording(name, data_location, generated_by, generation_metadata, channel_names, data_unit, time_step, channel_type=None, part_of=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.Trace

Multiple time series recorded during an experiment or simulation.: Time series may be recorded from multiple channels. If you have a file containing only a single recording from a single channel, you may instead use Trace.

Parameters:

name (str) –
data_location (Distribution) –
generated_by (PatchClampExperiment, ExtracellularElectrodeExperiment, ElectrodeArrayExperiment, EEGExperiment, ECoGExperiment) –
generation_metadata (QualifiedMultiTraceGeneration) –
channel_names (str) –
data_unit (str) –
time_step (QuantitativeValue) –
channel_type (ChannelType) –
part_of (Dataset) –

class fairgraph.electrophysiology.PatchedCell(name, brain_location, collection=None, putative_cell_type=None, cell_type=None, morphology_type=None, experiments=None, pipette_id=None, seal_resistance=None, pipette_resistance=None, start_membrane_potential=None, end_membrane_potential=None, pipette_solution=None, liquid_junction_potential=None, labeling_compound=None, reversal_potential_cl=None, description=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

A cell recorded in patch clamp.

Parameters:

name (str) –
brain_location (BrainRegion) –
collection (PatchedCellCollection) –
cell_type (CellType) –
experiments (PatchClampExperiment) –
pipette_id (str, int) –
seal_resistance (QuantitativeValue) –
pipette_resistance (QuantitativeValue) –
liquid_junction_potential (QuantitativeValue) –
start_membrane_potential (QuantitativeValue) –
end_membrane_potential (QuantitativeValue) –
pipette_solution (str) –
labeling_compound (str) –
reversal_potential_cl (QuantitativeValue) –
description (str) –

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)[source]¶: List all objects of this type in the Knowledge Graph

class fairgraph.electrophysiology.PatchedSlice(name, slice, recorded_cells, recording_activity=None, brain_location=None, bath_solution=None, description=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

A slice that has been recorded from using patch clamp.

Parameters:	name (str) – slice (Slice) – recorded_cells (PatchedCellCollection) – recording_activity (PatchClampActivity) – brain_location (BrainRegion) – bath_solution (QuantitativeValue) – description (str) –

class fairgraph.electrophysiology.PatchedCellCollection(name, cells, slice=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

A collection of patched cells.

Parameters:	name (str) – cells (PatchedCell) – slice (PatchedSlice) –

class fairgraph.electrophysiology.CellCulture(name, subject, cells, culturing_activity=None, experiment=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

A cell culture.

Parameters:	name (str) – subject (Subject) – cells (PatchedCell) – culturing_activity (CellCulturingActivity) – experiment (PatchClampActivity) –

class fairgraph.electrophysiology.PatchClampActivity(name, recorded_tissue, recorded_slice=None, protocol=None, people=None, start_time=None, end_time=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

A patch clamp recording session.

Parameters:	name (str) – recorded_tissue (CellCulture, Slice, CranialWindow) – recorded_slice (PatchedSlice) – protocol (str) – people (Person) – start_time (datetime) – end_time (datetime) –

class fairgraph.electrophysiology.PatchClampExperiment(name, recorded_cell, acquisition_device=None, stimulation=None, traces=None, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Stimulation of the neural tissue and recording of the responses during a patch clamp: recording session.

Parameters:	name (str) – recorded_cell (PatchedCell) – acquisition_device (Device) – stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) – traces (Trace, MultiChannelMultiTrialRecording) – start_time (datetime) – end_time (datetime) – people (Person) – protocol (Protocol) –

classmethod from_kg_instance(instance, client, resolved=False)[source]¶: docstring

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)[source]¶: List all objects of this type in the Knowledge Graph

class fairgraph.electrophysiology.QualifiedTraceGeneration(name, stimulus_experiment, sweep, repetition=None, at_time=None, provider_experiment_id=None, provider_experiment_name=None, holding_potential=None, measured_holding_potential=None, input_resistance=None, series_resistance=None, compensation_current=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Additional information about the generation of a single-channel electrophysiology trace.

Parameters:

name (str) –
stimulus_experiment (PatchClampExperiment, IntraCellularSharpElectrodeExperiment) –
sweep (int) –
repetition (int) –
at_time (datetime) –
provider_experiment_id (str) –
provider_experiment_name (str) –
holding_potential (QuantitativeValue) –
measured_holding_potential (QuantitativeValue) –
input_resistance (QuantitativeValue) –
series_resistance (QuantitativeValue) –
compensation_current (QuantitativeValue) –

class fairgraph.electrophysiology.ImplantedBrainTissue(name, subject, implantation_activity=None, experiment=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Brain tissue in which extracellular electrode was implanted.

Parameters:	name (str) – subject (Subject) – implantation_activity (ElectrodeImplantationActivity) – experiment (ExtracellularElectrodeExperiment) –

resolve(client, api='query', use_cache=True)[source]¶: To avoid having to check if a child attribute is a proxy or a real object, a real object resolves to itself.

class fairgraph.electrophysiology.ElectrodeArrayExperiment(name, device=None, implanted_brain_tissues=None, stimulation=None, sensors=None, digitized_head_points_coordinates=None, head_localization_coils_coordinates=None, digitized_head_points=False, digitized_landmarks=False, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Electrode array experiment (EEG, ECoG, MEG, ERP).

Parameters:

name (str) –
device (Device) –
implanted_brain_tissues (ImplantedBrainTissue) –
stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
sensors (Sensor) –
digitized_head_points_coordinates (Sensor) –
head_localization_coils_coordinates (Sensor) –
digitized_head_points (bool) –
digitized_landmarks (bool) –
start_time (datetime) –
end_time (datetime) –
people (Person) –
protocol (Protocol) –

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)[source]¶: List all objects of this type in the Knowledge Graph

class fairgraph.electrophysiology.ECoGExperiment(name, device=None, implanted_brain_tissues=None, stimulation=None, sensors=None, digitized_head_points_coordinates=None, head_localization_coils_coordinates=None, digitized_head_points=False, digitized_landmarks=False, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.ElectrodeArrayExperiment

Electrocorticography experiment.

Parameters:

name (str) –
device (Device) –
implanted_brain_tissues (ImplantedBrainTissue) –
stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
sensors (Sensor) –
digitized_head_points_coordinates (Sensor) –
head_localization_coils_coordinates (Sensor) –
digitized_head_points (bool) –
digitized_landmarks (bool) –
start_time (datetime) –
end_time (datetime) –
people (Person) –
protocol (Protocol) –

class fairgraph.electrophysiology.EEGExperiment(name, device=None, implanted_brain_tissues=None, stimulation=None, sensors=None, digitized_head_points_coordinates=None, head_localization_coils_coordinates=None, digitized_head_points=False, digitized_landmarks=False, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.ElectrodeArrayExperiment

Electroencephalography experiment.

Parameters:

name (str) –
device (Device) –
implanted_brain_tissues (ImplantedBrainTissue) –
stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
sensors (Sensor) –
digitized_head_points_coordinates (Sensor) –
head_localization_coils_coordinates (Sensor) –
digitized_head_points (bool) –
digitized_landmarks (bool) –
start_time (datetime) –
end_time (datetime) –
people (Person) –
protocol (Protocol) –

class fairgraph.electrophysiology.ElectrodePlacementActivity(name, subject, brain_location, device=None, protocol=None, people=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

docstring

Parameters:	name (str) – subject (Subject) – brain_location (BrainRegion) – device (Device) – protocol (Protocol) – people (Person) –

class fairgraph.electrophysiology.ElectrodeImplantationActivity(name, subject, brain_location, implanted_brain_tissues=None, device=None, cranial_window=None, protocol=None, anesthesia=None, start_time=None, end_time=None, people=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.ElectrodePlacementActivity

docstring

Parameters:	name (str) – subject (Subject) – brain_location (BrainRegion) – implanted_brain_tissues (ImplantedBrainTissue) – device (Device) – cranial_window (CranialWindow) – protocol (Protocol) – anesthesia (str) – start_time (datetime) – end_time (datetime) – people (Person) –

class fairgraph.electrophysiology.ExtracellularElectrodeExperiment(name, stimulation=None, recorded_cell=None, traces=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.PatchClampExperiment

Stimulation of the neural tissue and recording of the responses with: an extracellular electrode.

Parameters:	name (str) – stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) – recorded_cell (ImplantedBrainTissue) – traces (Trace) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeRecordedCell(name, brain_location, collection=None, putative_cell_type=None, cell_type=None, morphology_type=None, experiments=None, pipette_id=None, seal_resistance=None, pipette_resistance=None, start_membrane_potential=None, end_membrane_potential=None, pipette_solution=None, liquid_junction_potential=None, labeling_compound=None, reversal_potential_cl=None, description=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.PatchedCell

A cell recorded intracellularly with a sharp electrode.

Parameters:

name (str) –
brain_location (BrainRegion) –
collection (IntraCellularSharpElectrodeRecordedCellCollection) –
cell_type (CellType) –
experiments (IntraCellularSharpElectrodeExperiment) –
pipette_id (str, int) –
seal_resistance (QuantitativeValue) –
pipette_resistance (QuantitativeValue) –
liquid_junction_potential (QuantitativeValue) –
labeling_compound (str) –
reversal_potential_cl (QuantitativeValue) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeRecording(name, recorded_tissue, recorded_slice=None, protocol=None, people=None, start_time=None, end_time=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.PatchClampActivity

A sharp-electrode recording session.

Parameters:	name (str) – recorded_tissue (CellCulture, Slice, CranialWindow) – recorded_slice (IntraCellularSharpElectrodeRecordedSlice) – protocol (str) – people (Person) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeRecordedCellCollection(name, cells, slice=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.PatchedCellCollection

A collection of cells recorded with a sharp electrode.

Parameters:	name (str) – cells (IntraCellularSharpElectrodeRecordedCell) – slice (IntraCellularSharpElectrodeRecordedSlice) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeRecordedSlice(name, slice, recorded_cells, recording_activity=None, brain_location=None, bath_solution=None, description=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.PatchedSlice

A slice that has been recorded from using a sharp electrode.

Parameters:	name (str) – slice (Slice) – recorded_cells (IntraCellularSharpElectrodeRecordedCellCollection) – recording_activity (IntraCellularSharpElectrodeRecording) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeExperiment(name, recorded_cell, acquisition_device=None, stimulation=None, traces=None, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)[source]¶

Bases: fairgraph.electrophysiology.PatchClampExperiment

Stimulation of the neural tissue and recording of the responses with: a sharp intracellular electrode.

Parameters:	name (str) – recorded_cell (IntraCellularSharpElectrodeRecordedCell) – stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) – traces (Trace) – people (Person) –

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)[source]¶: List all objects of this type in the Knowledge Graph

class fairgraph.electrophysiology.QualifiedMultiTraceGeneration(name, stimulus_experiment, sweeps, channel_type=None, holding_potential=None, sampling_frequency=None, power_line_frequency=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Parameters:	name (str) – stimulus_experiment (ExtracellularElectrodeExperiment, IntraCellularSharpElectrodeExperiment, PatchClampExperiment, ElectrodeArrayExperiment) – sweeps (int) – channel_type (str) – holding_potential (QuantitativeValue) – sampling_frequency (QuantitativeValue) – power_line_frequency (QuantitativeValue) –

class fairgraph.electrophysiology.CellCulturingActivity(subject, cell_culture, brain_location=None, culture_type=None, culture_age=None, hemisphere=None, culture_solution=None, start_time=None, end_time=None, people=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

The activity of preparing a cell culture from whole brain.

Parameters:	subject (Subject) – cell_culture (CellCulture) – brain_location (BrainRegion) – culture_type (CultureType) – culture_age (QuantitativeValueRange) – hemisphere (str) – culture_solution (str) – start_time (datetime) – end_time (datetime) – people (Person) –

resolve(client, api='query', use_cache=True)[source]¶: To avoid having to check if a child attribute is a proxy or a real object, a real object resolves to itself.

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

fairgraph.electrophysiology.use_namespace(namespace)[source]¶: Set the namespace for all classes in this module.

brainsimulation¶

Metadata for model building, simulation and validation.

class fairgraph.brainsimulation.ModelProject(name, owners, authors, description, date_created, private, collab_id=None, alias=None, organization=None, pla_components=None, brain_region=None, species=None, celltype=None, abstraction_level=None, model_of=None, old_uuid=None, parents=None, instances=None, images=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject, fairgraph.base.HasAliasMixin

Representation of a neuroscience model or modelling project.

We distinguish a model in an abstract sense (this class), which may have multiple parameterizations and multiple implementations, from a specific version and parameterization of a model - see ModelInstance and ModelScript

Parameters:

name (str) –
owners (Person) –
authors (Person) –
description (str) –
date_created (datetime) –
private (bool) –
collab_id (str) –
alias (str) –
organization (Organization) –
pla_components (str) –
brain_region (BrainRegion) –
species (Species) –
celltype (CellType) –
abstraction_level (AbstractionLevel) –
model_of (ModelScope) –
old_uuid (str) –
parents (ModelProject) –
instances (ModelInstance, MEModel) –
images (dict) –

class fairgraph.brainsimulation.ModelInstance(name, main_script, version, timestamp=None, brain_region=None, species=None, model_of=None, release=None, part_of=None, description=None, parameters=None, old_uuid=None, alternate_of=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

A specific implementation, code version and parameterization of a model.

See also: ModelProject, MEModel, ModelScript

Parameters:

name (str) –
brain_region (BrainRegion) –
species (Species) –
model_of (CellType, BrainRegion) –
main_script (ModelScript) –
release (str) –
version (str) –
timestamp (datetime) –
part_of (KGObject) –
description (str) –
parameters (str) –
old_uuid (str) –
alternate_of (KGObject) –

class fairgraph.brainsimulation.MEModel(name, e_model, morphology, main_script, version, timestamp=None, brain_region=None, species=None, model_of=None, release=None, part_of=None, description=None, parameters=None, old_uuid=None, alternate_of=None, id=None, instance=None)[source]¶

Bases: fairgraph.brainsimulation.ModelInstance

A specific implementation, code version and parameterization of a single neuron model

with a defined morphology (M) and electrical (E) behaviour.

This is a specialized sub-class of ModelInstance.

Parameters:

name (str) –
brain_region (BrainRegion) –
species (Species) –
model_of (CellType, BrainRegion) –
main_script (ModelScript) –
release (str) –
version (str) –
timestamp (datetime) –
part_of (KGObject) –
description (str) –
parameters (str) –
old_uuid (str) –
alternate_of (KGObject) –
morphology (Morphology) –
e_model (EModel) –

class fairgraph.brainsimulation.Morphology(name, cell_type=None, morphology_file=None, distribution=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

The morphology of a single neuron model, typically defined as a set of cylinders or: truncated cones connected in a tree structure.

Parameters:	name (str) – cell_type (CellType) – distribution (Distribution) –

class fairgraph.brainsimulation.ModelScript(name, code_location=None, code_format=None, license=None, distribution=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Code or markup defining all or part of a model.

See also: ModelInstance, MEModel, EModel

Parameters:	name (str) – code_format (str) – license (str) – distribution (Distribution) –

class fairgraph.brainsimulation.EModel(name, main_script=None, version=None, timestamp=None, brain_region=None, species=None, model_of=None, release=None, part_of=None, description=None, parameters=None, old_uuid=None, id=None, instance=None)[source]¶

Bases: fairgraph.brainsimulation.ModelInstance

The electrical component of an MEModel

Parameters:	name (str) – brain_region (BrainRegion) – species (Species) – model_of (CellType, BrainRegion) – main_script (ModelScript) – release (str) – version (str) – timestamp (datetime) – part_of (KGObject) – description (str) – parameters (str) – old_uuid (str) –

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

Bases: fairgraph.base.KGObject, fairgraph.base.HasAliasMixin

Definition of a model validation test.

See also: ValidationScript, ValidationActivity, ValidationResult

Parameters:

name (str) –
authors (Person) –
description (str) –
date_created (date, datetime) –
alias (str) –
brain_region (BrainRegion) –
species (Species) –
celltype (CellType) –
test_type (str) –
age (Age) –
reference_data (KGObject) –
data_type (str) –
recording_modality (str) –
score_type (str) –
status (str) –
old_uuid (str) –

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

Bases: fairgraph.base.KGObject

Code implementing a particular model validation test.

See also: ValidationTestDefinition, ValidationActivity,

ValidationResult

Parameters:	name (str) – date_created (date, datetime) – repository (IRI) – version (str) – description (str) – parameters (str) – test_class (str) – test_definition (ValidationTestDefinition) – old_uuid (str) –

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

Bases: fairgraph.base.KGObject

The results of running a model validation test.

Including a numerical score, and optional additional data.

See also: ValidationTestDefinition, ValidationScript, ValidationActivity.

Parameters:	name (str) – generated_by (ValidationActivity) – description (str) – score (float, int) – normalized_score (float, int) – passed (bool) – timestamp (date, datetime) – additional_data (KGObject) – old_uuid (str) – collab_id (str) – hash (str) –

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

Bases: fairgraph.base.KGObject

Record of the validation of a model against experimental data.

Links a ModelInstance, a ValidationTestDefinition and a reference data set to a ValidationResult.

Parameters:	model_instance (ModelInstance, MEModel) – test_script (ValidationScript) – reference_data (Collection) – timestamp (datetime) – result (ValidationResult) – started_by (Person) – end_timestamp (datetime) –

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

Bases: fairgraph.base.KGObject

Parameters:

name (str) –
description (str) –
identifier (str) –
model_instance (ModelInstance, MEModel) –
config (SimulationConfiguration) –
timestamp (datetime) –
result (SimulationOutput) –
started_by (Person) –
end_timestamp (datetime) –
computing_environment (ComputingEnvironment) –
status (str) –
resource_usage (float) –
tags (str) –
job_id (str) –

class fairgraph.brainsimulation.SimulationConfiguration(name, config_file=None, description=None, identifier=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Parameters:	name (str) – identifier (str) – description (str) – config_file (Distribution, str) –

save(client)[source]¶: docstring

class fairgraph.brainsimulation.SimulationOutput(name, identifier=None, result_file=None, generated_by=None, derived_from=None, data_type=None, variable=None, target=None, description=None, timestamp=None, brain_region=None, species=None, celltype=None, id=None, instance=None)[source]¶

Bases: fairgraph.base.KGObject

Parameters:	name (str) – description (str) – identifier (str) – result_file (Distribution, str) – generated_by (Simulation) – derived_from (KGObject) – target (str) – data_type (str) – timestamp (datetime) – brain_region (BrainRegion) – species (Species) – celltype (CellType) –

save(client)[source]¶: docstring

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

fairgraph.brainsimulation.use_namespace(namespace)[source]¶: Set the namespace for all classes in this module.

software¶

Metadata about, or related to, software

class fairgraph.software.SoftwareCategory(label, iri=None, strict=False)[source]¶: Bases: fairgraph.base.OntologyTerm

class fairgraph.software.OperatingSystem(label, iri=None, strict=False)[source]¶: Bases: fairgraph.base.OntologyTerm

class fairgraph.software.ProgrammingLanguage(label, iri=None, strict=False)[source]¶: Bases: fairgraph.base.OntologyTerm

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

Bases: fairgraph.base.KGObject

Parameters:	identifier (str) – name (str) – description (str) – parent (SoftwareFeatureCategory) –

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

Bases: fairgraph.base.KGObject

Parameters:	name (str) – description (str) – category (SoftwareFeatureCategory) – identifier (str) –

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

Bases: fairgraph.base.KGObject

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

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

Bases: fairgraph.base.KGObject

Parameters:

name (str) –
description (str) –
citation (str) –
release_date (date) –
categories (SoftwareCategory) –
license (License) –
operating_system (OperatingSystem) –
release_notes (IRI) –
requirements (str) –
summary (str) –
contributors (Person) –
copyright (Person, Organization) –
homepage (IRI) –
documentation (IRI) –
help (IRI) –
source_code (IRI) –
programming_languages (ProgrammingLanguage) –
funding (Organization) –
components (Software) –
is_free (bool) –
keywords (Keyword) –
version (str) –
features (SoftwareFeature) –

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

fairgraph.software.use_namespace(namespace)[source]¶: Set the namespace for all classes in this module.

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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶: List all objects of this type in the Knowledge Graph

resolve(client, api='query', use_cache=True)[source]¶: 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)[source]¶

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)[source]¶: 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)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

Bases: fairgraph.base.KGObject

A collection of other metadata objects

Parameters:	name (str) – members (KGObject) –

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

fairgraph.core.use_namespace(namespace)[source]¶: Set the namespace for all classes in this module.

commons¶

class fairgraph.commons.Address(locality, country)[source]¶: Bases: fairgraph.base.StructuredMetadata

class fairgraph.commons.Group(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

The subject group

class fairgraph.commons.CultureType(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

The type of cell culture used

class fairgraph.commons.Species(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

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

class fairgraph.commons.Shape(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

Shape of a region of interest (ROI).

class fairgraph.commons.MorphologyType(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

The morphology of the cell used for recording.

class fairgraph.commons.SomaType(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

The type of soma of a reconstructed cell.

class fairgraph.commons.ObjectiveType(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

The type of objective used for microscopy.

class fairgraph.commons.Strain(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

An inbred sub-population within a species.

class fairgraph.commons.Genotype(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

Transgenic modification of the strain.

class fairgraph.commons.Sex(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

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

class fairgraph.commons.Handedness(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

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

class fairgraph.commons.ChannelType(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

The recording method used.

class fairgraph.commons.BrainRegion(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

A sub-structure or region with the brain.

class fairgraph.commons.CellType(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

A type of neuron or glial cell.

class fairgraph.commons.AbstractionLevel(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

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

class fairgraph.commons.ModelScope(label, iri=None, strict=False)[source]¶

Bases: fairgraph.base.OntologyTerm

docstring

class fairgraph.commons.License(label, iri=None, strict=False)[source]¶: Bases: fairgraph.base.OntologyTerm

class fairgraph.commons.StimulusType(label, iri=None, strict=False)[source]¶: Bases: fairgraph.base.OntologyTerm

class fairgraph.commons.Origin(label, iri=None, strict=False)[source]¶: Bases: fairgraph.base.OntologyTerm

class fairgraph.commons.QuantitativeValue(value, unit_text, unit_code=None)[source]¶

Bases: fairgraph.base.StructuredMetadata

docstring

class fairgraph.commons.QuantitativeValueRange(min, max, unit_text, unit_code=None)[source]¶

Bases: fairgraph.base.StructuredMetadata

docstring

class fairgraph.commons.Age(value, period)[source]¶

Bases: fairgraph.base.StructuredMetadata

Parameters:	value (str) – period (str) –

fairgraph currently provides the following modules for working with KG v2:

minds: “Minimal Information for Neuroscience DataSets” - metadata common to all neuroscience datasets independent of the type of investigation
uniminds: an updated version of MINDS
electrophysiology: metadata relating to patch clamp and sharp electrode intracellular recordings in vitro. Support for extracellular recording, tetrodes, multi-electrode arrays and in vivo recordings coming soon.
brainsimulation: metadata relating to modelling, simulation and validation
software: metadata relating to software used in neuroscience (for simulation, data analysis, stimulus presentation, etc.)
core: metadata for entities that are used in multiple contexts (e.g. in both electrophysiology and in simulation).
commons: metadata that are not specific to EBRAINS, typically these refer to URIs in standard ontologies, outside the Knowledge Graph.

Additional modules are planned, e.g. for fMRI, functional optical imaging. In addition, the base, commons, and utility modules provide additional tools for structuring metadata and for working with fairgraph objects.

Access permissions¶

Before accessing the Human Brain Project/EBRAINS Knowledge Graph through fairgraph, you must read and accept the Terms of Use, and then e-mail support@ebrains.eu to request access.

Contributing to fairgraph¶

Todo

add information about creating tickets, sending feedback, and a developers’ guide.

Getting help¶

In case of questions about fairgraph, please contact us via https://ebrains.eu/support/. If you find a bug or would like to suggest an enhancement or new feature, please open a ticket in the issue tracker.

Authors / contributors¶

The following people have contributed to fairgraph. Their affiliations at the time of the contributions are shown below.

Andrew Davison [1]
Onur Ates [1]
Yann Zerlaut [1]
Nico Feld [2]
Glynis Mattheisen[1]

Department of Integrative and Computational Neuroscience, Paris-Saclay Institute of Neuroscience, CNRS/Université Paris Saclay
Human-Computer Interaction, Department IV, Computer Science, Universität Trier

Acknowledgements¶

<div><img src=”https://www.braincouncil.eu/wp-content/uploads/2018/11/wsi-imageoptim-EU-Logo.jpg”: alt=”EU Logo” height=”23%” width=”15%” align=”right” style=”margin-left: 10px”></div>

This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270, No. 785907 and No. 945539 (Human Brain Project SGA1, SGA2 and SGA3).

Quickstart¶

Installation¶

To get the latest release:

pip install fairgraph

To get the development version:

git clone https://github.com/HumanBrainProject/fairgraph.git
pip install -r ./fairgraph/requirements.txt
pip install -U ./fairgraph

Basic setup¶

The basic idea of the library is to represent metadata nodes from the Knowledge Graph as Python objects. Communication with the Knowledge Graph service is through a client object, for which an access token associated with an EBRAINS account is needed.

If you are working in a Collaboratory Jupyter notebook, the client will take its access token from the notebook automatically:

from fairgraph import KGClient

client = KGClient()

If working outside the Collaboratory, you will need to obtain a token (for example from the KG Editor if you are a curator, or using clb_oauth.get_token() in a Collaboratory Jupyter notebook) and save it as an environment variable, e.g. at a shell prompt:

export KG_AUTH_TOKEN=eyJhbGci...nPq

and then in Python:

token = os.environ['KG_AUTH_TOKEN']

Once you have a token:

from fairgraph import KGClient

client = KGClient(token)

Retrieving metadata from the Knowledge Graph¶

The different metadata/data types available in the Knowledge Graph are grouped into modules within the openminds module. For example:

from fairgraph.openminds.core import DatasetVersion

Using these classes, it is possible to list all metadata matching a particular criterion, e.g.:

datasets = DatasetVersion.list(client, from_index=10, size=10)

If you know the unique identifier of an object, you can retrieve it directly:

dataset_of_interest = Dataset.from_id("153ec151-b1ae-417b-96b5-4ce9950a3c56", client)
dataset_of_interest.show()

Links between metadata in the Knowledge Graph are not followed automatically, to avoid unnecessary network traffic, but can be followed with the resolve() method:

dataset_license = dataset_of_interest.license.resolve(client)

The associated metadata are accessible as attributes of the Python objects, e.g.:

print(dataset_of_interest.description)

You can also access any associated data:

print(dataset.files)
dataset.download(dataset.files[0])

Advanced queries¶

While certain filters and queries are built in (such as the filter by brain region, above), more complex queries are possible using the Nexus query API.

from fairgraph.base import KGQuery
from fairgraph.minds import Dataset

query = {
   "path": "minds:specimen_group / minds:subjects / minds:samples / minds:methods / schema:name",
   "op": "in",
   "value": ["Electrophysiology recording",
            "Voltage clamp recording",
            "Single electrode recording",
            "functional magnetic resonance imaging"]
}
context = {
            "schema": "http://schema.org/",
            "minds": "https://schema.hbp.eu/minds/"
}

activity_datasets = KGQuery(Dataset, query, context).resolve(client)
for dataset in activity_datasets:
   print("* " + dataset.name)

Storing and editing metadata¶

For those users who have the necessary permissions to store and edit metadata in the Knowledge Graph, fairgraph objects can be created or edited in Python, and then saved back to the Knowledge Graph, e.g.:

from fairgraph.core import Person, Organization, use_namespace
from fairgraph.commons import Address

use_namespace("neuralactivity")

mgm = Organization("Metro-Goldwyn-Mayer")
mgm.save(client)
author = Person("Laurel", "Stan", "laurel@example.com", affiliation=mgm)
author.save(client)

mgm.address = Address(locality='Hollywood', country='United States')
mgm.save(client)

Getting help¶

In case of questions about fairgraph, please e-mail support@humanbrainproject.eu. If you find a bug or would like to suggest an enhancement or new feature, please open a ticket in the issue tracker.

Acknowledgements¶

This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270 and No. 785907 (Human Brain Project SGA1 and SGA2).