Metadata domains¶

fairgraph supports both openMINDS v4 and v5 schemas. By default, modules are imported from v4 for backwards compatibility:

import fairgraph.openminds.core as omcore          # v4 (default)
import fairgraph.openminds.v4.core as omcore4      # explicit v4
import fairgraph.openminds.v5.core as omcore5      # explicit v5

The two versions are entirely separate sets of classes: a v4 Person and a v5 Person are different Python classes, even though they share the same @type URI in the Knowledge Graph. Since the URI alone cannot tell them apart, the client has to be told which version to deserialize responses into, via the openminds_version argument. Omitting it keeps the v4 behaviour:

from fairgraph import KGClient
import fairgraph.openminds.v5.core as omcore

client = KGClient(host=host_serving_v5_metadata, openminds_version="v5")
people = omcore.Person.list(client)

Take care to import the classes you use from the same version the client was created with: passing a v4 class to a v5 client (or vice versa) will query for the wrong properties.

Note

The migration of the EBRAINS Knowledge Graph to openMINDS v5 is still in progress. The production and pre-production deployments serve openMINDS v4, which is what you should use against them. v5 metadata is so far only available from a development deployment with restricted access; if you need to work against it, contact EBRAINS Support.

openMINDS v4¶

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.controlled_terms: covers consistent definition of neuroscience terms.
openminds.chemicals: covers chemical substances and mixtures used in neuroscience.
openminds.computation: covers provenance of simulations, data analysis and visualizations in neuroscience.
openminds.ephys: covers in-depth metadata for electrophysiology recordings, extending the basic information in openMINDS/core.
openminds.specimen_prep: covers in-depth metadata for the preparation of specimens (e.g. cell culture, surgical procedures, tissue slicing).
openminds.stimulation: covers in-depth metadata about stimulation protocols in neuroscience experiments.
openminds.publications: covers scientific publications, particularly interactive publications such as live papers.

openMINDS v5¶

Warning

openMINDS v5 support is experimental.

The v5 classes have not yet been exercised against a fully populated Knowledge Graph (see the note above), so problems may remain that only real data will reveal. Until the KG migration completes, v5 support may be changed in backwards-incompatible ways in any release, without the deprecation period that applies to the rest of the API.

openMINDS v4 support is unaffected and remains the default. If you use v5 and hit a problem, please report it.

v5 includes all v4 modules plus a new neuroimaging module. Some classes have been renamed (e.g. BrainAtlas → AnatomicalAtlas), and new classes have been added.

openminds.v5.core: covers general origin, location and content of research products.
openminds.v5.sands: covers brain atlases, as well as anatomical locations and relations of non-atlas data.
openminds.v5.controlled_terms: covers consistent definition of neuroscience terms.
openminds.v5.chemicals: covers chemical substances and mixtures used in neuroscience.
openminds.v5.computation: covers provenance of simulations, data analysis and visualizations in neuroscience.
openminds.v5.ephys: covers in-depth metadata for electrophysiology recordings, extending the basic information in openMINDS/core.
openminds.v5.specimen_prep: covers in-depth metadata for the preparation of specimens (e.g. cell culture, surgical procedures, tissue slicing).
openminds.v5.stimulation: covers in-depth metadata about stimulation protocols in neuroscience experiments.
openminds.v5.publications: covers scientific publications, particularly interactive publications such as live papers.
openminds.v5.neuroimaging: covers in-depth metadata for neuroimaging data, particularly MRI acquisitions and devices.