WARNING: DEPRECATED REPOSITORY

openMINDS moved now to a new GitHub organization: https://github.com/openMetadataInitiative

This movement led to a couple of changes. SUMMARY OF CHANGES:

• ➡️ https://github.com/openMetadataInitiative/openMINDS
  • branch 'main' contains vocabulary and fully extended openMINDS schemas in openMINDS syntax
  • fully extended openMINDS schemas in openMINDS syntax use the extension *.schema.omi.json
  • schemas are build for openMINDS versions in dedicated folders in branch 'main'
  • code for gathering and extending schemas in the main branch is located in branch 'pipeline'
• ➡️ https://github.com/openMetadataInitiative/openMINDS_json-schema
  • branch 'main' contains extended openMINDS schemas (per openMINDS version) formatted in JSON-Schema
  • code for reformmating schemas is located in branch 'pipeline'
• ➡️ https://github.com/openMetadataInitiative/openMINDS_instances
  • branch 'main' contains libraries of controlled metadata instances and graph structures for selected schemas across openMINDS metadata models
  • instances and graph strucutres are build for openMINDS versions in dedicated folders in branch 'main'
• ➡️ https://github.com/openMetadataInitiative/openMINDS_Python
  • branch 'main' contains extended openMINDS schemas (per openMINDS version) coded as Python classes plus other code for openMINDS Python package
  • code for building openMINDS schema classes is located in branch 'pipeline'
• ➡️ https://github.com/openMetadataInitiative/openMINDS_MATLAB
  • branch 'main' contains extended openMINDS schemas (per openMINDS version) coded as Python classes plus other code for openMINDS MATLAB package
  • code for building openMINDS schema classes is located in branch 'pipeline'
• ➡️ https://github.com/openMetadataInitiative/openMINDS_documentation
  • builds the documentation for openMINDS on Read-The-Docs (https://openminds-documentation.readthedocs.io)

openMINDS_instances

The openMINDS_instances repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It contains well defined metadata representations (JSON-LDs) that are most likely to be reused across different research products. Currently, openMINDS provides predefined instances for all ControlledTerms, Licence, and ContentType schemas.

How to request new instances? Requests for adding new instances to this libraray can be made by getting in touch with the openMINDS development team (through the Issues or the support email: coming soon). The team will attend to a request as soon as possible. Note that instances should be well defined to be useful for the community. They should at least provide a one sentence definition, and where applicable a reference to a matching ontology term (for ControlledTerms) or another official resource (e.g., IANA for ContentType or SPDX for License). If you would like to contribute, cf. also CONTRIBUTING.

How to correctly define an openMINDS instance? openMINDS instances are written as JSON-LDs. A correctly instantiated openMINDS JSON-LD should always contain the following technical attributes, and at least the required properties of the respective schema type they are validated against:

{
  "@context": {
    "@vocab": "https://openminds.ebrains.eu/vocab/"
  },
  "@type": "OPENMINDS_SCHEMA_TYPE",
  "@id": "https://openminds.ebrains.eu/instances/OPENMINDS_SCHEMA_NAME/HUMAN_READABLE_INSTANCE_ID",
  "PROPERTY_NAME": "METADATA_VALUE"
}

The values written in capital letters need to be replaced accordingly. Here a full example of an instance for an openMINDS_controlledTerms schema type (cf. /instances/species/homoSapiens.jsonld):

{
  "@context": {
    "@vocab": "https://openminds.ebrains.eu/vocab/"
  },
  "@id": "https://openminds.ebrains.eu/instances/species/homoSapiens",
  "@type": "https://openminds.ebrains.eu/controlledTerms/Species",
  "definition": "The species *Homo sapiens* (humans) belongs to the family of *hominidae* (great apes).",
  "description": null,
  "interlexIdentifier": "http://uri.interlex.org/base/ilx_0105114",
  "knowledgeSpaceLink": "https://knowledge-space.org/wiki/NCBITaxon:9606#human",
  "name": "Homo sapiens",
  "preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/NCBITaxon_9606",
  "synonym": [
    "Homo sapien",
    "human",
    "man"
  ] 
}

Note that properties that are defined as optional in an openMINDS schema can either be provided with a null value in the JSON-LD or left out completely.

License

The work on this GitHub repository is licensed under the MIT License.