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openminds_matlab

A MATLAB toolbox for generating openMINDS-compliant linked metadata.

https://github.com/openmetadatainitiative/openminds_matlab

Science Score: 26.0%

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Keywords

linked-data metadata neuroscience openminds programming-package target
Last synced: 4 months ago · JSON representation

Repository

A MATLAB toolbox for generating openMINDS-compliant linked metadata.

Basic Info
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  • Open Issues: 12
  • Releases: 8
Topics
linked-data metadata neuroscience openminds programming-package target
Created over 2 years ago · Last pushed 4 months ago
Metadata Files
Readme License Codemeta

README.md

openMINDS-MATLAB-logo

openMINDS Metadata Models for MATLAB

Version Number Open in MATLAB Online View openMINDS_MATLAB on File Exchange MATLAB Tests codecov MATLAB Code Issues Maintenance

Requirements and Installation • Before you start • Getting Started • Acknowledgements

MATLAB toolbox for creating openMINDS compliant linked metadata, supporting import and export of metadata instances in JSON-LD format.

To learn more about the openMINDS metadata framework please go to :arrowright: ReadTheDocs.
You can test and learn how to use openMINDS in MATLAB by going through a small :arrowright: DEMO on MATLAB Online.

MathWorks provides a free basic version of MATLAB Online, but you need to register for a MathWorks Account.

Requirements and Installation

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openMINDS for MATLAB requires MATLAB R2022b or later. The toolbox can be installed from MATLAB's Add-On Explorer (recommended). It is also possible to download the MATLAB toolbox from FileExchange or from the Releases page of this repository and install it manually. If you are new to MATLAB, see the detailed installation instructions

Cloning the repository

matlab % This will install openMINDS_MATLAB in your current working directory !git clone https://github.com/openMetadataInitiative/openMINDS_MATLAB run(fullfile('openMINDS_MATLAB', 'code', 'setup.m'))

Before you start

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matlab % Verify that openMINDS_MATLAB is installed disp( openminds.toolboxversion )

TextOutput Version 0.9.1

If you have installed openMINDS_MATLAB and the above command does not work, most likely openMINDS_MATLAB is not added to MATLAB's search path.

Getting Started

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See also: Crew Member Collection Tutorial

Configure MATLAB's path to use the latest model versions

matlab % Schema classes for all the openMINDS model versions are available in this % toolbox. To ensure the latest version is used, run the following command: openminds.version("latest")

Import schemas from the core model

matlab import openminds.core.*

Create a Subject

matlab % Create a new demo subject subject1 = Subject('species', 'musMusculus', 'biologicalSex', 'male', 'lookupLabel', 'demo_subject1'); disp(subject1)

TextOutput Subject (https://openminds.ebrains.eu/core/Subject) with properties: biologicalSex: male (BiologicalSex) internalIdentifier: "" isPartOf: [None] (SubjectGroup) lookupLabel: "demo_subject1" species: Mus musculus (One of: Species, Strain) studiedState: [None] (SubjectState) Required Properties: species, studiedState

Create a Subject State

matlab subjectState = openminds.core.SubjectState('lookupLabel', 'demo_state')

TextOutput subjectState = SubjectState (https://openminds.ebrains.eu/core/SubjectState) with properties: additionalRemarks: "" age: [None] (One of: QuantitativeValue, QuantitativeValueRange) ageCategory: [None] (AgeCategory) attribute: [None] (SubjectAttribute) descendedFrom: [None] (SubjectState) handedness: [None] (Handedness) internalIdentifier: "" lookupLabel: "demo_state" pathology: [None] (Any of: Disease, DiseaseModel) relativeTimeIndication: [None] (One of: QuantitativeValue, QuantitativeValueRange) weight: [None] (One of: QuantitativeValue, QuantitativeValueRange) Required Properties: ageCategory

matlab % Add subject state to subject subject1.studiedState = subjectState; disp(subject1)

TextOutput Subject (https://openminds.ebrains.eu/core/Subject) with properties: biologicalSex: male (BiologicalSex) internalIdentifier: "" isPartOf: [None] (SubjectGroup) lookupLabel: "demo_subject1" species: Mus musculus (One of: Species, Strain) studiedState: demo_state (SubjectState) Required Properties: species, studiedState

```matlab % Update the value of the lookup label subjectState.lookupLabel = "demosubjectstatepre_recording";

% Create a new subject state subjectStatePost = openminds.core.SubjectState('lookupLabel', 'demosubjectstatepost_recording') ```

TextOutput subjectStatePost = SubjectState (https://openminds.ebrains.eu/core/SubjectState) with properties: additionalRemarks: "" age: [None] (One of: QuantitativeValue, QuantitativeValueRange) ageCategory: [None] (AgeCategory) attribute: [None] (SubjectAttribute) descendedFrom: [None] (SubjectState) handedness: [None] (Handedness) internalIdentifier: "" lookupLabel: "demo_subjectstate_post_recording" pathology: [None] (Any of: Disease, DiseaseModel) relativeTimeIndication: [None] (One of: QuantitativeValue, QuantitativeValueRange) weight: [None] (One of: QuantitativeValue, QuantitativeValueRange) Required Properties: ageCategory

matlab % Append the new subject state to the subject's studiedState property subject1.studiedState(end+1) = subjectStatePost; disp(subject1)

TextOutput Subject (https://openminds.ebrains.eu/core/Subject) with properties: biologicalSex: male (BiologicalSex) internalIdentifier: "" isPartOf: [None] (SubjectGroup) lookupLabel: "demo_subject1" species: Mus musculus (One of: Species, Strain) studiedState: [demo_subjectstate_pre_recording demo_subjectstate_post_recording] (SubjectState) Required Properties: species, studiedState

Detailed Installation Instructions

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The easiest way to install the openMINDS for MATLAB is to use the Add-on Explorer: 1. Launch the Add-on Explorer from MATLAB's Home tab. Click Add-Ons -> Get Add-Onsopenminds_installation_step1 2. Search for "openminds" 3. Select openMINDS Metadata Models for MATLABopenminds_installation_step2 4. Press the "Add" button.openminds_installation_step4

Acknowledgements

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EU Logo

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. 945539 (Human Brain Project SGA3).

Owner

  • Name: openMetadataInitiative
  • Login: openMetadataInitiative
  • Kind: organization

CodeMeta (codemeta.json) 

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "license": "https://spdx.org/licenses/MIT",
  "isPartOf": "https://github.com/openMetadataInitiative",
  "codeRepository": "https://github.com/openMetadataInitiative/openMINDS_MATLAB",
  "contIntegration": "https://github.com/openMetadataInitiative/openMINDS_MATLAB/actions",
  "issueTracker": "https://github.com/openMetadataInitiative/openMINDS_MATLAB/issues",
  "name": "openMINDS MATLAB",
  "description": "openMINDS MATLAB is a toolbox to support the creation and use of openMINDS metadata models and schemas in MATLAB, with import and export in JSON-LD format. The package contains all openMINDS schemas as MATLAB classes in addition to schema base classes and utility methods.",
  "applicationCategory": "neuroscience",
  "releaseNotes": "https://github.com/openMetadataInitiative/openMINDS_MATLAB/releases",
  "funding": "https://cordis.europa.eu/project/id/945539",
  "developmentStatus": "active",
  "funder": {
    "@type": "Organization",
    "name": "European Commission"
  },
  "programmingLanguage": [
    "MATLAB"
  ],
  "operatingSystem": [
    "Linux",
    "Windows",
    "macOS"
  ],
  "softwareRequirements": [
    "MATLAB R2022b or later"
  ],
  "relatedLink": [
    "https://openminds-documentation.readthedocs.io"
  ],
  "author": [
    {
      "@type": "Person",
      "@id": "https://orcid.org/0000-0002-8297-1753",
      "givenName": "Eivind",
      "familyName": "Hennestad"
    }
  ],
  "version": "0.9.7",
  "downloadUrl": "https://github.com/openMetadataInitiative/openMINDS_MATLAB/releases/download/v0.9.7/openMINDS_MATLAB_v0_9_7.mltbx",
  "dateModified": "2025-10-15"
}

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