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openMINDS pipeline
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+158
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‎schemas/v3.0/stimulation/activity/stimulationActivity.schema.omi.json‎

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@@ -84,8 +84,10 @@
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"type": "string"
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},
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"https://openminds.ebrains.eu/vocab/output": {
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"_instruction": "Add all states of the specimen(s) that were stimulated as a result of this activity.",
87+
"_instruction": "Add all states of the specimen(s) that were stimulated as a result of this activity, and all files or file bundles generated.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File",
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"https://openminds.ebrains.eu/core/FileBundle",
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"https://openminds.ebrains.eu/core/SubjectGroupState",
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"https://openminds.ebrains.eu/core/SubjectState",
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"https://openminds.ebrains.eu/core/TissueSampleCollectionState",
@@ -169,11 +171,14 @@
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},
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"https://openminds.ebrains.eu/vocab/stimulus": {
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"_instruction": "Add all stimuli used during this activity.",
172-
"_linkedTypes": [],
174+
"_linkedTypes": [
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"https://openminds.ebrains.eu/stimulation/EphysStimulus"
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],
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"label": "Stimulus",
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"labelPlural": "Stimuli",
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"minItems": 1,
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"name": "stimulus",
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"nameForReverseLink": null,
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"namePlural": "stimuli",
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"type": "array",
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"uniqueItems": true

‎schemas/v3.0/stimulation/stimulus/ephysStimulus.schema.omi.json‎

Lines changed: 94 additions & 1 deletion
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@@ -1,9 +1,99 @@
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{
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"_categories": [
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"stimulus"
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],
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"_module": "stimulation",
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"_type": "https://openminds.ebrains.eu/stimulation/EphysStimulus",
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"label": "Ephys stimulus",
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"name": "EphysStimulus",
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"properties": {
10+
"https://openminds.ebrains.eu/vocab/deliveredBy": {
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"_instruction": "Add the device used to deliver this stimulus.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/ephys/ElectrodeArrayUsage",
14+
"https://openminds.ebrains.eu/ephys/ElectrodeUsage",
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"https://openminds.ebrains.eu/ephys/PipetteUsage",
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"https://openminds.ebrains.eu/specimenPrep/SlicingDeviceUsage"
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],
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"label": "Delivered by",
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"labelPlural": "Delivered by",
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"name": "deliveredBy",
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"nameForReverseLink": null,
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"namePlural": "deliveredBy"
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},
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"https://openminds.ebrains.eu/vocab/description": {
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"_instruction": "Enter a short text describing this stimulus.",
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"description": "Longer statement or account giving the characteristics of someone or something.",
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"formatting": "text/markdown",
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"label": "Description",
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"labelPlural": "Descriptions",
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"multiline": true,
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"name": "description",
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"namePlural": "descriptions",
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"type": "string"
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},
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"https://openminds.ebrains.eu/vocab/epoch": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the total epoch length of this stimulus.",
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"label": "Epoch",
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"name": "epoch",
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"nameForReverseLink": null
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},
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"https://openminds.ebrains.eu/vocab/generatedBy": {
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"_instruction": "Add the device used to generate this stimulus.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/ephys/ElectrodeArrayUsage",
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"https://openminds.ebrains.eu/ephys/ElectrodeUsage",
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"https://openminds.ebrains.eu/ephys/PipetteUsage",
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"https://openminds.ebrains.eu/specimenPrep/SlicingDeviceUsage"
51+
],
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"label": "Generated by",
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"labelPlural": "Generated by",
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"name": "generatedBy",
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"nameForReverseLink": null,
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"namePlural": "generatedBy"
57+
},
58+
"https://openminds.ebrains.eu/vocab/internalIdentifier": {
59+
"_instruction": "Enter the identifier (or label) of this stimulus that is used within the corresponding data files to identify this stimulus.",
60+
"description": "Term or code that identifies someone or something within a particular product.",
61+
"formatting": "text/plain",
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"label": "Internal identifier",
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"labelPlural": "Internal identifiers",
64+
"multiline": false,
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"name": "internalIdentifier",
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"namePlural": "internalIdentifiers",
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"type": "string"
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},
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"https://openminds.ebrains.eu/vocab/lookupLabel": {
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"_instruction": "Enter a lookup label for this stimulus that may help you to find this instance more easily.",
71+
"formatting": "text/plain",
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"label": "Lookup label",
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"labelPlural": "Lookup labels",
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"multiline": false,
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"name": "lookupLabel",
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"namePlural": "lookupLabels",
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"type": "string"
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},
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"https://openminds.ebrains.eu/vocab/specification": {
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"_instruction": "Add the specification information for this stimulus.",
81+
"_linkedTypes": [
82+
"https://openminds.ebrains.eu/core/Configuration",
83+
"https://openminds.ebrains.eu/core/File",
84+
"https://openminds.ebrains.eu/core/FileBundle",
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"https://openminds.ebrains.eu/core/PropertyValueList"
86+
],
87+
"description": "Detailed and precise presentation of, or proposal for something.",
88+
"label": "Specification",
89+
"labelPlural": "Specifications",
90+
"minItems": 1,
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"name": "specification",
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"nameForReverseLink": null,
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"namePlural": "specifications",
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"type": "array",
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"uniqueItems": true
96+
},
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"https://openminds.ebrains.eu/vocab/type": {
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"_instruction": "Add the type that describe this electrical stimulus.",
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"_linkedTypes": [
@@ -16,5 +106,8 @@
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"nameForReverseLink": null,
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"namePlural": "types"
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}
19-
}
109+
},
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"required": [
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"https://openminds.ebrains.eu/vocab/internalIdentifier"
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]
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}

‎schemas/v4.0/Release Notes v4.0.json‎

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@@ -284,31 +284,10 @@
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},
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{
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"file": "stimulation/activity/stimulationActivity.schema.omi.json",
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"addedAttributes": [
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"properties.props:stimulus.nameForReverseLink"
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],
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"modifiedAttributes": [
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"properties.props:output._instruction",
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"properties.props:output._linkedTypes",
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"properties.props:stimulus._linkedTypes",
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"properties.props:studyTarget._linkedTypes"
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],
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"schemaType": "StimulationActivity"
297-
},
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{
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"file": "stimulation/stimulus/ephysStimulus.schema.omi.json",
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"addedAttributes": [
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"_categories",
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"required",
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"properties.props:deliveredBy",
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"properties.props:description",
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"properties.props:epoch",
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"properties.props:generatedBy",
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"properties.props:internalIdentifier",
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"properties.props:lookupLabel",
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"properties.props:specification"
310-
],
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"schemaType": "EphysStimulus"
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}
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]
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}

‎schemas/v4.0/Release Notes v4.0.txt‎

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Original file line numberDiff line numberDiff line change
@@ -142,19 +142,4 @@ Changes in specimenPrep/activity/tissueSampleSlicing.schema.omi.json:
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- Field 'required' modified.
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Changes in stimulation/activity/stimulationActivity.schema.omi.json:
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- Field 'properties.props:output._instruction' modified.
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- Field 'properties.props:output._linkedTypes' modified.
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- Field 'properties.props:stimulus.nameForReverseLink' added.
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- Field 'properties.props:stimulus._linkedTypes' modified.
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- Field 'properties.props:studyTarget._linkedTypes' modified.
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Changes in stimulation/stimulus/ephysStimulus.schema.omi.json:
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- Field '_categories' added.
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- Field 'required' added.
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- Field 'properties.props:deliveredBy' added.
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- Field 'properties.props:description' added.
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- Field 'properties.props:epoch' added.
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- Field 'properties.props:generatedBy' added.
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- Field 'properties.props:internalIdentifier' added.
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- Field 'properties.props:lookupLabel' added.
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- Field 'properties.props:specification' added.

‎vocab/categories.json‎

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@@ -461,6 +461,9 @@
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"ephys:Pipette",
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"specimenPrep:SlicingDevice"
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],
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"stimulus": [
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"stimulation:EphysStimulus"
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],
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"stimulusType": [
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"controlledTerms:AuditoryStimulusType",
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"controlledTerms:ElectricalStimulusType",

‎vocab/properties.json‎

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@@ -5173,6 +5173,12 @@
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"https://openminds.om-i.org/types/PipetteUsage",
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"https://openminds.om-i.org/types/SlicingDeviceUsage"
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],
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"v3.0": [
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"https://openminds.ebrains.eu/ephys/ElectrodeArrayUsage",
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"https://openminds.ebrains.eu/ephys/ElectrodeUsage",
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"https://openminds.ebrains.eu/ephys/PipetteUsage",
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"https://openminds.ebrains.eu/specimenPrep/SlicingDeviceUsage"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/ElectrodeArrayUsage",
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"https://openminds.om-i.org/types/ElectrodeUsage",
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"v4.0"
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],
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"namespace": "https://openminds.om-i.org/props/"
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},
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{
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"inVersions": [
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"v3.0"
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],
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"namespace": "https://openminds.ebrains.eu/vocab/"
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}
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],
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"label": "Delivered by",
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"latest": [
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"https://openminds.om-i.org/types/EphysStimulus"
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],
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"v3.0": [
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"https://openminds.ebrains.eu/stimulation/EphysStimulus"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/EphysStimulus"
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]
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"https://openminds.ebrains.eu/sands/CommonCoordinateSpaceVersion",
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"https://openminds.ebrains.eu/specimenPrep/CranialWindowPreparation",
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"https://openminds.ebrains.eu/specimenPrep/SlicingDevice",
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"https://openminds.ebrains.eu/stimulation/EphysStimulus",
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"https://openminds.ebrains.eu/stimulation/StimulationActivity"
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],
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"v4.0": [
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"latest": [
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"https://openminds.om-i.org/types/QuantitativeValue"
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],
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"v3.0": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/QuantitativeValue"
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]
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"v4.0"
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],
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"namespace": "https://openminds.om-i.org/props/"
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},
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{
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"inVersions": [
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"v3.0"
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],
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"namespace": "https://openminds.ebrains.eu/vocab/"
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}
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],
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"label": "Epoch",
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"latest": [
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"https://openminds.om-i.org/types/EphysStimulus"
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],
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"v3.0": [
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"https://openminds.ebrains.eu/stimulation/EphysStimulus"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/EphysStimulus"
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]
@@ -8326,6 +8354,12 @@
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"https://openminds.om-i.org/types/PipetteUsage",
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"https://openminds.om-i.org/types/SlicingDeviceUsage"
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],
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"v3.0": [
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"https://openminds.ebrains.eu/ephys/ElectrodeArrayUsage",
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"https://openminds.ebrains.eu/ephys/ElectrodeUsage",
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"https://openminds.ebrains.eu/ephys/PipetteUsage",
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"https://openminds.ebrains.eu/specimenPrep/SlicingDeviceUsage"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/ElectrodeArrayUsage",
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"https://openminds.om-i.org/types/ElectrodeUsage",
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"v4.0"
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],
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"namespace": "https://openminds.om-i.org/props/"
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},
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{
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"inVersions": [
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"v3.0"
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],
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"namespace": "https://openminds.ebrains.eu/vocab/"
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}
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],
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"label": "Generated by",
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"latest": [
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"https://openminds.om-i.org/types/EphysStimulus"
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],
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"v3.0": [
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"https://openminds.ebrains.eu/stimulation/EphysStimulus"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/EphysStimulus"
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]
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"https://openminds.ebrains.eu/ephys/Recording",
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"https://openminds.ebrains.eu/ephys/RecordingActivity",
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"https://openminds.ebrains.eu/sands/AtlasAnnotation",
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"https://openminds.ebrains.eu/sands/CustomAnnotation"
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"https://openminds.ebrains.eu/sands/CustomAnnotation",
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"https://openminds.ebrains.eu/stimulation/EphysStimulus"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/AtlasAnnotation",
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"https://openminds.ebrains.eu/specimenPrep/CranialWindowPreparation",
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"https://openminds.ebrains.eu/specimenPrep/SlicingDevice",
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"https://openminds.ebrains.eu/specimenPrep/SlicingDeviceUsage",
13093+
"https://openminds.ebrains.eu/stimulation/EphysStimulus",
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"https://openminds.ebrains.eu/stimulation/StimulationActivity"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/PropertyValueList"
1992419969
],
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"v3.0": [
19971+
"https://openminds.ebrains.eu/core/Configuration",
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"https://openminds.ebrains.eu/core/File",
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"https://openminds.ebrains.eu/core/FileBundle",
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"https://openminds.ebrains.eu/core/PropertyValueList"
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],
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"v4.0": [
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"v3.0": [
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"https://openminds.ebrains.eu/core/ContentType",
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"https://openminds.ebrains.eu/sands/AtlasAnnotation",
19988-
"https://openminds.ebrains.eu/sands/CustomAnnotation"
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"https://openminds.ebrains.eu/sands/CustomAnnotation",
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"https://openminds.ebrains.eu/stimulation/EphysStimulus"
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],
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"v4.0": [
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"https://openminds.om-i.org/types/AtlasAnnotation",
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"latest": [
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"https://openminds.om-i.org/types/EphysStimulus"
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],
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"v3.0": [
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"https://openminds.ebrains.eu/stimulation/EphysStimulus"
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],
2053120582
"v4.0": [
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"https://openminds.om-i.org/types/EphysStimulus"
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]

‎vocab/types.json‎

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}
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],
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"identical": [
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[
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"v3.0"
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],
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[
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"latest",
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"v3.0",
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"v4.0"
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]
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],

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