Wiki source code of Metadata models & schemas

Version 31.1 by oschmid on 2021/02/23 22:04
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lzehl 4.1 4 The openMINDS metadata models all consist of modular connectable metadata schemas. Each schema can be referenced by it's type and defines properties (including their expected value) for a set of related metadata.
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lzehl 21.1 7 A short overview for each openMINDS metadata model can be found below, including links to full HTML descriptions for all schemas and links to available metadata instances for selected schemas.
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lzehl 2.1 10 Note that all metadata models are licensed under the MIT license.
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lzehl 3.1 13 === openMINDS core ===
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lzehl 10.1 16 The openMINDS core metadata model contains schemas that can be used to describe the general origin, resource location, and content of research products in the field of neuroscience. Currently ( Feb 2021) this metadata model comprises 37 usable schemas, grouped into five classes:
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19 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
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oschmid 23.3 21 {{html}}
oschmid 28.1 22 <iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height: 28em"/>
oschmid 23.3 23 {{/html}}
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lzehl 7.1 25 {{container layoutStyle="columns"}}
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lzehl 8.1 28 **ACTORS**
lzehl 7.1 29 Affiliation
30 ContactInformation
31 Contribution
32 Organization
33 Person
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lzehl 8.1 35 **DATA**
lzehl 16.1 36 ContentType*
lzehl 7.1 37 Copyright
38 FileBundle
39 FileInstance
40 FileRepository
41 Hash
lzehl 16.1 42 License*
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lzehl 8.1 46 **MISCELLANEOUS**
lzehl 7.1 47 DigitalIdentifier
lzehl 16.1 48 DigitalIdentifierSchema*
lzehl 7.1 49 Funding
50 QuantitativeValue
51 QuantitativeValueRange
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lzehl 8.1 53 **PRODUCTS**
lzehl 7.1 54 Dataset
55 DatasetVersion
56 MetaDataModel
57 MetaDataModelVersion
58 Model
59 ModelVersion
60 Project
61 Software
62 SoftwareVersion
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lzehl 8.1 66 **RESEARCH**
lzehl 7.1 67 ParameterSetting
68 Protocol
69 ProtocolExecution
70 Subject
71 SubjectGroup
72 SubjectGroupState
73 SubjectState
74 TissueSample
75 TissueSampleCollection
76 TissueSampleCollectionState
77 TissueSampleState
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79 {{/container}}
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lzehl 16.1 82 In case of EBRAINS, metadata representations (instances) of the schemas marked with an asterisk are centrally defined and maintained on a separate GitHub to guarantee more consistency across the database instances of the Knowledge Graph (cf. section openMINDS instances).
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lzehl 14.1 85 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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lzehl 16.1 88 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
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lzehl 3.1 90 === openMINDS SANDS ===
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93 The openMINDS SANDS (**S**patial **A**nchoring for **N**euroscience **D**ata **S**tructures) metadata model contains schemas that can be used to capture the anatomical location of neuroscience data as well as to identify and highlight commonly used reference brain atlases and coordinate spaces. Currently (Feb 2021) this metadata model comprises 12 metadata schemas:
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lzehl 19.1 95 (% style="text-align: right;" %)
lzehl 23.1 96 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
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oschmid 28.1 98 (% style="text-align: right;" %)
oschmid 29.1 99 (% class="small" style="color:#7f8c8d" %){{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/SANDS.html" width="100%" style="border:0; height: 8em"/>{{/html}}
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lzehl 11.1 101 {{container layoutStyle="columns"}}
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104 AnatomicalEntity
105 AnatomicalEntityRelation
106 Annotation
107 AtlasTerminology
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111 BrainAtlas
112 BrainAtlasVersion
113 CoordinatePoint
114 CoordinateSpace
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118 Electrode
119 ElectrodeArray
120 ElectrodeContact
121 Image
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123 {{/container}}
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lzehl 14.1 125 (% class="wikigeneratedid" style="text-align: justify;" %)
126 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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129 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
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lzehl 12.1 131 === openMINDS controlledTerms - schemas ===
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lzehl 13.1 134 The openMINDS controlledTerms metadata model contains schemas that ensure consistent registration of well-defined terms, including linkages to existing ontological terms where applicable. Currently (Feb 2021) this metadata model comprises 38 nearly identical schemas:
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lzehl 23.1 137 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
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oschmid 30.1 139 (% style="text-align: right;" %)
oschmid 31.1 140 (% class="small" style="color:#7f8c8d" %){{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/controlledTerms.html" width="100%" style="border:0; height: 25em"/>{{/html}}
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lzehl 12.1 142 {{container layoutStyle="columns"}}
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145 AgeCategory
146 AnatomicalAxesOrientation
147 BehavioralTask
148 BiologicalSex
149 CellType
150 ContributionType
151 CriteriaQualityType
152 DatasetType
153 Disease
154 DiseaseModel
155 EthicsAssessment
156 FileBundleGrouping
lzehl 13.1 157 FileUsageRole
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161 Genotype
162 Language
163 Laterality
164 MetaDataModelType
165 Modality
166 ModelAbstractionLevel
167 ModelScope
168 OperatingDevice
169 OperatingSystem
170 Organ
171 Phenotype
lzehl 13.1 172 PreparationType
173 ProductAccessibility
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177 ProgrammingLanguage
178 QualitativeOverlap
179 SoftwareApplicationCategory
180 SoftwareFeature
181 Species
182 Strain
183 Technique
lzehl 16.1 184 TermSuggestion*
lzehl 12.1 185 Terminology
186 TissueSampleType
187 TypeOfUncertainty
188 UnitOfMeasurement
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190 {{/container}}
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lzehl 13.1 192 (% style="text-align: justify;" %)
lzehl 18.1 193 Except for TermSuggestion (marked with an asterisk), the openMINDS controlledTerms metadata schemas differ only in their type which defines the name of the terminology the correspondingly controlled terms are registered to (cf. openMINDS controlledTerms - terminologies).
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196 Compared to these schemas, the TermSuggestion has one additional property ("terminology") where users can state to which terminology the new suggested (not yet controlled) term belongs to. Within the EBRAINS Knowledge Graph, the metadata representations for TermSuggestion will be regularly reviewed by the openMINDS development team in order to integrate these community driven suggestions into the controlledTerms terminologies and corresponding ontology (where applicable).
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199 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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202 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
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lzehl 19.1 204 === openMINDS controlledTerms - terminologies ===
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206 The openMINDS instances repository holds a collection of metadata representations (instances) of selected schemas which content should be more controlled to ensure their consistent definition and usage for the entire EBRAINS Knowledge Graph. Currently the repository holds collections for the following schemas:
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lzehl 23.1 209 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
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211 {{container layoutStyle="columns"}}
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214 AgeCategory
215 AnatomicalAxesOrientation
216 BehavioralTask
217 BiologicalSex
218 CellType
219 ContributionType
220 CriteriaQualityType
221 DatasetType
222 Disease
223 DiseaseModel
224 EthicsAssessment
225 FileBundleGrouping
226 FileUsageRole
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229 (% class="small" %)
230 Genotype
231 Language
232 Laterality
233 MetaDataModelType
234 Modality
235 ModelAbstractionLevel
236 ModelScope
237 OperatingDevice
238 OperatingSystem
239 Organ
240 Phenotype
241 PreparationType
242 ProductAccessibility
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245 (% class="small" %)
246 ProgrammingLanguage
247 QualitativeOverlap
248 SoftwareApplicationCategory
249 SoftwareFeature
250 Species
251 Strain
252 Technique
253 Terminology
254 TissueSampleType
255 TypeOfUncertainty
256 UnitOfMeasurement
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258 {{/container}}
259
lzehl 2.1 260 === openMINDS instances ===
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lzehl 17.1 262 The openMINDS instances repository holds a collection of metadata representations (instances) of selected schemas which content should be more controlled to ensure their consistent definition and usage for the entire EBRAINS Knowledge Graph. Currently the repository holds collections for the following schemas:
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lzehl 19.1 264 (% style="text-align: right;" %)
lzehl 23.1 265 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
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lzehl 17.1 267 {{container layoutStyle="columns"}}
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270 contentType
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274 License
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277 (% class="small" %)
278 DigitalIdentifierSchema
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280 {{/container}}
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283 For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
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286 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
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