Wiki source code of Metadata models & schemas

Version 23.2 by oschmid on 2021/02/23 16:10
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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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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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10 Note that all metadata models are licensed under the MIT license.
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12
13 === openMINDS core ===
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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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24 **ACTORS**
25 Affiliation
26 ContactInformation
27 Contribution
28 Organization
29 Person
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31 **DATA**
32 ContentType*
33 Copyright
34 FileBundle
35 FileInstance
36 FileRepository
37 Hash
38 License*
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42 **MISCELLANEOUS**
43 DigitalIdentifier
44 DigitalIdentifierSchema*
45 Funding
46 QuantitativeValue
47 QuantitativeValueRange
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49 **PRODUCTS**
50 Dataset
51 DatasetVersion
52 MetaDataModel
53 MetaDataModelVersion
54 Model
55 ModelVersion
56 Project
57 Software
58 SoftwareVersion
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62 **RESEARCH**
63 ParameterSetting
64 Protocol
65 ProtocolExecution
66 Subject
67 SubjectGroup
68 SubjectGroupState
69 SubjectState
70 TissueSample
71 TissueSampleCollection
72 TissueSampleCollectionState
73 TissueSampleState
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75 {{/container}}
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78 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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81 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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84 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
85
86 === openMINDS SANDS ===
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89 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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92 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
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97 AnatomicalEntity
98 AnatomicalEntityRelation
99 Annotation
100 AtlasTerminology
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104 BrainAtlas
105 BrainAtlasVersion
106 CoordinatePoint
107 CoordinateSpace
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111 Electrode
112 ElectrodeArray
113 ElectrodeContact
114 Image
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116 {{/container}}
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119 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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122 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
123
124 === openMINDS controlledTerms - schemas ===
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127 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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130 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
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135 AgeCategory
136 AnatomicalAxesOrientation
137 BehavioralTask
138 BiologicalSex
139 CellType
140 ContributionType
141 CriteriaQualityType
142 DatasetType
143 Disease
144 DiseaseModel
145 EthicsAssessment
146 FileBundleGrouping
147 FileUsageRole
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151 Genotype
152 Language
153 Laterality
154 MetaDataModelType
155 Modality
156 ModelAbstractionLevel
157 ModelScope
158 OperatingDevice
159 OperatingSystem
160 Organ
161 Phenotype
162 PreparationType
163 ProductAccessibility
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167 ProgrammingLanguage
168 QualitativeOverlap
169 SoftwareApplicationCategory
170 SoftwareFeature
171 Species
172 Strain
173 Technique
174 TermSuggestion*
175 Terminology
176 TissueSampleType
177 TypeOfUncertainty
178 UnitOfMeasurement
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180 {{/container}}
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183 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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186 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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189 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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192 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
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194 === openMINDS controlledTerms - terminologies ===
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196 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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199 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
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201 {{container layoutStyle="columns"}}
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204 AgeCategory
205 AnatomicalAxesOrientation
206 BehavioralTask
207 BiologicalSex
208 CellType
209 ContributionType
210 CriteriaQualityType
211 DatasetType
212 Disease
213 DiseaseModel
214 EthicsAssessment
215 FileBundleGrouping
216 FileUsageRole
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220 Genotype
221 Language
222 Laterality
223 MetaDataModelType
224 Modality
225 ModelAbstractionLevel
226 ModelScope
227 OperatingDevice
228 OperatingSystem
229 Organ
230 Phenotype
231 PreparationType
232 ProductAccessibility
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235 (% class="small" %)
236 ProgrammingLanguage
237 QualitativeOverlap
238 SoftwareApplicationCategory
239 SoftwareFeature
240 Species
241 Strain
242 Technique
243 Terminology
244 TissueSampleType
245 TypeOfUncertainty
246 UnitOfMeasurement
247 )))
248 {{/container}}
249
250 === openMINDS instances ===
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252 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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255 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
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260 contentType
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264 License
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268 DigitalIdentifierSchema
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270 {{/container}}
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273 For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
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276 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
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openMINDS