Wiki source code of Metadata models & schemas

Version 27.1 by oschmid on 2021/02/23 22:01
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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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21 {{html}}
22 <iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height: 28em"/>
23 {{/html}}
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25 {{container layoutStyle="columns"}}
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28 **ACTORS**
29 Affiliation
30 ContactInformation
31 Contribution
32 Organization
33 Person
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35 **DATA**
36 ContentType*
37 Copyright
38 FileBundle
39 FileInstance
40 FileRepository
41 Hash
42 License*
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46 **MISCELLANEOUS**
47 DigitalIdentifier
48 DigitalIdentifierSchema*
49 Funding
50 QuantitativeValue
51 QuantitativeValueRange
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53 **PRODUCTS**
54 Dataset
55 DatasetVersion
56 MetaDataModel
57 MetaDataModelVersion
58 Model
59 ModelVersion
60 Project
61 Software
62 SoftwareVersion
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66 **RESEARCH**
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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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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85 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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88 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
89
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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96 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
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101 AnatomicalEntity
102 AnatomicalEntityRelation
103 Annotation
104 AtlasTerminology
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108 BrainAtlas
109 BrainAtlasVersion
110 CoordinatePoint
111 CoordinateSpace
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115 Electrode
116 ElectrodeArray
117 ElectrodeContact
118 Image
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120 {{/container}}
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123 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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126 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
127
128 === openMINDS controlledTerms - schemas ===
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131 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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134 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
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139 AgeCategory
140 AnatomicalAxesOrientation
141 BehavioralTask
142 BiologicalSex
143 CellType
144 ContributionType
145 CriteriaQualityType
146 DatasetType
147 Disease
148 DiseaseModel
149 EthicsAssessment
150 FileBundleGrouping
151 FileUsageRole
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155 Genotype
156 Language
157 Laterality
158 MetaDataModelType
159 Modality
160 ModelAbstractionLevel
161 ModelScope
162 OperatingDevice
163 OperatingSystem
164 Organ
165 Phenotype
166 PreparationType
167 ProductAccessibility
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171 ProgrammingLanguage
172 QualitativeOverlap
173 SoftwareApplicationCategory
174 SoftwareFeature
175 Species
176 Strain
177 Technique
178 TermSuggestion*
179 Terminology
180 TissueSampleType
181 TypeOfUncertainty
182 UnitOfMeasurement
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184 {{/container}}
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187 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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190 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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193 For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
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196 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
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198 === openMINDS controlledTerms - terminologies ===
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200 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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203 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
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205 {{container layoutStyle="columns"}}
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208 AgeCategory
209 AnatomicalAxesOrientation
210 BehavioralTask
211 BiologicalSex
212 CellType
213 ContributionType
214 CriteriaQualityType
215 DatasetType
216 Disease
217 DiseaseModel
218 EthicsAssessment
219 FileBundleGrouping
220 FileUsageRole
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223 (% class="small" %)
224 Genotype
225 Language
226 Laterality
227 MetaDataModelType
228 Modality
229 ModelAbstractionLevel
230 ModelScope
231 OperatingDevice
232 OperatingSystem
233 Organ
234 Phenotype
235 PreparationType
236 ProductAccessibility
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239 (% class="small" %)
240 ProgrammingLanguage
241 QualitativeOverlap
242 SoftwareApplicationCategory
243 SoftwareFeature
244 Species
245 Strain
246 Technique
247 Terminology
248 TissueSampleType
249 TypeOfUncertainty
250 UnitOfMeasurement
251 )))
252 {{/container}}
253
254 === openMINDS instances ===
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256 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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258 (% style="text-align: right;" %)
259 (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
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264 contentType
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268 License
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272 DigitalIdentifierSchema
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274 {{/container}}
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277 For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
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280 [[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
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openMINDS