Last modified by lzehl on 2021/07/02 17:06
From version 15.1
edited by lzehl
on 2021/02/22 16:21
Change comment: There is no comment for this version
To version 23.3
edited by oschmid
on 2021/02/23 16:21
Change comment: There is no comment for this version

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1 -XWiki.lzehl
1 +XWiki.oschmid
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4 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.
5 5  
6 6  (% style="text-align: justify;" %)
7 -Please find the HTML description for all schemas of each openMINDS metadata model in the corresponding sub-pages. A short overview for each openMINDS metadata model can be found below.
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.
8 8  
9 9  (% style="text-align: justify;" %)
10 10  Note that all metadata models are licensed under the MIT license.
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15 15  (% style="text-align: justify;" %)
16 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:
17 17  
18 +{{html}}
19 + <iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height:20em"/>
20 +{{/html}}
21 +
22 +(% style="text-align: right;" %)
23 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
24 +
18 18  {{container layoutStyle="columns"}}
19 19  (((
20 20  (% class="small" %)
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26 26  Person
27 27  (% class="small" %)
28 28  **DATA**
29 -ContentType
36 +ContentType*
30 30  Copyright
31 31  FileBundle
32 32  FileInstance
33 33  FileRepository
34 34  Hash
35 -License
42 +License*
36 36  )))
37 37  (((
38 38  (% class="small" %)
39 39  **MISCELLANEOUS**
40 40  DigitalIdentifier
41 -DigitalIdentifierSchema
48 +DigitalIdentifierSchema*
42 42  Funding
43 43  QuantitativeValue
44 44  QuantitativeValueRange
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72 72  {{/container}}
73 73  
74 74  (% class="wikigeneratedid" style="text-align: justify;" %)
75 -In case of EBRAINS, metadata representations (instances) of the schemas ContentType, License, and DigitalIdentifierSchema 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).
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).
76 76  
77 77  (% class="wikigeneratedid" style="text-align: justify;" %)
78 78  For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
79 79  
80 80  (% class="wikigeneratedid" %)
81 -[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel=" noopener noreferrer" target="_blank"]]
88 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
82 82  
83 83  === openMINDS SANDS ===
84 84  
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85 85  (% style="text-align: justify;" %)
86 86  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:
87 87  
95 +(% style="text-align: right;" %)
96 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
97 +
88 88  {{container layoutStyle="columns"}}
89 89  (((
90 90  (% class="small" %)
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120 120  (% style="text-align: justify;" %)
121 121  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:
122 122  
133 +(% style="text-align: right;" %)
134 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
135 +
123 123  {{container layoutStyle="columns"}}
124 124  (((
125 125  (% class="small" %)
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162 162  Species
163 163  Strain
164 164  Technique
165 -TermSuggestion
178 +TermSuggestion*
166 166  Terminology
167 167  TissueSampleType
168 168  TypeOfUncertainty
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171 171  {{/container}}
172 172  
173 173  (% style="text-align: justify;" %)
174 -Except for TermSuggestion, 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). 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.
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).
175 175  
189 +(% style="text-align: justify;" %)
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).
191 +
176 176  (% class="wikigeneratedid" style="text-align: justify;" %)
177 177  For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
178 178  
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179 179  (% class="wikigeneratedid" %)
180 180  [[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
181 181  
198 +=== openMINDS controlledTerms - terminologies ===
199 +
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:
201 +
202 +(% style="text-align: right;" %)
203 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
204 +
205 +{{container layoutStyle="columns"}}
206 +(((
207 +(% class="small" %)
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
221 +)))
222 +(((
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
237 +)))
238 +(((
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 +
182 182  === openMINDS instances ===
183 183  
184 -xxx
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:
257 +
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).
260 +
261 +{{container layoutStyle="columns"}}
262 +(((
263 +(% class="small" %)
264 +contentType
265 +)))
266 +(((
267 +(% class="small" %)
268 +License
269 +)))
270 +(((
271 +(% class="small" %)
272 +DigitalIdentifierSchema
273 +)))
274 +{{/container}}
275 +
276 +(% class="wikigeneratedid" style="text-align: justify;" %)
277 +For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
278 +
279 +(% class="wikigeneratedid" %)
280 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
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openMINDS