Last modified by lzehl on 2021/07/02 17:06
From version 14.1
edited by lzehl
on 2021/02/22 16:12
Change comment: There is no comment for this version
To version 28.1
edited by oschmid
on 2021/02/23 22:02
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 +(% style="text-align: right;" %)
19 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
20 +
21 +{{html}}
22 +<iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height: 28em"/>
23 +{{/html}}
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;" %)
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).
83 +
84 +(% class="wikigeneratedid" style="text-align: justify;" %)
75 75  For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
76 76  
77 77  (% class="wikigeneratedid" %)
78 -[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core]]
88 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
79 79  
80 80  === openMINDS SANDS ===
81 81  
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82 82  (% style="text-align: justify;" %)
83 83  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:
84 84  
95 +(% style="text-align: right;" %)
96 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
97 +
98 +(% style="text-align: right;" %)
99 +(% class="small" style="color:#7f8c8d" %){{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/SANDS.html" width="100%" style="border:0; height: 28em"/>{{/html}}
100 +
85 85  {{container layoutStyle="columns"}}
86 86  (((
87 87  (% class="small" %)
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117 117  (% style="text-align: justify;" %)
118 118  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:
119 119  
136 +(% style="text-align: right;" %)
137 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
138 +
120 120  {{container layoutStyle="columns"}}
121 121  (((
122 122  (% class="small" %)
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159 159  Species
160 160  Strain
161 161  Technique
162 -TermSuggestion
181 +TermSuggestion*
163 163  Terminology
164 164  TissueSampleType
165 165  TypeOfUncertainty
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168 168  {{/container}}
169 169  
170 170  (% style="text-align: justify;" %)
171 -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.
190 +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).
172 172  
192 +(% style="text-align: justify;" %)
193 +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).
194 +
173 173  (% class="wikigeneratedid" style="text-align: justify;" %)
174 174  For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
175 175  
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176 176  (% class="wikigeneratedid" %)
177 177  [[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
178 178  
201 +=== openMINDS controlledTerms - terminologies ===
202 +
203 +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:
204 +
205 +(% style="text-align: right;" %)
206 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
207 +
208 +{{container layoutStyle="columns"}}
209 +(((
210 +(% class="small" %)
211 +AgeCategory
212 +AnatomicalAxesOrientation
213 +BehavioralTask
214 +BiologicalSex
215 +CellType
216 +ContributionType
217 +CriteriaQualityType
218 +DatasetType
219 +Disease
220 +DiseaseModel
221 +EthicsAssessment
222 +FileBundleGrouping
223 +FileUsageRole
224 +)))
225 +(((
226 +(% class="small" %)
227 +Genotype
228 +Language
229 +Laterality
230 +MetaDataModelType
231 +Modality
232 +ModelAbstractionLevel
233 +ModelScope
234 +OperatingDevice
235 +OperatingSystem
236 +Organ
237 +Phenotype
238 +PreparationType
239 +ProductAccessibility
240 +)))
241 +(((
242 +(% class="small" %)
243 +ProgrammingLanguage
244 +QualitativeOverlap
245 +SoftwareApplicationCategory
246 +SoftwareFeature
247 +Species
248 +Strain
249 +Technique
250 +Terminology
251 +TissueSampleType
252 +TypeOfUncertainty
253 +UnitOfMeasurement
254 +)))
255 +{{/container}}
256 +
179 179  === openMINDS instances ===
180 180  
181 -xxx
259 +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:
260 +
261 +(% style="text-align: right;" %)
262 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
263 +
264 +{{container layoutStyle="columns"}}
265 +(((
266 +(% class="small" %)
267 +contentType
268 +)))
269 +(((
270 +(% class="small" %)
271 +License
272 +)))
273 +(((
274 +(% class="small" %)
275 +DigitalIdentifierSchema
276 +)))
277 +{{/container}}
278 +
279 +(% class="wikigeneratedid" style="text-align: justify;" %)
280 +For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
281 +
282 +(% class="wikigeneratedid" %)
283 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
Public

openMINDS