Last modified by lzehl on 2021/07/02 17:06
From version 11.1
edited by lzehl
on 2021/02/22 15:22
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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12 12  
13 13  === openMINDS core ===
14 14  
15 +(% style="text-align: justify;" %)
15 15  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:
16 16  
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 +
17 17  {{container layoutStyle="columns"}}
18 18  (((
19 19  (% class="small" %)
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25 25  Person
26 26  (% class="small" %)
27 27  **DATA**
28 -ContentType
36 +ContentType*
29 29  Copyright
30 30  FileBundle
31 31  FileInstance
32 32  FileRepository
33 33  Hash
34 -License
42 +License*
35 35  )))
36 36  (((
37 37  (% class="small" %)
38 38  **MISCELLANEOUS**
39 39  DigitalIdentifier
40 -DigitalIdentifierSchema
48 +DigitalIdentifierSchema*
41 41  Funding
42 42  QuantitativeValue
43 43  QuantitativeValueRange
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70 70  )))
71 71  {{/container}}
72 72  
81 +(% 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;" %)
85 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
86 +
87 +(% class="wikigeneratedid" %)
88 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
89 +
73 73  === openMINDS SANDS ===
74 74  
75 -The openMINDS SANDS (Spatial Anchoring for Neuroscience Data Structures) 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:
92 +(% style="text-align: justify;" %)
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:
76 76  
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 +
77 77  {{container layoutStyle="columns"}}
78 78  (((
79 79  (% class="small" %)
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98 98  )))
99 99  {{/container}}
100 100  
101 -=== openMINDS controlledTerms ===
125 +(% class="wikigeneratedid" style="text-align: justify;" %)
126 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
102 102  
103 -The openMINDS controlledTerms metadata model contains schemas that ensure consistent registration of well-defined terms, including linkages to existing ontological terms where applicable.
128 +(% class="wikigeneratedid" %)
129 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
104 104  
131 +=== openMINDS controlledTerms - schemas ===
132 +
133 +(% style="text-align: justify;" %)
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:
135 +
136 +(% style="text-align: right;" %)
137 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
138 +
139 +{{container layoutStyle="columns"}}
140 +(((
141 +(% class="small" %)
142 +AgeCategory
143 +AnatomicalAxesOrientation
144 +BehavioralTask
145 +BiologicalSex
146 +CellType
147 +ContributionType
148 +CriteriaQualityType
149 +DatasetType
150 +Disease
151 +DiseaseModel
152 +EthicsAssessment
153 +FileBundleGrouping
154 +FileUsageRole
155 +)))
156 +(((
157 +(% class="small" %)
158 +Genotype
159 +Language
160 +Laterality
161 +MetaDataModelType
162 +Modality
163 +ModelAbstractionLevel
164 +ModelScope
165 +OperatingDevice
166 +OperatingSystem
167 +Organ
168 +Phenotype
169 +PreparationType
170 +ProductAccessibility
171 +)))
172 +(((
173 +(% class="small" %)
174 +ProgrammingLanguage
175 +QualitativeOverlap
176 +SoftwareApplicationCategory
177 +SoftwareFeature
178 +Species
179 +Strain
180 +Technique
181 +TermSuggestion*
182 +Terminology
183 +TissueSampleType
184 +TypeOfUncertainty
185 +UnitOfMeasurement
186 +)))
187 +{{/container}}
188 +
189 +(% style="text-align: justify;" %)
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).
191 +
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 +
195 +(% class="wikigeneratedid" style="text-align: justify;" %)
196 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
197 +
198 +(% class="wikigeneratedid" %)
199 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
200 +
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 +
105 105  === openMINDS instances ===
106 106  
107 -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]]
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openMINDS