Last modified by lzehl on 2021/07/02 17:06
From version 13.1
edited by lzehl
on 2021/02/22 16:03
Change comment: There is no comment for this version
To version 30.1
edited by oschmid
on 2021/02/23 22:04
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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71 71  )))
72 72  {{/container}}
73 73  
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 +
74 74  === openMINDS SANDS ===
75 75  
76 76  (% style="text-align: justify;" %)
77 77  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:
78 78  
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: 8em"/>{{/html}}
100 +
79 79  {{container layoutStyle="columns"}}
80 80  (((
81 81  (% class="small" %)
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100 100  )))
101 101  {{/container}}
102 102  
125 +(% class="wikigeneratedid" style="text-align: justify;" %)
126 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
127 +
128 +(% class="wikigeneratedid" %)
129 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
130 +
103 103  === openMINDS controlledTerms - schemas ===
104 104  
105 105  (% style="text-align: justify;" %)
106 106  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:
107 107  
136 +(% style="text-align: right;" %)
137 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
138 +
139 +(% style="text-align: right;" %)
140 +(% class="small" style="color:#7f8c8d" %){{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/SANDS.html" width="100%" style="border:0; height: 25em"/>{{/html}}
141 +
108 108  {{container layoutStyle="columns"}}
109 109  (((
110 110  (% class="small" %)
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147 147  Species
148 148  Strain
149 149  Technique
150 -TermSuggestion
184 +TermSuggestion*
151 151  Terminology
152 152  TissueSampleType
153 153  TypeOfUncertainty
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156 156  {{/container}}
157 157  
158 158  (% style="text-align: justify;" %)
159 -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.
193 +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).
160 160  
195 +(% style="text-align: justify;" %)
196 +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).
197 +
198 +(% class="wikigeneratedid" style="text-align: justify;" %)
199 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
200 +
201 +(% class="wikigeneratedid" %)
202 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
203 +
204 +=== openMINDS controlledTerms - terminologies ===
205 +
206 +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:
207 +
208 +(% style="text-align: right;" %)
209 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
210 +
211 +{{container layoutStyle="columns"}}
212 +(((
213 +(% class="small" %)
214 +AgeCategory
215 +AnatomicalAxesOrientation
216 +BehavioralTask
217 +BiologicalSex
218 +CellType
219 +ContributionType
220 +CriteriaQualityType
221 +DatasetType
222 +Disease
223 +DiseaseModel
224 +EthicsAssessment
225 +FileBundleGrouping
226 +FileUsageRole
227 +)))
228 +(((
229 +(% class="small" %)
230 +Genotype
231 +Language
232 +Laterality
233 +MetaDataModelType
234 +Modality
235 +ModelAbstractionLevel
236 +ModelScope
237 +OperatingDevice
238 +OperatingSystem
239 +Organ
240 +Phenotype
241 +PreparationType
242 +ProductAccessibility
243 +)))
244 +(((
245 +(% class="small" %)
246 +ProgrammingLanguage
247 +QualitativeOverlap
248 +SoftwareApplicationCategory
249 +SoftwareFeature
250 +Species
251 +Strain
252 +Technique
253 +Terminology
254 +TissueSampleType
255 +TypeOfUncertainty
256 +UnitOfMeasurement
257 +)))
258 +{{/container}}
259 +
161 161  === openMINDS instances ===
162 162  
163 -xxx
262 +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:
263 +
264 +(% style="text-align: right;" %)
265 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
266 +
267 +{{container layoutStyle="columns"}}
268 +(((
269 +(% class="small" %)
270 +contentType
271 +)))
272 +(((
273 +(% class="small" %)
274 +License
275 +)))
276 +(((
277 +(% class="small" %)
278 +DigitalIdentifierSchema
279 +)))
280 +{{/container}}
281 +
282 +(% class="wikigeneratedid" style="text-align: justify;" %)
283 +For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
284 +
285 +(% class="wikigeneratedid" %)
286 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
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openMINDS