Last modified by lzehl on 2021/07/02 17:06
From version 23.4
edited by oschmid
on 2021/02/23 16:21
Change comment: There is no comment for this version
To version 10.1
edited by lzehl
on 2021/02/22 11:37
Change comment: There is no comment for this version

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1 -XWiki.oschmid
1 +XWiki.lzehl
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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 -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.
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.
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;" %)
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 -
25 25  {{container layoutStyle="columns"}}
26 26  (((
27 27  (% class="small" %)
... ... @@ -33,19 +33,19 @@
33 33  Person
34 34  (% class="small" %)
35 35  **DATA**
36 -ContentType*
28 +ContentType
37 37  Copyright
38 38  FileBundle
39 39  FileInstance
40 40  FileRepository
41 41  Hash
42 -License*
34 +License
43 43  )))
44 44  (((
45 45  (% class="small" %)
46 46  **MISCELLANEOUS**
47 47  DigitalIdentifier
48 -DigitalIdentifierSchema*
40 +DigitalIdentifierSchema
49 49  Funding
50 50  QuantitativeValue
51 51  QuantitativeValueRange
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78 78  )))
79 79  {{/container}}
80 80  
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 -
90 90  === openMINDS SANDS ===
91 91  
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:
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:
94 94  
95 -(% style="text-align: right;" %)
96 -(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
77 +=== openMINDS controlledTerms ===
97 97  
98 -{{container layoutStyle="columns"}}
99 -(((
100 -(% class="small" %)
101 -AnatomicalEntity
102 -AnatomicalEntityRelation
103 -Annotation
104 -AtlasTerminology
105 -)))
106 -(((
107 -(% class="small" %)
108 -BrainAtlas
109 -BrainAtlasVersion
110 -CoordinatePoint
111 -CoordinateSpace
112 -)))
113 -(((
114 -(% class="small" %)
115 -Electrode
116 -ElectrodeArray
117 -ElectrodeContact
118 -Image
119 -)))
120 -{{/container}}
79 +The openMINDS controlledTerms metadata model contains schemas that ensure consistent registration of well-defined terms, including linkages to existing ontological terms where applicable.
121 121  
122 -(% class="wikigeneratedid" style="text-align: justify;" %)
123 -For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
124 -
125 -(% class="wikigeneratedid" %)
126 -[[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
127 -
128 -=== openMINDS controlledTerms - schemas ===
129 -
130 -(% style="text-align: justify;" %)
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:
132 -
133 -(% style="text-align: right;" %)
134 -(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
135 -
136 -{{container layoutStyle="columns"}}
137 -(((
138 -(% class="small" %)
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
152 -)))
153 -(((
154 -(% class="small" %)
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
168 -)))
169 -(((
170 -(% class="small" %)
171 -ProgrammingLanguage
172 -QualitativeOverlap
173 -SoftwareApplicationCategory
174 -SoftwareFeature
175 -Species
176 -Strain
177 -Technique
178 -TermSuggestion*
179 -Terminology
180 -TissueSampleType
181 -TypeOfUncertainty
182 -UnitOfMeasurement
183 -)))
184 -{{/container}}
185 -
186 -(% style="text-align: justify;" %)
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).
188 -
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 -
192 -(% class="wikigeneratedid" style="text-align: justify;" %)
193 -For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
194 -
195 -(% class="wikigeneratedid" %)
196 -[[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
197 -
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 -
254 254  === openMINDS instances ===
255 255  
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]]
83 +xxx
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openMINDS