Last modified by lzehl on 2021/07/02 17:06
From version 6.1
edited by lzehl
on 2021/02/18 17:38
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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12 12  
13 13  === openMINDS core ===
14 14  
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 this metadata model comprises 37 usable schemas:
15 +(% style="text-align: justify;" %)
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:
16 16  
17 -* Affiliation
18 -* ContactInformation
19 -* Contribution
20 -* Organization
21 -* Person
22 -* ContentType
23 -* Copyright
24 -* FileBundle
25 -* FileInstance
26 -* FileRepository
27 -* Hash
28 -* License
29 -* DigitalIdentifier
30 -* DigitalIdentifierSchema
31 -* Funding
32 -* QuantitativeValue
33 -* QuantitativeValueRange
34 -* Dataset
35 -* DatasetVersion
36 -* MetaDataModel
37 -* MetaDataModelVersion
38 -* Model
39 -* ModelVersion
40 -* Project
41 -* Software
42 -* SoftwareVersion
43 -* ParameterSetting
44 -* Protocol
45 -* ProtocolExecution
46 -* Subject
47 -* SubjectGroup
48 -* SubjectGroupState
49 -* SubjectState
50 -* TissueSample
51 -* TissueSampleCollection
52 -* TissueSampleCollectionState
53 -* TissueSampleState
18 +(% style="text-align: right;" %)
19 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
54 54  
21 +{{html}}
22 +<iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height: 28em"/>
23 +{{/html}}
24 +
25 +{{container layoutStyle="columns"}}
26 +(((
27 +(% class="small" %)
28 +**ACTORS**
29 +Affiliation
30 +ContactInformation
31 +Contribution
32 +Organization
33 +Person
34 +(% class="small" %)
35 +**DATA**
36 +ContentType*
37 +Copyright
38 +FileBundle
39 +FileInstance
40 +FileRepository
41 +Hash
42 +License*
43 +)))
44 +(((
45 +(% class="small" %)
46 +**MISCELLANEOUS**
47 +DigitalIdentifier
48 +DigitalIdentifierSchema*
49 +Funding
50 +QuantitativeValue
51 +QuantitativeValueRange
52 +(% class="small" %)
53 +**PRODUCTS**
54 +Dataset
55 +DatasetVersion
56 +MetaDataModel
57 +MetaDataModelVersion
58 +Model
59 +ModelVersion
60 +Project
61 +Software
62 +SoftwareVersion
63 +)))
64 +(((
65 +(% class="small" %)
66 +**RESEARCH**
67 +ParameterSetting
68 +Protocol
69 +ProtocolExecution
70 +Subject
71 +SubjectGroup
72 +SubjectGroupState
73 +SubjectState
74 +TissueSample
75 +TissueSampleCollection
76 +TissueSampleCollectionState
77 +TissueSampleState
78 +)))
79 +{{/container}}
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 +
55 55  === openMINDS SANDS ===
56 56  
57 -xxx
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:
58 58  
59 -=== openMINDS controlledTerms ===
95 +(% style="text-align: right;" %)
96 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
60 60  
61 -xxx
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}}
62 62  
101 +{{container layoutStyle="columns"}}
102 +(((
103 +(% class="small" %)
104 +AnatomicalEntity
105 +AnatomicalEntityRelation
106 +Annotation
107 +AtlasTerminology
108 +)))
109 +(((
110 +(% class="small" %)
111 +BrainAtlas
112 +BrainAtlasVersion
113 +CoordinatePoint
114 +CoordinateSpace
115 +)))
116 +(((
117 +(% class="small" %)
118 +Electrode
119 +ElectrodeArray
120 +ElectrodeContact
121 +Image
122 +)))
123 +{{/container}}
124 +
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 +
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 +(% 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 +
142 +{{container layoutStyle="columns"}}
143 +(((
144 +(% class="small" %)
145 +AgeCategory
146 +AnatomicalAxesOrientation
147 +BehavioralTask
148 +BiologicalSex
149 +CellType
150 +ContributionType
151 +CriteriaQualityType
152 +DatasetType
153 +Disease
154 +DiseaseModel
155 +EthicsAssessment
156 +FileBundleGrouping
157 +FileUsageRole
158 +)))
159 +(((
160 +(% class="small" %)
161 +Genotype
162 +Language
163 +Laterality
164 +MetaDataModelType
165 +Modality
166 +ModelAbstractionLevel
167 +ModelScope
168 +OperatingDevice
169 +OperatingSystem
170 +Organ
171 +Phenotype
172 +PreparationType
173 +ProductAccessibility
174 +)))
175 +(((
176 +(% class="small" %)
177 +ProgrammingLanguage
178 +QualitativeOverlap
179 +SoftwareApplicationCategory
180 +SoftwareFeature
181 +Species
182 +Strain
183 +Technique
184 +TermSuggestion*
185 +Terminology
186 +TissueSampleType
187 +TypeOfUncertainty
188 +UnitOfMeasurement
189 +)))
190 +{{/container}}
191 +
192 +(% style="text-align: justify;" %)
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).
194 +
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 +
63 63  === openMINDS instances ===
64 64  
65 -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