Last modified by lzehl on 2021/07/02 17:06
From version 6.1
edited by lzehl
on 2021/02/18 17:38
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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 -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: 28em"/>{{/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 +{{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 +
63 63  === openMINDS instances ===
64 64  
65 -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