Last modified by lzehl on 2021/07/02 17:06
From version 43.1
edited by oschmid
on 2021/02/24 11:53
Change comment: There is no comment for this version
To version 11.1
edited by lzehl
on 2021/02/22 15:22
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 -(% style="text-align: right;" %)
19 -(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
20 -{{html clean="false"}}<span>
21 -<script>
22 -function resize(evt){
23 -alert('hello world');
24 -}
25 -</script>
26 -
27 -<iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height: 28em" onload="resize"/>
28 -</span>{{/html}}
29 -
30 -(% class="wikigeneratedid" style="text-align: justify;" %)
31 -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).
32 -
33 -(% class="wikigeneratedid" style="text-align: justify;" %)
34 -For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
35 -
36 -(% class="wikigeneratedid" %)
37 -[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
38 -
39 -=== openMINDS SANDS ===
40 -
41 -(% style="text-align: justify;" %)
42 -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:
43 -
44 -(% style="text-align: right;" %)
45 -(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
46 -{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/SANDS.html" width="100%" style="border:0; height: 8em"/>{{/html}}
47 -
48 -(% class="wikigeneratedid" style="text-align: justify;" %)
49 -For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
50 -
51 -(% class="wikigeneratedid" %)
52 -[[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
53 -
54 -=== openMINDS controlledTerms - schemas ===
55 -
56 -(% style="text-align: justify;" %)
57 -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:
58 -
59 -(% style="text-align: right;" %)
60 -(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
61 -{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/controlledTerms.html" width="100%" style="border:0; height: 25em"/>{{/html}}
62 -
63 -(% style="text-align: justify;" %)
64 -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).
65 -
66 -(% style="text-align: justify;" %)
67 -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).
68 -
69 -(% class="wikigeneratedid" style="text-align: justify;" %)
70 -For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
71 -
72 -(% class="wikigeneratedid" %)
73 -[[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
74 -
75 -=== openMINDS controlledTerms - terminologies ===
76 -
77 -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:
78 -
79 -(% style="text-align: right;" %)
80 -(% class="small" style="color:#7f8c8d" %)//**Coming soon:** //Click on a schema to discover its available instances.
81 -
82 82  {{container layoutStyle="columns"}}
83 83  (((
84 84  (% class="small" %)
85 -AgeCategory
86 -AnatomicalAxesOrientation
87 -BehavioralTask
88 -BiologicalSex
89 -CellType
90 -ContributionType
91 -CriteriaQualityType
92 -DatasetType
93 -Disease
94 -DiseaseModel
95 -EthicsAssessment
96 -FileBundleGrouping
97 -FileUsageRole
20 +**ACTORS**
21 +Affiliation
22 +ContactInformation
23 +Contribution
24 +Organization
25 +Person
26 +(% class="small" %)
27 +**DATA**
28 +ContentType
29 +Copyright
30 +FileBundle
31 +FileInstance
32 +FileRepository
33 +Hash
34 +License
98 98  )))
99 99  (((
100 100  (% class="small" %)
101 -Genotype
102 -Language
103 -Laterality
104 -MetaDataModelType
105 -Modality
106 -ModelAbstractionLevel
107 -ModelScope
108 -OperatingDevice
109 -OperatingSystem
110 -Organ
111 -Phenotype
112 -PreparationType
113 -ProductAccessibility
38 +**MISCELLANEOUS**
39 +DigitalIdentifier
40 +DigitalIdentifierSchema
41 +Funding
42 +QuantitativeValue
43 +QuantitativeValueRange
44 +(% class="small" %)
45 +**PRODUCTS**
46 +Dataset
47 +DatasetVersion
48 +MetaDataModel
49 +MetaDataModelVersion
50 +Model
51 +ModelVersion
52 +Project
53 +Software
54 +SoftwareVersion
114 114  )))
115 115  (((
116 116  (% class="small" %)
117 -ProgrammingLanguage
118 -QualitativeOverlap
119 -SoftwareApplicationCategory
120 -SoftwareFeature
121 -Species
122 -Strain
123 -Technique
124 -Terminology
125 -TissueSampleType
126 -TypeOfUncertainty
127 -UnitOfMeasurement
58 +**RESEARCH**
59 +ParameterSetting
60 +Protocol
61 +ProtocolExecution
62 +Subject
63 +SubjectGroup
64 +SubjectGroupState
65 +SubjectState
66 +TissueSample
67 +TissueSampleCollection
68 +TissueSampleCollectionState
69 +TissueSampleState
128 128  )))
129 129  {{/container}}
130 130  
131 -=== openMINDS instances ===
73 +=== openMINDS SANDS ===
132 132  
133 -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:
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:
134 134  
135 -(% style="text-align: right;" %)
136 -(% class="small" style="color:#7f8c8d" %)//**Coming soon:**// Click on a schema to discover its available instances.
137 -
138 138  {{container layoutStyle="columns"}}
139 139  (((
140 140  (% class="small" %)
141 -contentType
80 +AnatomicalEntity
81 +AnatomicalEntityRelation
82 +Annotation
83 +AtlasTerminology
142 142  )))
143 143  (((
144 144  (% class="small" %)
145 -License
87 +BrainAtlas
88 +BrainAtlasVersion
89 +CoordinatePoint
90 +CoordinateSpace
146 146  )))
147 147  (((
148 148  (% class="small" %)
149 -DigitalIdentifierSchema
94 +Electrode
95 +ElectrodeArray
96 +ElectrodeContact
97 +Image
150 150  )))
151 151  {{/container}}
152 152  
153 -(% class="wikigeneratedid" style="text-align: justify;" %)
154 -For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
101 +=== openMINDS controlledTerms ===
155 155  
156 -(% class="wikigeneratedid" %)
157 -[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
103 +The openMINDS controlledTerms metadata model contains schemas that ensure consistent registration of well-defined terms, including linkages to existing ontological terms where applicable.
104 +
105 +=== openMINDS instances ===
106 +
107 +xxx
Public

openMINDS