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 43.1
edited by oschmid
on 2021/02/24 11:53
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.
20 +{{html clean="false"}}<span>
21 +<script>
22 +function resize(evt){
23 +alert('hello world');
24 +}
25 +</script>
54 54  
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 +
55 55  === openMINDS SANDS ===
56 56  
57 -xxx
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:
58 58  
59 -=== openMINDS controlledTerms ===
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}}
60 60  
61 -xxx
48 +(% class="wikigeneratedid" style="text-align: justify;" %)
49 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
62 62  
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 +{{container layoutStyle="columns"}}
83 +(((
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
98 +)))
99 +(((
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
114 +)))
115 +(((
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
128 +)))
129 +{{/container}}
130 +
63 63  === openMINDS instances ===
64 64  
65 -xxx
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:
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 +{{container layoutStyle="columns"}}
139 +(((
140 +(% class="small" %)
141 +contentType
142 +)))
143 +(((
144 +(% class="small" %)
145 +License
146 +)))
147 +(((
148 +(% class="small" %)
149 +DigitalIdentifierSchema
150 +)))
151 +{{/container}}
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:
155 +
156 +(% class="wikigeneratedid" %)
157 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
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openMINDS