Last modified by lzehl on 2021/07/02 17:06
From version 7.1
edited by lzehl
on 2021/02/18 17:56
Change comment: There is no comment for this version
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, grouped into five classes:
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  
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 +
17 17  {{container layoutStyle="columns"}}
18 18  (((
19 19  (% class="small" %)
20 -ACTORS
21 -Affiliation
22 -ContactInformation
23 -Contribution
24 -Organization
25 -Person
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
26 26  )))
27 27  (((
28 28  (% class="small" %)
29 -DATA
30 -ContentType
31 -Copyright
32 -FileBundle
33 -FileInstance
34 -FileRepository
35 -Hash
36 -License
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
37 37  )))
38 38  (((
39 39  (% class="small" %)
40 -MISCELLANEOUS
41 -DigitalIdentifier
42 -DigitalIdentifierSchema
43 -Funding
44 -QuantitativeValue
45 -QuantitativeValueRange
117 +ProgrammingLanguage
118 +QualitativeOverlap
119 +SoftwareApplicationCategory
120 +SoftwareFeature
121 +Species
122 +Strain
123 +Technique
124 +Terminology
125 +TissueSampleType
126 +TypeOfUncertainty
127 +UnitOfMeasurement
46 46  )))
129 +{{/container}}
130 +
131 +=== openMINDS instances ===
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:
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"}}
47 47  (((
48 48  (% class="small" %)
49 -PRODUCTS
50 -Dataset
51 -DatasetVersion
52 -MetaDataModel
53 -MetaDataModelVersion
54 -Model
55 -ModelVersion
56 -Project
57 -Software
58 -SoftwareVersion
141 +contentType
59 59  )))
60 60  (((
61 61  (% class="small" %)
62 -RESEARCH
63 -ParameterSetting
64 -Protocol
65 -ProtocolExecution
66 -Subject
67 -SubjectGroup
68 -SubjectGroupState
69 -SubjectState
70 -TissueSample
71 -TissueSampleCollection
72 -TissueSampleCollectionState
73 -TissueSampleState
145 +License
74 74  )))
147 +(((
148 +(% class="small" %)
149 +DigitalIdentifierSchema
150 +)))
75 75  {{/container}}
76 76  
77 -=== openMINDS SANDS ===
153 +(% class="wikigeneratedid" style="text-align: justify;" %)
154 +For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
78 78  
79 -xxx
80 -
81 -=== openMINDS controlledTerms ===
82 -
83 -xxx
84 -
85 -=== openMINDS instances ===
86 -
87 -xxx
156 +(% class="wikigeneratedid" %)
157 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
Public

openMINDS