Last modified by lzehl on 2021/07/02 17:06
From version 11.1
edited by lzehl
on 2021/02/22 15:22
Change comment: There is no comment for this version
To version 35.1
edited by oschmid
on 2021/02/24 11:49
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 +(% style="text-align: justify;" %)
15 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 ( 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}}<iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height: 28em" onload="e -> alert(e)"/>
21 +{{/html}}
22 +
23 +(% class="wikigeneratedid" style="text-align: justify;" %)
24 +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).
25 +
26 +(% class="wikigeneratedid" style="text-align: justify;" %)
27 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
28 +
29 +(% class="wikigeneratedid" %)
30 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
31 +
32 +=== openMINDS SANDS ===
33 +
34 +(% style="text-align: justify;" %)
35 +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:
36 +
37 +(% style="text-align: right;" %)
38 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
39 +{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/SANDS.html" width="100%" style="border:0; height: 8em"/>{{/html}}
40 +
41 +(% class="wikigeneratedid" style="text-align: justify;" %)
42 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
43 +
44 +(% class="wikigeneratedid" %)
45 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
46 +
47 +=== openMINDS controlledTerms - schemas ===
48 +
49 +(% style="text-align: justify;" %)
50 +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:
51 +
52 +(% style="text-align: right;" %)
53 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
54 +{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/controlledTerms.html" width="100%" style="border:0; height: 25em"/>{{/html}}
55 +
56 +(% style="text-align: justify;" %)
57 +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).
58 +
59 +(% style="text-align: justify;" %)
60 +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).
61 +
62 +(% class="wikigeneratedid" style="text-align: justify;" %)
63 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
64 +
65 +(% class="wikigeneratedid" %)
66 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
67 +
68 +=== openMINDS controlledTerms - terminologies ===
69 +
70 +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:
71 +
72 +(% style="text-align: right;" %)
73 +(% class="small" style="color:#7f8c8d" %)//**Coming soon:** //Click on a schema to discover its available instances.
74 +
17 17  {{container layoutStyle="columns"}}
18 18  (((
19 19  (% class="small" %)
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
78 +AgeCategory
79 +AnatomicalAxesOrientation
80 +BehavioralTask
81 +BiologicalSex
82 +CellType
83 +ContributionType
84 +CriteriaQualityType
85 +DatasetType
86 +Disease
87 +DiseaseModel
88 +EthicsAssessment
89 +FileBundleGrouping
90 +FileUsageRole
35 35  )))
36 36  (((
37 37  (% class="small" %)
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
94 +Genotype
95 +Language
96 +Laterality
97 +MetaDataModelType
98 +Modality
99 +ModelAbstractionLevel
100 +ModelScope
101 +OperatingDevice
102 +OperatingSystem
103 +Organ
104 +Phenotype
105 +PreparationType
106 +ProductAccessibility
55 55  )))
56 56  (((
57 57  (% class="small" %)
58 -**RESEARCH**
59 -ParameterSetting
60 -Protocol
61 -ProtocolExecution
62 -Subject
63 -SubjectGroup
64 -SubjectGroupState
65 -SubjectState
66 -TissueSample
67 -TissueSampleCollection
68 -TissueSampleCollectionState
69 -TissueSampleState
110 +ProgrammingLanguage
111 +QualitativeOverlap
112 +SoftwareApplicationCategory
113 +SoftwareFeature
114 +Species
115 +Strain
116 +Technique
117 +Terminology
118 +TissueSampleType
119 +TypeOfUncertainty
120 +UnitOfMeasurement
70 70  )))
71 71  {{/container}}
72 72  
73 -=== openMINDS SANDS ===
124 +=== openMINDS instances ===
74 74  
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:
126 +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:
76 76  
128 +(% style="text-align: right;" %)
129 +(% class="small" style="color:#7f8c8d" %)//**Coming soon:**// Click on a schema to discover its available instances.
130 +
77 77  {{container layoutStyle="columns"}}
78 78  (((
79 79  (% class="small" %)
80 -AnatomicalEntity
81 -AnatomicalEntityRelation
82 -Annotation
83 -AtlasTerminology
134 +contentType
84 84  )))
85 85  (((
86 86  (% class="small" %)
87 -BrainAtlas
88 -BrainAtlasVersion
89 -CoordinatePoint
90 -CoordinateSpace
138 +License
91 91  )))
92 92  (((
93 93  (% class="small" %)
94 -Electrode
95 -ElectrodeArray
96 -ElectrodeContact
97 -Image
142 +DigitalIdentifierSchema
98 98  )))
99 99  {{/container}}
100 100  
101 -=== openMINDS controlledTerms ===
146 +(% class="wikigeneratedid" style="text-align: justify;" %)
147 +For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
102 102  
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
149 +(% class="wikigeneratedid" %)
150 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
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openMINDS