Last modified by lzehl on 2021/07/02 17:06
From version 58.2
edited by lzehl
on 2021/05/02 14:25
Change comment: Update document after refactoring.
To version 16.1
edited by lzehl
on 2021/02/22 16:27
Change comment: There is no comment for this version

Summary

Details

Page properties
Parent
... ... @@ -1,1 +1,1 @@
1 -Collabs.openminds.Documentation on.WebHome
1 +Collabs.openminds.openMINDS core.WebHome
Content
... ... @@ -4,7 +4,7 @@
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 to available metadata instances for selected schemas (for the latest openMINDS release).
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.
... ... @@ -13,44 +13,172 @@
13 13  === openMINDS core ===
14 14  
15 15  (% style="text-align: justify;" %)
16 -The openMINDS core metadata model contains schemas that you can use to describe the general origin, resource location, and content of your research products in the field of neuroscience. Currently this metadata model comprises the following schemas, grouped into five classes:
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}}<iframe id="coreFrame" src="https://humanbrainproject.github.io/openMINDS/v2/core.html" width="100%" style="border:0; height: 35em"/>{{/html}}
18 +{{container layoutStyle="columns"}}
19 +(((
20 +(% class="small" %)
21 +**ACTORS**
22 +Affiliation
23 +ContactInformation
24 +Contribution
25 +Organization
26 +Person
27 +(% class="small" %)
28 +**DATA**
29 +ContentType*
30 +Copyright
31 +FileBundle
32 +FileInstance
33 +FileRepository
34 +Hash
35 +License*
36 +)))
37 +(((
38 +(% class="small" %)
39 +**MISCELLANEOUS**
40 +DigitalIdentifier
41 +DigitalIdentifierSchema*
42 +Funding
43 +QuantitativeValue
44 +QuantitativeValueRange
45 +(% class="small" %)
46 +**PRODUCTS**
47 +Dataset
48 +DatasetVersion
49 +MetaDataModel
50 +MetaDataModelVersion
51 +Model
52 +ModelVersion
53 +Project
54 +Software
55 +SoftwareVersion
56 +)))
57 +(((
58 +(% class="small" %)
59 +**RESEARCH**
60 +ParameterSetting
61 +Protocol
62 +ProtocolExecution
63 +Subject
64 +SubjectGroup
65 +SubjectGroupState
66 +SubjectState
67 +TissueSample
68 +TissueSampleCollection
69 +TissueSampleCollectionState
70 +TissueSampleState
71 +)))
72 +{{/container}}
21 21  
22 22  (% class="wikigeneratedid" style="text-align: justify;" %)
23 -In case of EBRAINS, metadata representations (instances) of a few selected schemas (**##ContentType##**, **##DititalIdentifierSchema##**, **##License##**) are centrally defined and maintained in a library on a separate [[openMINDS instances GitHub>>https://github.com/HumanBrainProject/openMINDS_instances/||rel="noopener noreferrer" target="_blank"]] to guarantee more consistency across the database instances of the EBRAINS Knowledge Graph. Feel free to explore these instances and to use them also outside of the EBRAINS Knowledge Graph.
75 +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).
24 24  
25 25  (% class="wikigeneratedid" style="text-align: justify;" %)
26 -For further details on this metadata model, please check out the [[openMINDS core GitHub repository>>https://github.com/HumanBrainProject/openMINDS_core]].
78 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
27 27  
80 +(% class="wikigeneratedid" %)
81 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
82 +
28 28  === openMINDS SANDS ===
29 29  
30 30  (% style="text-align: justify;" %)
31 -The openMINDS SANDS (**S**patial **A**nchoring for **N**euroscience **D**ata **S**tructures) metadata model contains schemas that you can use to capture the anatomical location of your neuroscience data as well as to identify and highlight commonly used reference brain atlases and coordinate spaces. Currently this metadata model comprises the following schemas:
86 +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:
32 32  
33 -(% style="text-align: right;" %)
34 -(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
35 -{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/v2/SANDS.html" width="100%" style="border:0; height: 20em"/>{{/html}}
88 +{{container layoutStyle="columns"}}
89 +(((
90 +(% class="small" %)
91 +AnatomicalEntity
92 +AnatomicalEntityRelation
93 +Annotation
94 +AtlasTerminology
95 +)))
96 +(((
97 +(% class="small" %)
98 +BrainAtlas
99 +BrainAtlasVersion
100 +CoordinatePoint
101 +CoordinateSpace
102 +)))
103 +(((
104 +(% class="small" %)
105 +Electrode
106 +ElectrodeArray
107 +ElectrodeContact
108 +Image
109 +)))
110 +{{/container}}
36 36  
37 37  (% class="wikigeneratedid" style="text-align: justify;" %)
38 -For further details on this metadata model, please check out the [[openMINDS SANDS GitHub repository>>https://github.com/HumanBrainProject/openMINDS_SANDS]].
113 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
39 39  
40 -=== openMINDS controlledTerms ===
115 +(% class="wikigeneratedid" %)
116 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
41 41  
118 +=== openMINDS controlledTerms - schemas ===
119 +
42 42  (% style="text-align: justify;" %)
43 -The openMINDS controlledTerms metadata model contains schemas that ensure consistent registration of well-defined terms, including linkages to existing ontological terms where applicable. Currently this metadata model comprises the following schemas:
121 +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:
44 44  
45 -(% style="text-align: right;" %)
46 -(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
47 -{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/v2/controlledTerms.html" width="100%" style="border:0; height: 25em"/>{{/html}}
123 +{{container layoutStyle="columns"}}
124 +(((
125 +(% class="small" %)
126 +AgeCategory
127 +AnatomicalAxesOrientation
128 +BehavioralTask
129 +BiologicalSex
130 +CellType
131 +ContributionType
132 +CriteriaQualityType
133 +DatasetType
134 +Disease
135 +DiseaseModel
136 +EthicsAssessment
137 +FileBundleGrouping
138 +FileUsageRole
139 +)))
140 +(((
141 +(% class="small" %)
142 +Genotype
143 +Language
144 +Laterality
145 +MetaDataModelType
146 +Modality
147 +ModelAbstractionLevel
148 +ModelScope
149 +OperatingDevice
150 +OperatingSystem
151 +Organ
152 +Phenotype
153 +PreparationType
154 +ProductAccessibility
155 +)))
156 +(((
157 +(% class="small" %)
158 +ProgrammingLanguage
159 +QualitativeOverlap
160 +SoftwareApplicationCategory
161 +SoftwareFeature
162 +Species
163 +Strain
164 +Technique
165 +TermSuggestion*
166 +Terminology
167 +TissueSampleType
168 +TypeOfUncertainty
169 +UnitOfMeasurement
170 +)))
171 +{{/container}}
48 48  
49 -(% class="wikigeneratedid" style="text-align: justify;" %)
50 -Except for **##TermSuggestion##**, the openMINDS controlledTerms metadata schemas differ only in their schema type which defines the terminology to which correspondingly created metadata representations (instances) belong to. In order to guarantee more consistency across the database instances of the EBRAINS Knowledge Graph, instances for all controlled terms (except **##TermSuggestion##**) are centrally defined and maintained in a library on a separate [[openMINDS instances GitHub>>https://github.com/HumanBrainProject/openMINDS_instances/||rel="noopener noreferrer" target="_blank"]]. Feel free to explore these instances and to use them also outside of the EBRAINS Knowledge Graph.
51 -
52 52  (% style="text-align: justify;" %)
53 -We expect the list of controlled terms (schema as well as instances) to grow based on your feedback. For instances within the EBRAINS Knowledge Graph that are entries for the property ##"studyTarget"##, you can provide this feedback directly through the schema **##TermSuggestion##**. For all other instances (e.g., of type **##Technique##** or **##BehavioralTask##**) or if you work independent of the EBRAINS Knowledge Graph, please provide your feedback through the [[openMINDS instances GitHub Issue Tracker>>https://github.com/HumanBrainProject/openMINDS_instances/issues||rel="noopener noreferrer" target="_blank"]]. The openMINDS development team reviews all your feedback regularly, in order to integrate all community-driven suggestions into the openMINDS_controlledTerms and openMINDS_instances (where applicable). In addition, your term suggestions will be evaluated as possible extensions for the SciGraph ontologies, powered by the FAIR Data Informatics (FDI) Lab - SciCrunch Infrastrucutre and the INCF Knowledge Space team.
174 +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). 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.
54 54  
55 55  (% class="wikigeneratedid" style="text-align: justify;" %)
56 -For further details on this metadata model, please check out the [[openMINDS controlledTerms GitHub repository>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]].
177 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
178 +
179 +(% class="wikigeneratedid" %)
180 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
181 +
182 +=== openMINDS instances ===
183 +
184 +xxx
Public

openMINDS