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 66.1
edited by lzehl
on 2021/07/02 17:06
Change comment: There is no comment for this version

Summary

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1 -Metadata models & schemas
1 +Metadata models and schemas
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1 -Collabs.openminds.openMINDS core.WebHome
1 +Collabs.openminds.Documentation.WebHome
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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 across all versions. Note that for some schemas, openMINDS provides also a library of controlled instances. The available controlled instances are listed in the HTML view for the respective schema.
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 ( Feb 2021) 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 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 (default: latest stable version):
16 16  
17 -{{container layoutStyle="columns"}}
18 -(((
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
35 -)))
36 -(((
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
55 -)))
56 -(((
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
70 -)))
71 -{{/container}}
18 +(% style="text-align: right;" %)
19 +(% class="small" style="color:#7f8c8d" %)Select a version and click on a schema to discover its full HTML description.
20 +{{html}}<iframe id="coreFrame" src="https://humanbrainproject.github.io/openMINDS/v2.0.0/core.html" width="100%" style="border:0; height: 35em"/>{{/html}}
72 72  
22 +(% class="wikigeneratedid" style="text-align: justify;" %)
23 +For the schemas **##ContentType##**, **##License##**, and **##Protocol##**, openMINDS provides a library of controlled instances that were defined and reviewed by corresponding experts of the openMINDS development team (cf. also below). In particular within EBRAINS, the usage of these controlled instances increase the level of data integration inside the EBRAINS Knowledge Graph. Feel free to explore these instances (in the HTML view or on the GitHub) and make use them, inside or outside of EBRAINS.
24 +
25 +(% class="wikigeneratedid" style="text-align: justify;" %)
26 +For further details or to review schemas of an older version of this metadata model, please check out the [[openMINDS core GitHub repository>>https://github.com/HumanBrainProject/openMINDS_core]].
27 +
73 73  === openMINDS SANDS ===
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:
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 (default: latest stable version):
76 76  
77 -{{container layoutStyle="columns"}}
78 -(((
79 -(% class="small" %)
80 -AnatomicalEntity
81 -AnatomicalEntityRelation
82 -Annotation
83 -AtlasTerminology
84 -)))
85 -(((
86 -(% class="small" %)
87 -BrainAtlas
88 -BrainAtlasVersion
89 -CoordinatePoint
90 -CoordinateSpace
91 -)))
92 -(((
93 -(% class="small" %)
94 -Electrode
95 -ElectrodeArray
96 -ElectrodeContact
97 -Image
98 -)))
99 -{{/container}}
33 +(% style="text-align: right;" %)
34 +(% class="small" style="color:#7f8c8d" %)Select a version and click on a schema to discover its full HTML description.
35 +{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/v2.0.0/SANDS.html" width="100%" style="border:0; height: 20em"/>{{/html}}
100 100  
37 +(% class="wikigeneratedid" style="text-align: justify;" %)
38 +For further details or to review schemas of an older version of this metadata model, please check out the [[openMINDS SANDS GitHub repository>>https://github.com/HumanBrainProject/openMINDS_SANDS]].
39 +
101 101  === openMINDS controlledTerms ===
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.
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 (default: latest stable version):
104 104  
45 +(% style="text-align: right;" %)
46 +(% class="small" style="color:#7f8c8d" %)Select a version and click on a schema to discover its full HTML description.
47 +{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/v2.0.0/controlledTerms.html" width="100%" style="border:0; height: 25em"/>{{/html}}
48 +
49 +(% 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 the correspondingly created metadata representations (instances) belong to.
51 +
52 +(% style="text-align: justify;" %)
53 +For all controlled terms schemas (except **##TermSuggestion##**), openMINDS provides a library of controlled instances that were defined and reviewed by corresponding experts of the openMINDS development team (cf. also below). In particular within EBRAINS, the usage of these controlled instances increase the level of data integration inside the EBRAINS Knowledge Graph. Feel free to explore these instances (in the HTML view or on the GitHub) and make use them, inside or outside of EBRAINS.
54 +
55 +(% style="text-align: justify;" %)
56 +The **##TermSuggestion##** schema was introduced to facilitate community-driven requests for new controlled terms and respective instances for the properties **##"studyOption"##** and **##"studyTarget"##** (which needs are particularly difficult to predict). Correspondingly suggested metadata instances will be frequently evaluated and integrated as proper controlled instances on the GitHub repository be the openMINDS development team.
57 +
58 +(% style="text-align: justify;" %)
59 +For further details or to review schemas of an older version of this metadata model, please check out the [[openMINDS controlledTerms GitHub repository>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]].
60 +
61 +=== openMINDS computation ===
62 +
63 +(% style="text-align: justify;" %)
64 +The openMINDS computation metadata model contains schemas that you can use to capture the provenance of simulations, data analysis and visualizations. Currently this metadata model comprises the following schemas (default: dev):
65 +
66 +(% style="text-align: right;" %)
67 +(% class="small" style="color:#7f8c8d" %)Select a version and click on a schema to discover its full HTML description.
68 +{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/v3/computation.html" width="100%" style="border:0; height: 20em"/>{{/html}}
69 +
70 +(% class="wikigeneratedid" style="text-align: justify;" %)
71 +For further details or to review schemas of an older version of this metadata model, please check out the [[openMINDS computation GitHub repository>>https://github.com/HumanBrainProject/openMINDS_computation]].
72 +
73 +=== openMINDS computation ===
74 +
75 +(% style="text-align: justify;" %)
76 +(% style="color:#7f8c8d" %)(//**coming soon**//)
77 +
105 105  === openMINDS instances ===
106 106  
107 -xxx
80 +(% style="text-align: justify;" %)
81 +For selected schemas, openMINDS provides a library of controlled instances that were defined and reviewed by corresponding experts of the openMINDS development team (cf. above). These instances are stored on the GitHub repository of the metadata model the respective schema belongs to. In particular within EBRAINS, the usage of these controlled instances increase the level of data integration inside the EBRAINS Knowledge Graph. Feel free to explore these instances (in the HTML view or on the GitHub) and make use them, inside or outside of EBRAINS.
82 +
83 +(% style="text-align: justify;" %)
84 +The libraries of these controlled instances will grow based on your feedback. If you miss an instance or terminology, feel free to make a corresponding request via our support email ([[openminds@ebrains.eu>>mailto:openminds@ebrains.eu]]) or raise an issue on the respective GitHub repository. Within EBRAINS, new controlled terms and respective instances for the properties **##"studyOption"##** and **##"studyTarget"##** (which needs are particularly difficult to predict) can also be made by filling out a **##TermSuggestion##** (cf. above).
85 +
86 +(% style="text-align: justify;" %)
87 +All your request are reviewed regularly by the openMINDS development team, in order to integrate all community-driven suggestions (where applicable). In addition, your 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.
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openMINDS