Changes for page Metadata models and schemas

Last modified by lzehl on 2021/07/02 17:06

From 30.1 to 29.1 From 48.1 to 47.1

From version 47.1

edited by lzehl
on 2021/03/17 16:08

Change comment: There is no comment for this version

To version 30.1

edited by oschmid
on 2021/02/23 22:04

Change comment: There is no comment for this version

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@@ -1,1 +1,1 @@
--XWiki.lzehl
++XWiki.oschmid

Content

@@ -4,7 +4,7 @@
  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.
  (% style="text-align: justify;" %)
--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.
++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.
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  Note that all metadata models are licensed under the MIT license.
@@ -13,17 +13,76 @@
  === openMINDS core ===
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--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 ( Feb 2021) this metadata model comprises 37 usable schemas, grouped into five classes:
++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:
  (% style="text-align: right;" %)
  (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
--{{html}}<iframe id="coreFrame" src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height: 28em"/>{{/html}}
++{{html}}
++<iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height: 28em"/>
++{{/html}}
++
++{{container layoutStyle="columns"}}
++(((
++(% class="small" %)
++**ACTORS**
++Affiliation
++ContactInformation
++Contribution
++Organization
++Person
++(% class="small" %)
++**DATA**
++ContentType*
++Copyright
++FileBundle
++FileInstance
++FileRepository
++Hash
++License*
++)))
++(((
++(% class="small" %)
++**MISCELLANEOUS**
++DigitalIdentifier
++DigitalIdentifierSchema*
++Funding
++QuantitativeValue
++QuantitativeValueRange
++(% class="small" %)
++**PRODUCTS**
++Dataset
++DatasetVersion
++MetaDataModel
++MetaDataModelVersion
++Model
++ModelVersion
++Project
++Software
++SoftwareVersion
++)))
++(((
++(% class="small" %)
++**RESEARCH**
++ParameterSetting
++Protocol
++ProtocolExecution
++Subject
++SubjectGroup
++SubjectGroupState
++SubjectState
++TissueSample
++TissueSampleCollection
++TissueSampleCollectionState
++TissueSampleState
++)))
++{{/container}}
++
  (% class="wikigeneratedid" style="text-align: justify;" %)
--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.
++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).
  (% class="wikigeneratedid" style="text-align: justify;" %)
--For details on, contributing to, or reviewing examples of the openMINDS core metadata model please checkout the dedicated GitHub repository:
++For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
  (% class="wikigeneratedid" %)
  [[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
@@ -31,19 +31,45 @@
  === openMINDS SANDS ===
  (% style="text-align: justify;" %)
--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 (Feb 2021) this metadata model comprises 12 metadata schemas:
++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:
  (% style="text-align: right;" %)
  (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
--{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/SANDS.html" width="100%" style="border:0; height: 8em"/>{{/html}}
++(% style="text-align: right;" %)
++(% class="small" style="color:#7f8c8d" %){{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/SANDS.html" width="100%" style="border:0; height: 8em"/>{{/html}}
++
++{{container layoutStyle="columns"}}
++(((
++(% class="small" %)
++AnatomicalEntity
++AnatomicalEntityRelation
++Annotation
++AtlasTerminology
++)))
++(((
++(% class="small" %)
++BrainAtlas
++BrainAtlasVersion
++CoordinatePoint
++CoordinateSpace
++)))
++(((
++(% class="small" %)
++Electrode
++ElectrodeArray
++ElectrodeContact
++Image
++)))
++{{/container}}
++
  (% class="wikigeneratedid" style="text-align: justify;" %)
--For details on, contributing to, or reviewing examples of the openMINDS SANDS metadata model please checkout the dedicated GitHub repository:
++For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
  (% class="wikigeneratedid" %)
  [[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
--=== openMINDS controlledTerms ===
++=== openMINDS controlledTerms - schemas ===
  (% style="text-align: justify;" %)
  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:
@@ -50,16 +50,152 @@
  (% style="text-align: right;" %)
  (% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
--{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/controlledTerms.html" width="100%" style="border:0; height: 25em"/>{{/html}}
--(% class="wikigeneratedid" style="text-align: justify;" %)
--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 are centrally defined and maintained in a library on the openMINDS controlledTerms GitHub under [[**##terminologies/##**>>https://github.com/HumanBrainProject/openMINDS_controlledTerms/tree/v1/terminologies]]. Feel free to explore these instances and to use them also outside of the EBRAINS Knowledge Graph.
++(% style="text-align: right;" %)
++(% class="small" style="color:#7f8c8d" %){{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/SANDS.html" width="100%" style="border:0; height: 25em"/>{{/html}}
++{{container layoutStyle="columns"}}
++(((
++(% class="small" %)
++AgeCategory
++AnatomicalAxesOrientation
++BehavioralTask
++BiologicalSex
++CellType
++ContributionType
++CriteriaQualityType
++DatasetType
++Disease
++DiseaseModel
++EthicsAssessment
++FileBundleGrouping
++FileUsageRole
++)))
++(((
++(% class="small" %)
++Genotype
++Language
++Laterality
++MetaDataModelType
++Modality
++ModelAbstractionLevel
++ModelScope
++OperatingDevice
++OperatingSystem
++Organ
++Phenotype
++PreparationType
++ProductAccessibility
++)))
++(((
++(% class="small" %)
++ProgrammingLanguage
++QualitativeOverlap
++SoftwareApplicationCategory
++SoftwareFeature
++Species
++Strain
++Technique
++TermSuggestion*
++Terminology
++TissueSampleType
++TypeOfUncertainty
++UnitOfMeasurement
++)))
++{{/container}}
++
  (% style="text-align: justify;" %)
--We expect the list of controlled terms (schema as well as instances) to grow based on your feedback. The schema **##TermSuggestion##**, provides you therefore with the possibility to define your own controlled term that is still missing in our library. For this purpose, the **##TermSuggestion##** has two more properties ("addExistingTerminology", "suggestNewTerminology") where you can state to which terminology the new suggested (not yet controlled) term should belong 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 ontologies (where applicable).
++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).
++(% style="text-align: justify;" %)
++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).
++
  (% class="wikigeneratedid" style="text-align: justify;" %)
--For details on, contributing to, or reviewing examples of the openMINDS controlledTerms metadata model please checkout the dedicated GitHub repository:
++For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
  (% class="wikigeneratedid" %)
  [[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
++
++=== openMINDS controlledTerms - terminologies ===
++
++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:
++
++(% style="text-align: right;" %)
++(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
++
++{{container layoutStyle="columns"}}
++(((
++(% class="small" %)
++AgeCategory
++AnatomicalAxesOrientation
++BehavioralTask
++BiologicalSex
++CellType
++ContributionType
++CriteriaQualityType
++DatasetType
++Disease
++DiseaseModel
++EthicsAssessment
++FileBundleGrouping
++FileUsageRole
++)))
++(((
++(% class="small" %)
++Genotype
++Language
++Laterality
++MetaDataModelType
++Modality
++ModelAbstractionLevel
++ModelScope
++OperatingDevice
++OperatingSystem
++Organ
++Phenotype
++PreparationType
++ProductAccessibility
++)))
++(((
++(% class="small" %)
++ProgrammingLanguage
++QualitativeOverlap
++SoftwareApplicationCategory
++SoftwareFeature
++Species
++Strain
++Technique
++Terminology
++TissueSampleType
++TypeOfUncertainty
++UnitOfMeasurement
++)))
++{{/container}}
++
++=== openMINDS instances ===
++
++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:
++
++(% style="text-align: right;" %)
++(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
++
++{{container layoutStyle="columns"}}
++(((
++(% class="small" %)
++contentType
++)))
++(((
++(% class="small" %)
++License
++)))
++(((
++(% class="small" %)
++DigitalIdentifierSchema
++)))
++{{/container}}
++
++(% class="wikigeneratedid" style="text-align: justify;" %)
++For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
++
++(% class="wikigeneratedid" %)
++[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]