Changes for page Metadata models and schemas

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

From 29.1 to 30.1 From 63.1 to 64.1

From version 30.1

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

Change comment: There is no comment for this version

To version 63.1

edited by lzehl
on 2021/07/02 17:00

Change comment: There is no comment for this version

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Title

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--Metadata models & schemas
++Metadata models and schemas

Parent

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--Collabs.openminds.openMINDS core.WebHome
++Collabs.openminds.Documentation.WebHome

Author

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--XWiki.oschmid
++XWiki.lzehl

Content

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  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 links 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 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.
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  Note that all metadata models are licensed under the MIT license.
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  === openMINDS core ===
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--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:
++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):
  (% style="text-align: right;" %)
--(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
++(% class="small" style="color:#7f8c8d" %)Select a version and click on a schema to discover its full HTML description.
++{{html}}<iframe id="coreFrame" src="https://humanbrainproject.github.io/openMINDS/v2.0.0/core.html" width="100%" style="border:0; height: 35em"/>{{/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 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).
++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.
  (% class="wikigeneratedid" style="text-align: justify;" %)
--For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
++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]].
--(% class="wikigeneratedid" %)
--[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
--
  === openMINDS SANDS ===
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--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:
++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):
  (% style="text-align: right;" %)
--(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
++(% class="small" style="color:#7f8c8d" %)Select a version and click on a schema to discover its full HTML description.
++{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/v2.0.0/SANDS.html" width="100%" style="border:0; height: 20em"/>{{/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, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
++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]].
--(% class="wikigeneratedid" %)
--[[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
++=== openMINDS controlledTerms ===
--=== openMINDS controlledTerms - schemas ===
--
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--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:
++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):
  (% style="text-align: right;" %)
--(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
++(% class="small" style="color:#7f8c8d" %)Select a version and click on a schema to discover its full HTML description.
++{{html}}<iframe src="https://humanbrainproject.github.io/openMINDS/v2.0.0/controlledTerms.html" width="100%" style="border:0; height: 25em"/>{{/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: 25em"/>{{/html}}
++(% style="text-align: justify;" %)
++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.
--{{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;" %)
++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.
  (% style="text-align: justify;" %)
--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).
++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.
  (% 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).
++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]].
--(% class="wikigeneratedid" style="text-align: justify;" %)
--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: justify;" %)
++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.
--(% style="text-align: right;" %)
--(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
++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) 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).
--{{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]]
++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.