Difference between revisions of "Schema Representations"
From Meta-Omics Data of Collection Objects
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| − | Conceptual and procedural schemas and community standards are established to provide a common understanding of the meaning or semantics of data and data pipelines. They are built on sets of vocabulary/ ontology terms which can be used to describe resources for the purposes of discovery. Schema(s) and standard(s) enable structured data management and data exchange between data storage structures. Schema(s) might rely on standard vocabularies. In the MOD-CO context meta-omics-related vocabularies | + | Conceptual and procedural schemas and community standards are established to provide a common understanding of the meaning or semantics of data, concepts and data pipelines. They are built on sets of vocabulary/ ontology terms and naming conventions which can be used to describe resources for the purposes of discovery. Schema(s) and standard(s) enable structured data management and data exchange between data storage structures relying on them. Schema(s) might rely on standard vocabularies. In the MOD-CO project context meta-omics-related vocabularies were evaluated and a generic naming convention for schema elements was set up. |
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| + | The conceptual and procedural meta-omics schema is developed as part of the [https://www.mod-co.net/wiki/Main_Page MOD-CO project]. It is entitled with '''"MOD-CO schema – a conceptual schema for processing sample data in meta’omics research"''' and published in various kind of schema representations. With that, the MOD-CO schema is a generic and comprehensive schema providing specifications useful for later software implementation and facilitates international standardisation processes. Certain [[Implementations| Implementations and Use Cases]] are provided. | ||
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=== Access to MOD-CO schema === | === Access to MOD-CO schema === | ||
| − | + | '''Representation 1:''' versioned MOD-CO version 1.0 namespace scheme publication (static, snapshot): '''https://www.mod-co.net/wiki/MOD-CO_Schema_Reference''' | |
<div style="overflow:hidden;"> | <div style="overflow:hidden;"> | ||
{| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | {| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | ||
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|} | |} | ||
</div> | </div> | ||
| − | + | '''Representation 2:''' LOD-compliant MOD-CO version 1.0 namespace scheme publication under '''https://www.mod-co.net/wiki/MOD-CO''' with 2,463 [https://www.mod-co.net/wiki/Class:Concept 'concepts'], including 653 concepts (= [https://www.mod-co.net/wiki/Class:Class 'concept classes'] according to TDWG-compliant MediaWiki structure) and 1,810 (predefined) concept values (= [https://www.mod-co.net/wiki/Class:Property 'concept properties'] according to TDWG-compliant MediaWiki structure) | |
<div style="overflow:hidden;"> | <div style="overflow:hidden;"> | ||
{| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | {| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | ||
|- | |- | ||
! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:SemanticMediaWiki.png|x250px|thumb|Concept collections and concepts (LOD overview page)]] | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:SemanticMediaWiki.png|x250px|thumb|Concept collections and concepts (LOD overview page)]] | ||
| − | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File: | + | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:SMWconcept.png|x250px|thumb|Concept (LOD single unit page)]] |
|} | |} | ||
</div> | </div> | ||
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:* The editorial work will be followed by a regular data export and data import in the MOD-CO wiki for web access. | :* The editorial work will be followed by a regular data export and data import in the MOD-CO wiki for web access. | ||
:* The "View history" function of each wiki page is used to document the history of published editorial changes and have a documentation of the "issue date" and “modified date” for each single concept page. | :* The "View history" function of each wiki page is used to document the history of published editorial changes and have a documentation of the "issue date" and “modified date” for each single concept page. | ||
| − | + | '''Representation 3:''' SDD-structured XML document of MOD-CO version 1.0: '''MODCOschema1.0_SDDstructured.xml''' for download as ZIP archive [[:Media:MODCOschema1.0_SDDstructured.zip|'''here''']]. | |
<div style="overflow:hidden;"> | <div style="overflow:hidden;"> | ||
{| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | {| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | ||
|- | |- | ||
| − | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:SDD.png|x250px|thumb|SDD structured XML]] | + | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:SDD.png|x250px|thumb|SDD structured XML with descriptive concepts]] |
| − | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File: | + | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:SDDcharater.png|x250px|thumb|SDD structured XML with character definitions]] |
|} | |} | ||
</div> | </div> | ||
| − | + | *This XML representation might be imported in any installation of the ''DiversityDescriptions'' application or other applications with interfaces for data exchange with SDD. For download of ''DiversityDescriptions'' database and client see https://diversityworkbench.net/Portal/DiversityDescriptions. For SDD as a metastandard see [https://www.tdwg.org/standards/sdd/ Standard Description Download] and [http://rs.tdwg.org/UBIF/2006/Schema/SDD1.1rev5.zip SDD Schema files SDD1.1rev5]. | |
| − | * | + | *A zip archive with SDD-structured XML document of MOD-CO version 1.0 will be available as data publication through [https://www.gfbio.org/ GFBio] data pipelines with appropriate GFBio parameter assignments and SNSB as GFBio data center. |
| − | + | '''Representation 4:''' two ''DiversityDescriptions'' installations at the SNSB IT Center with MOD-CO schema version 1.0, one as read-only access for anonymous DWB users ([https://diversityworkbench.net/Portal/DWB_cloud_services DWB cloud services]) and the other for training and outreach purposes, i.e., '''integrated in the''' [https://diversityworkbench.net/Portal/DWB_training_environment '''DWB Training environment''']. | |
<div style="overflow:hidden;"> | <div style="overflow:hidden;"> | ||
{| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | {| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | ||
|- | |- | ||
! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:DescriptorTree2.png|x250px|thumb|Descriptor tree view in DiversityDescriptions]] | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:DescriptorTree2.png|x250px|thumb|Descriptor tree view in DiversityDescriptions]] | ||
| − | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File: | + | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:DD3.png|x250px|thumb| Descriptor=concept in DiversityDescriptions]] |
|} | |} | ||
</div> | </div> | ||
| − | + | '''Representation 5:''' '''Normative XSD (= XML Schema Definition)''' for MOD-CO schema version 1.0 is available under http://schema.mod-co.net/MOD-CO_1.0.xsd'''. | |
<div style="overflow:hidden;"> | <div style="overflow:hidden;"> | ||
{| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | {| cellpadding='0' align='left' width='800' style="border: 1px #FFFFFF solid; border-radius: 5px;" | ||
|- | |- | ||
! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:XSD.png|x250px|thumb|XML schema definition for MOD-CO]] | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:XSD.png|x250px|thumb|XML schema definition for MOD-CO]] | ||
| − | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File: | + | ! bgcolor='#FFFFFF' style="border-left: 1px #FFFFFF solid;"|[[File:XSDenum.png|x250px|thumb|XML schema definition for MOD-CO: Definition of enumerations]] |
|} | |} | ||
</div> | </div> | ||
| − | + | *The generation of the XSD with ''DiversityDescriptions'' is explained under [[MOD-CO normative XSD representation]]. The XSD is for validation of any external XML document assumed to be structured according MOD-CO concerning well-formedness. Validation might be done using any online XML validator. <!--, e.g. [https://www.freeformatter.com/xml-validator-xsd.html].--> | |
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===[[Feedback area]]=== | ===[[Feedback area]]=== | ||
Latest revision as of 17:07, 26 January 2021
Conceptual and procedural schemas and community standards are established to provide a common understanding of the meaning or semantics of data, concepts and data pipelines. They are built on sets of vocabulary/ ontology terms and naming conventions which can be used to describe resources for the purposes of discovery. Schema(s) and standard(s) enable structured data management and data exchange between data storage structures relying on them. Schema(s) might rely on standard vocabularies. In the MOD-CO project context meta-omics-related vocabularies were evaluated and a generic naming convention for schema elements was set up.
The conceptual and procedural meta-omics schema is developed as part of the MOD-CO project. It is entitled with "MOD-CO schema – a conceptual schema for processing sample data in meta’omics research" and published in various kind of schema representations. With that, the MOD-CO schema is a generic and comprehensive schema providing specifications useful for later software implementation and facilitates international standardisation processes. Certain Implementations and Use Cases are provided.
MOD-CO schema namespace in numbers
see under modco
Access to MOD-CO schema
Representation 1: versioned MOD-CO version 1.0 namespace scheme publication (static, snapshot): https://www.mod-co.net/wiki/MOD-CO_Schema_Reference
Representation 2: LOD-compliant MOD-CO version 1.0 namespace scheme publication under https://www.mod-co.net/wiki/MOD-CO with 2,463 'concepts', including 653 concepts (= 'concept classes' according to TDWG-compliant MediaWiki structure) and 1,810 (predefined) concept values (= 'concept properties' according to TDWG-compliant MediaWiki structure)
- The editing of concepts etc. for future versions is done in a master installation of DiversityDescriptions with export function.
- The editorial work will be followed by a regular data export and data import in the MOD-CO wiki for web access.
- The "View history" function of each wiki page is used to document the history of published editorial changes and have a documentation of the "issue date" and “modified date” for each single concept page.
Representation 3: SDD-structured XML document of MOD-CO version 1.0: MODCOschema1.0_SDDstructured.xml for download as ZIP archive here.
- This XML representation might be imported in any installation of the DiversityDescriptions application or other applications with interfaces for data exchange with SDD. For download of DiversityDescriptions database and client see https://diversityworkbench.net/Portal/DiversityDescriptions. For SDD as a metastandard see Standard Description Download and SDD Schema files SDD1.1rev5.
- A zip archive with SDD-structured XML document of MOD-CO version 1.0 will be available as data publication through GFBio data pipelines with appropriate GFBio parameter assignments and SNSB as GFBio data center.
Representation 4: two DiversityDescriptions installations at the SNSB IT Center with MOD-CO schema version 1.0, one as read-only access for anonymous DWB users (DWB cloud services) and the other for training and outreach purposes, i.e., integrated in the DWB Training environment.
Representation 5: Normative XSD (= XML Schema Definition) for MOD-CO schema version 1.0 is available under http://schema.mod-co.net/MOD-CO_1.0.xsd.
- The generation of the XSD with DiversityDescriptions is explained under MOD-CO normative XSD representation. The XSD is for validation of any external XML document assumed to be structured according MOD-CO concerning well-formedness. Validation might be done using any online XML validator.
