Template:Workflow: Difference between revisions

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T4 reidelbach (talk | contribs)
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539 edits
T4 reidelbach (talk | contribs)
private
539 edits
 
(23 intermediate revisions by the same user not shown)
Line 158: Line 158:
       (GROUP_CONCAT(DISTINCT ?outputLink; separator=", ") AS ?Output)
       (GROUP_CONCAT(DISTINCT ?outputLink; separator=", ") AS ?Output)
       (GROUP_CONCAT(DISTINCT ?methodLink; separator=", ") AS ?Method)
       (GROUP_CONCAT(DISTINCT ?methodLink; separator=", ") AS ?Method)
       (GROUP_CONCAT(DISTINCT ?environmentLabel; separator=", ") AS ?Environment)
       (GROUP_CONCAT(DISTINCT ?environmentLink; separator=", ") AS ?Environment)
       (GROUP_CONCAT(DISTINCT ?disciplineLink; separator=", ") AS ?Discipline)
       (GROUP_CONCAT(DISTINCT ?disciplineLink; separator=", ") AS ?Discipline)


Line 221: Line 221:
     ?environmentID rdfs:label ?environmentLabel.
     ?environmentID rdfs:label ?environmentLabel.
     FILTER (lang(?environmentLabel) = 'en')
     FILTER (lang(?environmentLabel) = 'en')
    BIND(replace( xsd:string(?environmentID),
      'https://portal.mardi4nfdi.de/entity/',
      '') as ?environmentQID)
    BIND (CONCAT('<a href=\'/wiki/Item:',?environmentQID,'\'>',?environmentLabel,'</a>') as ?environmentLink)
   }
   }
    
    
Line 245: Line 249:
}}
}}
</div>
</div>
=== Applied methods ===
=== Applied methods ===
<div class='no-pagination no-filter'>
<div class='no-pagination no-filter'>
{{#sparql:
{{#sparql:
SELECT ?ID
SELECT ?Name
      ?Name
       ?Description
       ?Description
       (GROUP_CONCAT(DISTINCT ?stepLink; separator=", ") AS ?ProcessStep)
       (GROUP_CONCAT(DISTINCT ?stepLink; separator=", ") AS ?Process_Step)
       (GROUP_CONCAT(DISTINCT ?softwareLink; separator=", ") AS ?ImplementedBy)
       (GROUP_CONCAT(DISTINCT ?softwareLink; separator=", ") AS ?Implemented_By)
        
        
WHERE {
WHERE {
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<div class='no-pagination no-filter'>
<div class='no-pagination no-filter'>
{{#sparql:
{{#sparql:
SELECT ?ID
SELECT ?Name
      ?Name
       ?Description
       ?Description
       ?Version
       ?Version
       (GROUP_CONCAT(DISTINCT ?plLink; separator=", ") AS ?ProgrammingLanguage)
       (GROUP_CONCAT(DISTINCT ?plLink; separator=", ") AS ?Programming_Language)
       (GROUP_CONCAT(DISTINCT ?dpLink; separator=", ") AS ?Dependencies)
       (GROUP_CONCAT(DISTINCT ?dpLink; separator=", ") AS ?Dependencies)
       ?versioned
       ?versioned
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<div class='no-pagination no-filter'>
<div class='no-pagination no-filter'>
{{#sparql:
{{#sparql:
SELECT ?ID
SELECT ?Name
      ?Name
       ?Description
       ?Description
       (GROUP_CONCAT(DISTINCT ?processorLink; separator=", ") AS ?Processor)
       (GROUP_CONCAT(DISTINCT ?processorLink; separator=", ") AS ?Processor)
       (GROUP_CONCAT(DISTINCT ?nodes; separator=", ") AS ?NumberOfNodes)
       (GROUP_CONCAT(DISTINCT ?nodes; separator=", ") AS ?Node_Number)
       (GROUP_CONCAT(DISTINCT ?cores; separator=", ") AS ?NumberOfCores)
       (GROUP_CONCAT(DISTINCT ?cores; separator=", ") AS ?Core_Number)
        
        
WHERE {
WHERE {
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</div>
</div>


=== Input data ===
=== Data Sets ===
<div class="no-pagination no-filter">  
<div class="no-pagination no-filter">  
{{#sparql:
{{#sparql:
SELECT ?ID
SELECT ?Name
       ?Name
       ?Description
       ?Size
       ?Size
       ?DataStructure
       (?DataType AS ?Data_Type)
       ?ExchangeFormat
       (?RepresentationFormat AS ?Representation_Format)
       ?BinaryOrText
       (?FileFormat AS ?File_Format)
      (?BinaryOrText AS ?Binary_Text)
       ?Proprietary
       ?Proprietary
       ?toPublish
       (?toPublish AS ?to_Publish)
       ?toArchive
       (?toArchive AS ?to_Archive)
        
        
WHERE {
WHERE {
Line 463: Line 466:
   # Get Data
   # Get Data
   OPTIONAL {
   OPTIONAL {
     ?stepID wdt:P1605 ?inputID.
     {?stepID wdt:P1605 ?inputID.}
    UNION
    {?stepID wdt:P1606 ?inputID.}
     ?inputID rdfs:label ?NameLabel.
     ?inputID rdfs:label ?NameLabel.
     FILTER (lang(?NameLabel) = 'en')
     FILTER (lang(?NameLabel) = 'en')
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     BIND(CONCAT('mardi:','<a href=\'/wiki/Item:',?qid,'\'>',?qid,'</a>') as ?ID)
     BIND(CONCAT('mardi:','<a href=\'/wiki/Item:',?qid,'\'>',?qid,'</a>') as ?ID)
     BIND(CONCAT('<a href=\'/wiki/Item:',?qid,'\'>',?NameLabel,'</a>') as ?Name)
     BIND(CONCAT('<a href=\'/wiki/Item:',?qid,'\'>',?NameLabel,'</a>') as ?Name)
  OPTIONAL {
    ?inputID schema:description ?Description.
    FILTER (lang(?Description) = 'en')}


   # Data Size (maps to Size if File etc size is provided)
   # Data Size (maps to Size if File etc size is provided)
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}
}
    
    
   # Number of Records (maps to Size if Number of Entries in a Database etc is provided=
   # Number of Records (maps to Size if Number of Entries in a Database etc is provided
   OPTIONAL {
   OPTIONAL {
     ?inputID wdt:P139 ?Sizeraw
     ?inputID wdt:P139 ?Sizeraw
Line 491: Line 500:
   }
   }
    
    
   # Data Structure
   # Data Type
   OPTIONAL {
   OPTIONAL {
     ?inputID wdt:P1193 ?DataStructure
     ?inputID p:P557 ?statement_dt.
    ?statement_dt ps:P557 ?datatypeID.
    ?statement_dt pq:P560 ?qualifier.
    FILTER (?qualifier = wd:Q78802)
    ?datatypeID rdfs:label ?datatypeLabel. 
    FILTER (lang(?datatypeLabel) = 'en')
    BIND(replace( xsd:string(?datatypeID),
        'https://portal.mardi4nfdi.de/entity/',
        '') as ?datatypeQID) 
 
    BIND (CONCAT('<a href=\'/wiki/Item:',?datatypeQID,'\'>',?datatypeLabel,'</a>') as ?DataType)
     }
     }
      
      
   # Exchange Format
   # Representation Format
   OPTIONAL {
   OPTIONAL {
     ?inputID wdt:P921 ?ExchangeFormat
    ?inputID p:P557 ?statement_rf.
    ?statement_rf ps:P557 ?representationID.
    ?statement_rf pq:P560 ?qualifier2.
    FILTER (?qualifier2 = wd:Q6534222)
    ?representationID rdfs:label ?representationLabel. 
    FILTER (lang(?representationLabel) = 'en')
    BIND(replace( xsd:string(?representationID),
        'https://portal.mardi4nfdi.de/entity/',
        '') as ?representationQID) 
 
    BIND (CONCAT('<a href=\'/wiki/Item:',?representationQID,'\'>',?representationLabel,'</a>') as ?RepresentationFormat)
    }
   
  # File Format
  OPTIONAL {
     ?inputID wdt:P921 ?FileFormat
     }
     }
    
    
Line 546: Line 580:
      
      
   }
   }
} GROUP BY ?ID ?Name ?Size ?DataStructure ?ExchangeFormat ?BinaryOrText ?Proprietary ?toPublish ?toArchive
} GROUP BY ?ID ?Name ?Description ?Size ?DataType ?RepresentationFormat ?FileFormat ?BinaryOrText ?Proprietary ?toPublish ?toArchive
 
| chart=bordercloud.visualization.DataTable
| options=width=100%!
| endpoint=https://query.portal.mardi4nfdi.de/proxy/wdqs/bigdata/namespace/wdq/sparql
}}
</div>
 
=== Output data ===
<div class="no-pagination no-filter">
{{#sparql:
SELECT ?ID
      ?Name
      ?Size
      ?DataStructure
      ?ExchangeFormat
      ?BinaryOrText
      ?Proprietary
      ?toPublish
      ?toArchive
     
WHERE {
 
  # Get Step
  wd:{{#invoke:Wd|label|raw|}} p:P557 ?mainStatement.
  ?mainStatement ps:P557 ?stepID.
  ?stepID wdt:P31 wd:Q6486603.           
 
  # Get Data
  OPTIONAL {
    ?stepID wdt:P1606 ?outputID.
    ?outputID rdfs:label ?NameLabel.
    FILTER (lang(?NameLabel) = 'en')
   
    BIND(replace( xsd:string(?outputID),
      'https://portal.mardi4nfdi.de/entity/',
      '') as ?qid)
   
    BIND(CONCAT('mardi:','<a href=\'/wiki/Item:',?qid,'\'>',?qid,'</a>') as ?ID)
    BIND(CONCAT('<a href=\'/wiki/Item:',?qid,'\'>',?NameLabel,'</a>') as ?Name)
 
  # Data Size (maps to Size if File etc size is provided)
  OPTIONAL {
    ?outputID p:P1542 ?statementNode.         
    ?statementNode psv:P1542 ?valueNode.     
    ?valueNode wikibase:quantityAmount ?size;
              wikibase:quantityUnit ?unit.
    ?unit rdfs:label ?unitlabel.
    FILTER (lang(?unitlabel) = 'en')
    BIND(CONCAT(STR(?size), ' ', STR(?unitlabel)) AS ?Size)
}
 
  # Number of Records (maps to Size if Number of Entries in a Database etc is provided=
  OPTIONAL {
    ?outputID wdt:P139 ?Sizeraw
    BIND(CONCAT(STR(?Sizeraw),' Items') as ?Size)
  }
 
  # Data Structure
  OPTIONAL {
    ?outputID wdt:P1193 ?DataStructure
    }
   
  # Exchange Format
  OPTIONAL {
    ?outputID wdt:P921 ?ExchangeFormat
    }
 
  # Binary or Text
  BIND(IF(EXISTS { ?outputID wdt:P31 wd:Q6480276 }, "binary", IF(EXISTS { ?outputID wdt:P31 wd:Q6534207 }, "text", "" )) AS ?BinaryOrText)
 
  # Proprietary
  BIND(IF(EXISTS { ?outputID wdt:P31 wd:Q6480367 }, "yes", IF(EXISTS { ?outputID wdt:P31 wd:Q6480313 }, "no", "" )) AS ?Proprietary)
 
  # Bind DOI and URL if they exist
  OPTIONAL { ?outputID wdt:P23 ?doi. }
  OPTIONAL { ?outputID wdt:P188 ?url. }
 
  # Data Publishing
  BIND(
  IF(EXISTS { ?outputID wdt:P1563 wd:Q6480291 },
    IF(EXISTS { ?outputID wdt:P27 ?doi },
        CONCAT('<a href="', 'https://dx.doi.org', STR(?doi), '">yes</a>'),
        IF(EXISTS { ?outputID wdt:P188 ?url },
          CONCAT('<a href="', STR(?url), '">yes</a>'),
          "yes"
        )
    ),
    "no"
  ) AS ?toPublish
)
 
# Data Archiving
 
  OPTIONAL {
  ?outputID p:P1563 ?statementNode.
  ?statementNode ps:P1563 wd:Q6480370.
  OPTIONAL {
    ?statementNode pq:P411 ?endTime.
  }
}
 
BIND(
  IF(BOUND(?statementNode),
    IF(BOUND(?endTime),
        SUBSTR(STR(?endTime), 1, 4),
        "yes"
    ),
    "no"
  ) AS ?toArchive
)
   
  }
} GROUP BY ?ID ?Name ?Size ?DataStructure ?ExchangeFormat ?BinaryOrText ?Proprietary ?toPublish ?toArchive


| chart=bordercloud.visualization.DataTable
| chart=bordercloud.visualization.DataTable
Line 670: Line 591:
<div class='no-pagination no-filter'>
<div class='no-pagination no-filter'>
{{#sparql:
{{#sparql:
SELECT ?math_result
SELECT ?Mathematically
       ?run_result
       ?Runtime
       ?res_result
       ?Result
       ?plat_result
       (?OriginalPlatform AS ?Original_Platform)
       ?xplat_result
       (?CrossPlatform AS ?Cross_Platform)
       ?Transferability
       ?Transferability
        
        
WHERE {
WHERE {
 
 
   # Mathematical Reproducibility  
   # Mathematical Reproducibility
  BIND("No" AS ?math_result)
   OPTIONAL {
   OPTIONAL {
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?math_statement.
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?math_statement.
     ?math_statement ps:P31 wd:Q6534210.
     ?math_statement ps:P31 wd:Q6534210.
     BIND("Yes" AS ?math_result)
     BIND("Yes" AS ?math_hasTriple)
     OPTIONAL {
     OPTIONAL {
       ?math_statement pq:P8 ?math_text.
       ?math_statement pq:P8 ?math_text.
       BIND(CONCAT("Yes: ", STR(?math_text)) AS ?math_result)
       BIND(CONCAT("Yes: ", STR(?math_text)) AS ?math_result)
    }
      }
   }
   }
  BIND(IF(BOUND(?math_result), ?math_result, IF(BOUND(?math_hasTriple), "Yes", "No")) AS ?Mathematically)
    
    
   # Runtime Reproducibility  
   # Runtime Reproducibility
  BIND("No" AS ?run_result)
   OPTIONAL {
   OPTIONAL {
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?run_statement.
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?run_statement.
     ?run_statement ps:P31 wd:Q6534211.
     ?run_statement ps:P31 wd:Q6534211.
     BIND("Yes" AS ?run_result)
     BIND("Yes" AS ?run_hasTriple)
     OPTIONAL {
     OPTIONAL {
       ?run_statement pq:P8 ?run_text.
       ?run_statement pq:P8 ?run_text.
       BIND(CONCAT("Yes: ", GROUP_CONCAT(DISTINCT STR(?run_text); separator=", ")) AS ?run_result)
       BIND(CONCAT("Yes: ", STR(?run_text)) AS ?run_result)
    }
      }
   }
   }
  BIND(IF(BOUND(?run_result), ?run_result, IF(BOUND(?run_hasTriple), "Yes", "No")) AS ?Runtime)
    
    
   # Result Reproducibility  
   # Result Reproducibility
  BIND("No" AS ?res_result)
   OPTIONAL {
   OPTIONAL {
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?res_statement.
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?res_statement.
     ?res_statement ps:P31 wd:Q6534212.
     ?res_statement ps:P31 wd:Q6534212.
     BIND("Yes" AS ?res_result)
     BIND("Yes" AS ?res_hasTriple)
     OPTIONAL {
     OPTIONAL {
       ?res_statement pq:P8 ?res_text.
       ?res_statement pq:P8 ?res_text.
       BIND(CONCAT("Yes: ", GROUP_CONCAT(DISTINCT STR(?res_text); separator=", ")) AS ?res_result)
       BIND(CONCAT("Yes: ", STR(?res_text)) AS ?res_result)
    }
      }
   }
   }
  BIND(IF(BOUND(?res_result), ?res_result, IF(BOUND(?res_hasTriple), "Yes", "No")) AS ?Result)
    
    
   # Original Platform Reproducibility  
   # Original Platform Reproducibility
  BIND("No" AS ?plat_result)
   OPTIONAL {
   OPTIONAL {
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?plat_statement.
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?plat_statement.
     ?plat_statement ps:P31 wd:Q6534213.
     ?plat_statement ps:P31 wd:Q6534213.
     BIND("Yes" AS ?plat_result)
     BIND("Yes" AS ?plat_hasTriple)
     OPTIONAL {
     OPTIONAL {
       ?plat_statement pq:P8 ?plat_text.
       ?plat_statement pq:P8 ?plat_text.
       BIND(CONCAT("Yes: ", GROUP_CONCAT(DISTINCT STR(?plat_text); separator=", ")) AS ?plat_result)
       BIND(CONCAT("Yes: ", STR(?plat_text)) AS ?plat_result)
    }
      }
   }
   }
  BIND(IF(BOUND(?plat_result), ?plat_result, IF(BOUND(?plat_hasTriple), "Yes", "No")) AS ?OriginalPlatform)
    
    
   # Other Platform Reproducibility  
   # Cross Platform Reproducibility
  BIND("No" AS ?xplat_result)
   OPTIONAL {
   OPTIONAL {
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?xplat_statement.
     wd:{{#invoke:Wd|label|raw|}} p:P31 ?xplat_statement.
     ?xplat_statement ps:P31 wd:Q6534214.
     ?xplat_statement ps:P31 wd:Q6534214.
     BIND("Yes" AS ?xplat_result)
     BIND("Yes" AS ?xplat_hasTriple)
     OPTIONAL {
     OPTIONAL {
       ?xplat_statement pq:P8 ?xplat_text.
       ?xplat_statement pq:P8 ?xplat_text.
       BIND(CONCAT("Yes: ", GROUP_CONCAT(DISTINCT STR(?xplat_text); separator=", ")) AS ?xplat_result)
       BIND(CONCAT("Yes: ", STR(?xplat_text)) AS ?xplat_result)
    }
      }
   }
   }
  BIND(IF(BOUND(?xplat_result), ?xplat_result, IF(BOUND(?xplat_hasTriple), "Yes", "No")) AS ?CrossPlatform)
    
    
   # Transferability  
   # Transferability  
Line 751: Line 672:
   BIND(IF(BOUND(?trans_result), ?trans_result, IF(BOUND(?trans_hasTriple), "Yes", "No")) AS ?Transferability)
   BIND(IF(BOUND(?trans_result), ?trans_result, IF(BOUND(?trans_hasTriple), "Yes", "No")) AS ?Transferability)
}
}
GROUP BY ?math_result ?run_result ?res_result ?plat_result ?xplat_result ?Transferability
GROUP BY ?Mathematically ?Runtime ?Result ?OriginalPlatform ?CrossPlatform ?Transferability


| chart=bordercloud.visualization.DataTable
| chart=bordercloud.visualization.DataTable

Latest revision as of 11:54, 3 January 2025


Available identifiers

Problem statement

Object of research and objective

Involved disciplines

    Model

    Variables

    Parameters

    Process information

    Process steps

    Applied methods

    Software used

    Hardware

    Data Sets

    Reproducibility

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