Help:WikiPathways Metabolomics

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} order by desc(?count)
} order by desc(?count)
</pre>
</pre>
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== All metabolites from one source ==
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=== All KEGG identifiers ===
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prefix wp:      <http://vocabularies.wikipathways.org/wp#>
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prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
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prefix dcterms:  <http://purl.org/dc/terms/>
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select distinct ?identifier
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where {
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  ?mb a wp:Metabolite ;
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    dc:source "Kegg Compound"^^xsd:string ;
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    dc:identifier ?identifier .
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  FILTER (!isIRI(?identifier))
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} order by ?identifier
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=== All HMDB identifiers ===
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 +
prefix wp:      <http://vocabularies.wikipathways.org/wp#>
 +
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
 +
prefix dcterms:  <http://purl.org/dc/terms/>
 +
 +
select distinct ?identifier
 +
where {
 +
  ?mb a wp:Metabolite ;
 +
    dc:source "Kegg Compound"^^xsd:string ;
 +
    dc:identifier ?identifier .
 +
  FILTER (!isIRI(?identifier))
 +
} order by ?identifier
= Metabolic Pathways =
= Metabolic Pathways =

Revision as of 05:15, 7 January 2013

On this page we collect SPARQL queries to see the state of the Metabolome in WikiPathways. Triggered by User:Andra's RDF / SPARQL work, curation started with metabolites without database identifiers. But this soon led to the observation that metabolites are often not even annotated as being a metabolite (using <Label> rather than <DataNode>). Therefore, User:Egonw started at Pathway:WP1 to curate them one by one and fix these issues:

  • connect lines between metabolites
  • convert metabolites to use <Label> rather than <DataNode>

The reason for this is that these are some basic underlying properties we need for metabolomics research fields.

Contents

[hide]

Metabolome

The following queries provide an overview of the Metabolome captures by WikiPathways.

The key type for metabolites is the wp:Metabolite. We can see all available properties with: 

prefix wp:      <http://vocabularies.wikipathways.org/wp#>

select distinct ?p where {
  ?mb a wp:Metabolite ;
    ?p [] .
}

All Metabolites

Count 

prefix wp:      <http://vocabularies.wikipathways.org/wp#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms:  <http://purl.org/dc/terms/>

select count(?mb) where {
  ?mb a wp:Metabolite .
}

List 

prefix wp:      <http://vocabularies.wikipathways.org/wp#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms:  <http://purl.org/dc/terms/>

select ?mb ?label where {
  ?mb a wp:Metabolite ;
     rdfs:label ?label .
}

Metabolic Data Sources

Sorted by use 

prefix wp:      <http://vocabularies.wikipathways.org/wp#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms:  <http://purl.org/dc/terms/>

select ?datasource count(?identifier) as ?count
where {
  ?mb a wp:Metabolite ;
    dc:source ?datasource ;
    dc:identifier ?identifier .
} order by desc(?count)

All metabolites from one source

All KEGG identifiers

prefix wp: <http://vocabularies.wikipathways.org/wp#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix dcterms: <http://purl.org/dc/terms/>

select distinct ?identifier where { 

 ?mb a wp:Metabolite ;
   dc:source "Kegg Compound"^^xsd:string ;
   dc:identifier ?identifier .
 FILTER (!isIRI(?identifier))

} order by ?identifier

All HMDB identifiers

prefix wp: <http://vocabularies.wikipathways.org/wp#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix dcterms: <http://purl.org/dc/terms/>

select distinct ?identifier where { 

 ?mb a wp:Metabolite ;
   dc:source "Kegg Compound"^^xsd:string ;
   dc:identifier ?identifier .
 FILTER (!isIRI(?identifier))

} order by ?identifier

Metabolic Pathways

Curation

Metabolites not classified as such

One can list all data sources for non-metabolites with this query: 

prefix wp:      <http://vocabularies.wikipathways.org/wp#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms:  <http://purl.org/dc/terms/>

select ?datasource count(?identifier) as ?count
where {
  ?mb dc:source ?datasource ;
    dc:identifier ?identifier .
  FILTER NOT EXISTS { ?mb a wp:Metabolite }
} order by desc(?count)

That mostly lists gene identifier sources, etc, but watch out for the metabolite identifier data sources. For example, metabolites not marked as such but with a metabolite identifier can be found this way.

Non-Metabolites with CAS identifier 

prefix wp:      <http://vocabularies.wikipathways.org/wp#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms: <http://purl.org/dc/terms/>
prefix xsd:     <http://www.w3.org/2001/XMLSchema#>

select distinct ?pathway ?mb ?identifier 
where {
  ?mb dc:source "CAS"^^xsd:string ;
    dc:identifier ?identifier ;
    dcterms:isPartOf ?pathway .
  FILTER NOT EXISTS { ?mb a wp:Metabolite }
  FILTER (!isIRI(?identifier))
} order by ?pathway

Non-Metabolites with PubChem identifier

These might have been curated by the time of reading. 

prefix wp:      <http://vocabularies.wikipathways.org/wp#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms: <http://purl.org/dc/terms/>
prefix xsd:     <http://www.w3.org/2001/XMLSchema#>

select distinct ?pathway ?mb ?identifier 
where {
  ?mb dc:source "PubChem"^^xsd:string ;
    dc:identifier ?identifier ;
    dcterms:isPartOf ?pathway .
  FILTER NOT EXISTS { ?mb a wp:Metabolite }
  FILTER (!isIRI(?identifier))
} order by ?pathway
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