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Revision as of 15:23, 5 January 2013 (view source) Egonw (Talk | contribs) (→All Metabolites) ← Previous diff		Revision as of 15:24, 5 January 2013 (view source) Egonw (Talk | contribs) (→All Metabolites) Next diff →
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	== All Metabolites ==		== All Metabolites ==
		+
		+	=== Count ===
	<pre>		<pre>
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	select count(?mb) where {		select count(?mb) where {
	?mb a wp:Metabolite .		?mb a wp:Metabolite .
		+	}
		+	</pre>
		+
		+	=== List ===
		+
		+	<pre>
		+	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 .
	}		}
	</pre>		</pre>

---

Revision as of 15:24, 5 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 1 Metabolome 1.1 All Metabolites 1.1.1 Count 1.1.2 List

Metabolome

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

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 .
}