From WikiPathways

Revision as of 07:37, 9 December 2012 (view source) Egonw (Talk | contribs) (New page: 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 databa...) ← Previous diff		Revision as of 15:23, 5 January 2013 (view source) Egonw (Talk | contribs) (→All Metabolites) Next diff →
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	== All Metabolites ==		== All Metabolites ==
		+
		+	<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 count(?mb) where {
		+	?mb a wp:Metabolite .
		+	}
		+	</pre>

---

Revision as of 15:23, 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.

Metabolome

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

All Metabolites

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 .
}