From WikiPathways

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 2 Metabolic Pathways 3 Curation 3.1 Metabolites not classified as such

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 Pathways

Curation

Metabolites not classified as such