Help:WikiPathways Metabolomics
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 |
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 [] .
}
To only get analysis of the most recent pathways, add this snippet to your SPARQL, assuming ?pathway is the used variable name:
?mb dcterms:isPartOf ?pathway . ?mb dcterms:isPartOf ?pathway2 . ?pathway2 pav:version ?version2 . FILTER (?version2 > ?version)
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
Note that a CAS identifier can also refer to mixtures, compound classes, etc.
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
Metabolites with an identifier but undefined data source
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 a wp:Metabolite ;
dc:source ""^^xsd:string ;
dc:identifier ?identifier ;
dcterms:isPartOf ?pathway .
FILTER (!isIRI(?identifier))
FILTER (str(?identifier) != "")
} order by ?pathway
Metabolites with an Entrez Gene 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 a wp:Metabolite ; dc:source "Entrez Gene"^^xsd:string ; dc:identifier ?identifier ; dcterms:isPartOf ?pathway . FILTER (!isIRI(?identifier)) FILTER (str(?identifier) != "")
} order by ?pathway
