Help:WikiPathways Metabolomics
From WikiPathways
(→Metabolic Data Sources) |
(→Curation) |
||
| Line 70: | Line 70: | ||
== Metabolites not classified as such == | == Metabolites not classified as such == | ||
| + | |||
| + | One can list all data sources for non-metabolites with this query: | ||
| + | |||
| + | <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 ?datasource count(?identifier) as ?count | ||
| + | where { | ||
| + | ?mb dc:source ?datasource ; | ||
| + | dc:identifier ?identifier . | ||
| + | FILTER NOT EXISTS { ?mb a wp:Metabolite } | ||
| + | } order by desc(?count) | ||
| + | </pre> | ||
| + | |||
| + | 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 === | ||
| + | |||
| + | <pre> | ||
| + | </pre> | ||
Revision as of 15:47, 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 |
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)
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.
