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View Code? Open in Web Editor NEWSPARQL queries for Web API
License: Apache License 2.0
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Input parameter of getQTLsPerArticle query not shown in the UI
Rename repo
queries -> api
Graph IRI enumaration does not work
Can't use GROUP_CONCAT in the query
See query: getGeneAnnotations.rq
?go_id -> GROUP_CONCAT(?go_id, ', ') AS ?uniprot_goa
...
GROUP BY ...
Input parameters do not show up in the grlc UI
@c-martinez: Any ideas why begin and end parameters are absent? (see /getFeaturesInInterval endpoint or query).
Issue related to #201.
Add NCBITaxon ID to the output of the getQTLs query
Lines 13 to 14 in ec1662a
Improve/add SPARQL queries
- List all QTLs in an articles (using PMCID)
- List all trait IDs give a trait term
- List all QTLs associated with a trait ID
- List all genes in a QTL given a QTL ID
- List all genes associated with a QTL(s) given a trait ID
- List all features given start/end position on a chromosome
- Get annotations from SGN and UniProt given a gene ID
- Get orthologs of tomato/potato genes in potato/tomato
- Get paralogs in potato/tomato
- Set default value(s) for input parameters (e.g., gene, QTL or trait ID)
- Summarize QTLs per species
Input parameter of getQTLs query not shown in the UI
Query1: List all QTLS in an article not working.
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX so: <http://purl.obolibrary.org/obo/so#>
SELECT
?qtl_uri
?qtl_id
?pmc_id
WHERE {
GRAPH <http://europepmc.org/articles> {
?qtl_uri a obo:SO_0000771 ;
dcterms:identifier ?qtl_id;
dcterms:isReferencedBy ?pmc_id.
BIND(uri(concat("http://identifiers.org/pmc/", ?_pmc_id )) AS ?user_pmc_id)
BIND(bif:strcontains(?pmc_id,?user_pmc_id ) AS ?match)
FILTER(?match = 1)
}
}
# EXAMPLE: ?pmc_id = PMC4266912
Add keywords labels/names to Uniprot keyword query
related to #1
Update getGeneAnnotations query
Currently, GO IDs are returned for a gene ID only if there is a gene name (via uniprot:encodedBy/skos:prefLabel predicate)->make these independent (or optional). In addition to GO IDs return also the corresponding GO terms.
Change graph IRI
related to issue candYgene/pbg-ld#40
Add uniprot:core/existence to Uniprot Annotation query
Can't set default parameter values
For example, see this query.
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