Comments (3)
Error vanishes after
make restart-srv
from pbg-ld.
They do seem to run (even all together in one query) with
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT
str(?g1) AS ?g1
str(?feature_name) AS ?feature_name
?feature_id
COUNT(*) AS ?n
FROM NAMED <http://solgenomics.net/genome/Solanum_lycopersicum>
FROM NAMED <http://solgenomics.net/genome/Solanum_pennellii>
FROM NAMED <http://solgenomics.net/genome/Solanum_tuberosum>
FROM NAMED <http://plants.ensembl.org/Solanum_lycopersicum>
FROM NAMED <http://plants.ensembl.org/Solanum_tuberosum>
FROM NAMED <http://purl.obolibrary.org/obo/so.owl>
WHERE {
GRAPH ?g1 {
?ft a ?feature_type .
FILTER regex(?feature_type, obo:SO_) .
BIND(concat('[', replace(replace(str(?feature_type), '.+\\/', ''), '_', ':'), '](', ?feature_type, ')') AS ?feature_id)
}
GRAPH ?g2 {
?feature_type rdfs:label ?feature_name
}
}
GROUP BY ?g1 ?g2 ?feature_name ?feature_id
ORDER BY ASC(?g1) DESC(?n)
resulting in
from pbg-ld.
And to improve performance, it can be simplified to
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT
STR(?g1) AS ?g1
STR(?feature_name) AS ?feature_name
CONCAT('[', replace(replace(str(?feature_type), '.+\\/', ''), '_', ':'), '](', ?feature_type, ')') AS ?feature_id
COUNT(*) AS ?n
FROM NAMED <http://solgenomics.net/genome/Solanum_lycopersicum>
FROM NAMED <http://solgenomics.net/genome/Solanum_pennellii>
FROM NAMED <http://solgenomics.net/genome/Solanum_tuberosum>
FROM NAMED <http://plants.ensembl.org/Solanum_lycopersicum>
FROM NAMED <http://plants.ensembl.org/Solanum_tuberosum>
FROM NAMED <http://purl.obolibrary.org/obo/so.owl>
WHERE {
GRAPH ?g1 {
?ft a ?feature_type .
}
GRAPH ?g2 {
?feature_type rdfs:label ?feature_name
}
}
GROUP BY ?g1 ?g2 ?feature_name ?feature_type
ORDER BY ASC(?g1) DESC(?n)
from pbg-ld.
Related Issues (20)
- Create & orchestrate Docker images HOT 1
- FCT browser link is not resolvable is the new commit
- Some flanking markers require additional validation & post-processing HOT 3
- Enable additional annotation tracks in JBrowse
- Update user documentation
- Error The estimated execution time exceeds the limit of 400 (sec). HOT 2
- Link genes to JBrowse
- Add tests for WebAPI HOT 1
- Change graph IRI
- Add DC terms identifiers for chromosomes
- Use Makefile to fetch remote RDF data
- Add updated Jupyter Notebooks HOT 1
- Use permanent identifiers in production
- Add genome graph of the potato cultivar M6 HOT 1
- Update README
- Update chromosome labels HOT 1
- Rename Docker image HOT 1
- Run Docker services on subdomains
- Fix chromosome labels HOT 1
- Failed to connect to host HOT 3
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from pbg-ld.