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networks/species-pathways/sparql/species-pathways-proteins.md
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# SPARQL endpoints | ||
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* Gene Ontology: https://geneontology.org/sparql | ||
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* UniProt (better): https://sparql.uniprot.org/sparql | ||
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# Wnt signaling pathway (GO:0016055) | ||
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* URI: https://amigo.geneontology.org/amigo/term/GO:0016055 | ||
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## All superclasses of the pathway | ||
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~~~sparql | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
SELECT DISTINCT ?super ?labels | ||
WHERE { | ||
obo:GO_0016055 rdfs:subClassOf ?super . | ||
?super rdfs:label ?labels . | ||
} | ||
~~~ | ||
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## All subclasses of the pathway | ||
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~~~sparql | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
SELECT DISTINCT ?sub ?label | ||
WHERE { | ||
?sub rdfs:subClassOf obo:GO_0016055 . | ||
?sub rdfs:label ?label . | ||
} | ||
~~~ | ||
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## All properties and objects related to the pathway | ||
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~~~sparql | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
SELECT DISTINCT ?property ?object | ||
WHERE { | ||
obo:GO_0016055 ?property ?object . | ||
} | ||
~~~ | ||
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## All subjects and properties related to the pathway | ||
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~~~sparql | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
SELECT DISTINCT ?subject ?property | ||
WHERE { | ||
?subject ?property obo:GO_0016055 . | ||
} | ||
~~~ | ||
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## All subjects (URI and label) classified with the pathway | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
SELECT DISTINCT ?uri ?label | ||
WHERE { | ||
?uri up_core:classifiedWith obo:GO_0016055 . | ||
?uri rdfs:label ?label . | ||
} | ||
~~~ | ||
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## All proteins (URI and label) classified with the pathway | ||
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~~~sparql | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
SELECT DISTINCT ?protein ?label | ||
WHERE { | ||
?protein up_core:classifiedWith obo:GO_0016055 . | ||
?protein rdf:type up_core:Protein . | ||
?protein rdfs:label ?label . | ||
} | ||
~~~ | ||
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# PRICKLE2 - Prickle-like protein 2 (UniProtKB:Q7Z3G6) | ||
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* URI: http://purl.uniprot.org/uniprot/Q7Z3G6 | ||
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## All subjects related to the protein | ||
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~~~sparql | ||
PREFIX up: <http://purl.uniprot.org/uniprot/> | ||
SELECT DISTINCT ?subject ?property | ||
WHERE { | ||
?subject ?property up:Q7Z3G6 . | ||
} | ||
~~~ | ||
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## All properties and objects related to the protein | ||
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~~~sparql | ||
PREFIX up: <http://purl.uniprot.org/uniprot/> | ||
SELECT DISTINCT ?property ?object | ||
WHERE { | ||
up:Q7Z3G6 ?property ?object . | ||
} | ||
~~~ | ||
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## All proteins URI with the label "Prickle-like protein 2" | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
SELECT DISTINCT ?protein ?label | ||
WHERE { | ||
?protein rdfs:label "Prickle-like protein 2" . | ||
} | ||
~~~ | ||
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## All objects classified with the protein | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up: <http://purl.uniprot.org/uniprot/> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
SELECT DISTINCT ?object ?label | ||
WHERE { | ||
up:Q7Z3G6 up_core:classifiedWith ?object . | ||
?object rdfs:label ?label . | ||
} | ||
~~~ | ||
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~~~csv | ||
object, label | ||
http://purl.obolibrary.org/obo/GO_0005737,"cytoplasm" | ||
http://purl.obolibrary.org/obo/GO_0031965,"nuclear membrane" | ||
http://purl.obolibrary.org/obo/GO_0008270,"zinc ion binding" | ||
http://purl.obolibrary.org/obo/GO_0060071,"Wnt signaling pathway, planar cell polarity pathway" | ||
~~~ | ||
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## Organism related to this protein | ||
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~~~sparql | ||
PREFIX up: <http://purl.uniprot.org/uniprot/> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
SELECT DISTINCT ?protein ?taxon ?scientific_name | ||
WHERE { | ||
up:Q7Z3G6 up_core:organism ?taxon . | ||
?taxon up_core:scientificName ?scientific_name . | ||
} | ||
~~~ | ||
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## Gene related to this protein | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up: <http://purl.uniprot.org/uniprot/> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
SELECT DISTINCT ?gene ?label | ||
WHERE { | ||
up:Q7Z3G6 up_core:encodedBy ?gene . | ||
?gene rdfs:label ?label . | ||
} | ||
~~~ | ||
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# Wnt signaling pathway, planar cell polarity pathway (GO:0060071) | ||
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## All proteins classified with the pathway | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
SELECT DISTINCT ?protein ?label | ||
WHERE { | ||
?protein up_core:classifiedWith obo:GO_0060071 . | ||
?protein rdf:type up_core:Protein . | ||
?protein rdfs:label ?label . | ||
} | ||
~~~ | ||
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## All proteins classified with the pathway and their organism | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
SELECT DISTINCT ?protein ?label ?organism | ||
WHERE { | ||
?protein up_core:classifiedWith obo:GO_0060071 . | ||
?protein rdf:type up_core:Protein . | ||
?protein rdfs:label ?label . | ||
?protein up_core:organism ?organism . | ||
} | ||
~~~ | ||
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## All proteins classified with the pathway and their organism with the scientific name | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
SELECT DISTINCT ?protein ?label ?organism ?scientific_name | ||
WHERE { | ||
?protein up_core:classifiedWith obo:GO_0060071 . | ||
?protein rdf:type up_core:Protein . | ||
?protein rdfs:label ?label . | ||
?protein up_core:organism ?organism . | ||
?organism up_core:scientificName ?scientific_name . | ||
} | ||
~~~ | ||
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# Wnt signaling pathway (GO:0016055) | ||
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## All proteins classified with the pathway and their organism with the scientific name | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
SELECT DISTINCT ?protein ?label ?organism ?scientific_name | ||
WHERE { | ||
?protein up_core:classifiedWith obo:GO_0016055 . | ||
?protein rdf:type up_core:Protein . | ||
?protein rdfs:label ?label . | ||
?protein up_core:organism ?organism . | ||
?organism up_core:scientificName ?scientific_name . | ||
} | ||
~~~ | ||
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## All proteins classified with the pathway for the organism Homo sapiens (taxon:9606) | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> | ||
SELECT DISTINCT ?protein ?label | ||
WHERE { | ||
?protein up_core:classifiedWith obo:GO_0016055 . | ||
?protein rdf:type up_core:Protein . | ||
?protein rdfs:label ?label . | ||
?protein up_core:organism taxon:9606 . | ||
} | ||
~~~ | ||
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## All proteins classified with the pathway for the organism Mus musculus (taxon:10090) | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> | ||
SELECT DISTINCT ?protein ?label | ||
WHERE { | ||
?protein up_core:classifiedWith obo:GO_0016055 . | ||
?protein rdf:type up_core:Protein . | ||
?protein rdfs:label ?label . | ||
?protein up_core:organism taxon:10090 . | ||
} | ||
~~~ | ||
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# Cluster Casein kinase I isoform delta - 100% (UniRef100_Q9DC28) | ||
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## All subjects and properties related to the cluster | ||
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~~~sparql | ||
PREFIX up_ref: <http://purl.uniprot.org/uniref/> | ||
SELECT DISTINCT ?subject ?property | ||
WHERE { | ||
?subject ?property up_ref:UniRef100_Q9DC28 . | ||
} | ||
~~~ | ||
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## All properties and objects related to the cluster | ||
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~~~sparql | ||
PREFIX up_ref: <http://purl.uniprot.org/uniref/> | ||
SELECT DISTINCT ?property ?object | ||
WHERE { | ||
up_ref:UniRef100_Q9DC28 ?property ?object . | ||
} | ||
~~~ | ||
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## The UniParc which this cluster is member of | ||
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~~~sparql | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
PREFIX up_ref: <http://purl.uniprot.org/uniref/> | ||
SELECT DISTINCT ?uniparc ?label | ||
WHERE { | ||
up_ref:UniRef100_Q9DC28 up_core:member ?uniparc . | ||
?uniparc rdfs:label ?label . | ||
} | ||
~~~ | ||
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~~~ | ||
uniparc | ||
UPI0000027B20 | ||
~~~ | ||
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## All properties and objects related to the UniParc | ||
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~~~sparql | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX up_core: <http://purl.uniprot.org/core/> | ||
PREFIX up_arc: <http://purl.uniprot.org/uniparc/> | ||
SELECT DISTINCT ?protein ?organism ?scientific_name | ||
WHERE { | ||
up_arc:UPI0000027B20 up_core:sequenceFor ?protein . | ||
?protein rdf:type up_core:Protein . | ||
?protein up_core:organism ?organism . | ||
?organism up_core:scientificName ?scientific_name . | ||
} | ||
~~~ |
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