From 426ed0649a2641ed617bf5403c705983f16a02a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Santanch=C3=A8?= Date: Tue, 28 May 2024 07:06:09 -0300 Subject: [PATCH] feat (networks/sp): new examples and markdown --- .../sparql/species-pathways-proteins.md | 336 ++++++++++++++++++ .../sparql/species-pathways-proteins.sparql | 29 +- 2 files changed, 364 insertions(+), 1 deletion(-) create mode 100644 networks/species-pathways/sparql/species-pathways-proteins.md diff --git a/networks/species-pathways/sparql/species-pathways-proteins.md b/networks/species-pathways/sparql/species-pathways-proteins.md new file mode 100644 index 0000000..63ff7da --- /dev/null +++ b/networks/species-pathways/sparql/species-pathways-proteins.md @@ -0,0 +1,336 @@ +# SPARQL endpoints + +* Gene Ontology: https://geneontology.org/sparql + +* UniProt (better): https://sparql.uniprot.org/sparql + +# Wnt signaling pathway (GO:0016055) + +* URI: https://amigo.geneontology.org/amigo/term/GO:0016055 + +## All superclasses of the pathway + +~~~sparql +PREFIX obo: +PREFIX rdfs: + +SELECT DISTINCT ?super ?labels +WHERE { + obo:GO_0016055 rdfs:subClassOf ?super . + ?super rdfs:label ?labels . +} +~~~ + +## All subclasses of the pathway + +~~~sparql +PREFIX obo: +PREFIX rdfs: + +SELECT DISTINCT ?sub ?label +WHERE { + ?sub rdfs:subClassOf obo:GO_0016055 . + ?sub rdfs:label ?label . +} +~~~ + +## All properties and objects related to the pathway + +~~~sparql +PREFIX obo: + +SELECT DISTINCT ?property ?object +WHERE { + obo:GO_0016055 ?property ?object . +} +~~~ + +## All subjects and properties related to the pathway + +~~~sparql +PREFIX obo: + +SELECT DISTINCT ?subject ?property +WHERE { + ?subject ?property obo:GO_0016055 . +} +~~~ + +## All subjects (URI and label) classified with the pathway + +~~~sparql +PREFIX rdfs: +PREFIX obo: +PREFIX up_core: + +SELECT DISTINCT ?uri ?label +WHERE { + ?uri up_core:classifiedWith obo:GO_0016055 . + ?uri rdfs:label ?label . +} +~~~ + +## All proteins (URI and label) classified with the pathway + +~~~sparql +PREFIX rdf: +PREFIX rdfs: +PREFIX obo: +PREFIX up_core: + +SELECT DISTINCT ?protein ?label +WHERE { + ?protein up_core:classifiedWith obo:GO_0016055 . + ?protein rdf:type up_core:Protein . + ?protein rdfs:label ?label . +} +~~~ + +# PRICKLE2 - Prickle-like protein 2 (UniProtKB:Q7Z3G6) + +* URI: http://purl.uniprot.org/uniprot/Q7Z3G6 + +## All subjects related to the protein + +~~~sparql +PREFIX up: + +SELECT DISTINCT ?subject ?property +WHERE { + ?subject ?property up:Q7Z3G6 . +} +~~~ + +## All properties and objects related to the protein + +~~~sparql +PREFIX up: + +SELECT DISTINCT ?property ?object +WHERE { + up:Q7Z3G6 ?property ?object . +} +~~~ + +## All proteins URI with the label "Prickle-like protein 2" + +~~~sparql +PREFIX rdfs: + +SELECT DISTINCT ?protein ?label +WHERE { + ?protein rdfs:label "Prickle-like protein 2" . +} +~~~ + +## All objects classified with the protein + +~~~sparql +PREFIX rdfs: +PREFIX up: +PREFIX up_core: + +SELECT DISTINCT ?object ?label +WHERE { + up:Q7Z3G6 up_core:classifiedWith ?object . + ?object rdfs:label ?label . +} +~~~ + +~~~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" +~~~ + +## Organism related to this protein + +~~~sparql +PREFIX up: +PREFIX up_core: + +SELECT DISTINCT ?protein ?taxon ?scientific_name +WHERE { + up:Q7Z3G6 up_core:organism ?taxon . + ?taxon up_core:scientificName ?scientific_name . +} +~~~ + +## Gene related to this protein + +~~~sparql +PREFIX rdfs: +PREFIX up: +PREFIX up_core: + +SELECT DISTINCT ?gene ?label +WHERE { + up:Q7Z3G6 up_core:encodedBy ?gene . + ?gene rdfs:label ?label . +} +~~~ + +# Wnt signaling pathway, planar cell polarity pathway (GO:0060071) + +## All proteins classified with the pathway + +~~~sparql +PREFIX rdfs: +PREFIX up_core: +PREFIX obo: + +SELECT DISTINCT ?protein ?label +WHERE { + ?protein up_core:classifiedWith obo:GO_0060071 . + ?protein rdf:type up_core:Protein . + ?protein rdfs:label ?label . +} +~~~ + +## All proteins classified with the pathway and their organism + +~~~sparql +PREFIX rdfs: +PREFIX up_core: +PREFIX 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 . +} +~~~ + +## All proteins classified with the pathway and their organism with the scientific name + +~~~sparql +PREFIX rdfs: +PREFIX up_core: +PREFIX 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 . +} +~~~ + +# Wnt signaling pathway (GO:0016055) + +## All proteins classified with the pathway and their organism with the scientific name + +~~~sparql +PREFIX rdfs: +PREFIX up_core: +PREFIX 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 . +} +~~~ + +## All proteins classified with the pathway for the organism Homo sapiens (taxon:9606) + +~~~sparql +PREFIX rdfs: +PREFIX up_core: +PREFIX obo: +PREFIX taxon: + +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 . +} +~~~ + +## All proteins classified with the pathway for the organism Mus musculus (taxon:10090) + +~~~sparql +PREFIX rdfs: +PREFIX up_core: +PREFIX obo: +PREFIX taxon: + +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 . +} +~~~ + +# Cluster Casein kinase I isoform delta - 100% (UniRef100_Q9DC28) + +## All subjects and properties related to the cluster + +~~~sparql +PREFIX up_ref: + +SELECT DISTINCT ?subject ?property +WHERE { + ?subject ?property up_ref:UniRef100_Q9DC28 . +} +~~~ + +## All properties and objects related to the cluster + +~~~sparql +PREFIX up_ref: + +SELECT DISTINCT ?property ?object +WHERE { + up_ref:UniRef100_Q9DC28 ?property ?object . +} +~~~ + +## The UniParc which this cluster is member of + +~~~sparql +PREFIX rdfs: +PREFIX up_core: +PREFIX up_ref: + +SELECT DISTINCT ?uniparc ?label +WHERE { + up_ref:UniRef100_Q9DC28 up_core:member ?uniparc . + ?uniparc rdfs:label ?label . +} +~~~ + +~~~ +uniparc +UPI0000027B20 +~~~ + +## All properties and objects related to the UniParc + +~~~sparql +PREFIX rdf: +PREFIX rdfs: +PREFIX up_core: +PREFIX up_arc: + +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 . +} +~~~ \ No newline at end of file diff --git a/networks/species-pathways/sparql/species-pathways-proteins.sparql b/networks/species-pathways/sparql/species-pathways-proteins.sparql index 35647ac..08971ff 100644 --- a/networks/species-pathways/sparql/species-pathways-proteins.sparql +++ b/networks/species-pathways/sparql/species-pathways-proteins.sparql @@ -78,6 +78,8 @@ WHERE { # PRICKLE2 - Prickle-like protein 2 (UniProtKB:Q7Z3G6) # ---------------------------------------------------- +* URI: http://purl.uniprot.org/uniprot/Q7Z3G6 + # All subjects related to the protein PREFIX up: @@ -125,6 +127,31 @@ http://purl.obolibrary.org/obo/GO_0008270,"zinc ion binding" http://purl.obolibrary.org/obo/GO_0060071,"Wnt signaling pathway, planar cell polarity pathway" ----- +# Organism related to this protein + +PREFIX up: +PREFIX up_core: + +SELECT DISTINCT ?protein ?taxon ?scientific_name +WHERE { + up:Q7Z3G6 up_core:organism ?taxon . + ?taxon up_core:scientificName ?scientific_name . +} + +# Gene related to this protein + +PREFIX rdfs: +PREFIX up: +PREFIX up_core: + +SELECT DISTINCT ?gene ?label +WHERE { + up:Q7Z3G6 up_core:encodedBy ?gene . + ?gene rdfs:label ?label . +} + + + # Wnt signaling pathway, planar cell polarity pathway (GO:0060071) # ---------------------------------------------------------------- @@ -244,7 +271,7 @@ WHERE { PREFIX rdfs: PREFIX up_core: -PREFIX up_ref: +PREFIX up_ref: SELECT DISTINCT ?uniparc ?label WHERE {