testing with a few initial oma sparql querries #3
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,20 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:1 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Find all Rattus norvegicus' proteins present in OMA RDF database.""" ; | ||
| sh:select """SELECT ?protein ?OMA_link | ||
| WHERE | ||
| { | ||
| ?protein a orth:Protein. | ||
| ?protein orth:organism ?organism. | ||
| ?inTaxon rdfs:label 'in taxon'@en. | ||
| ?organism ?inTaxon ?taxon. | ||
| ?taxon up:scientificName 'Rattus norvegicus'. | ||
| ?protein rdfs:seeAlso ?OMA_link. | ||
| }""" . | ||
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|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:2 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
|
There was a problem hiding this comment. this can also work on the uniprot sparql endpoint and the bgee one. you can add |
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| rdfs:comment """Which species are available on OMA database and their scientific names?""" ; | ||
| sh:select """SELECT ?species ?sciname WHERE | ||
| { | ||
| ?species a up:Taxon. | ||
| ?species up:scientificName ?sciname. | ||
| ?species up:rank up:Species. | ||
| }""" . | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:3 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all proteins in OMA that is encoded by the INS gene and their mnemonics and evidence types from Uniprot database (federated query).""" ; | ||
| sh:select """SELECT DISTINCT ?proteinOMA ?species ?mnemonic ?evidenceType ?UniProt_URI | ||
| WHERE { | ||
| ?proteinOMA a orth:Protein; | ||
| orth:organism/obo:RO_0002162/up:scientificName ?species; | ||
| rdfs:label 'INS'. | ||
| ?proteinOMA lscr:xrefUniprot ?UniProt_URI. | ||
| #Search the INS gene mnemonics and evidence types from Uniprot database. | ||
| service <http://sparql.uniprot.org/sparql> { | ||
| ?UniProt_URI up:mnemonic ?mnemonic; | ||
| up:existence/rdfs:label ?evidenceType. } | ||
| }""" . | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:4 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all genes that are orthologous to ENSLACG00000002497 Ensembl gene (identifier)""" ; | ||
| sh:select """select ?protein2 ?OMA_LINK | ||
| where { | ||
| #The three that contains Orthologs. The leafs are proteins. | ||
| #This graph pattern defines the relationship protein1 is Orthologs to protein2 | ||
| ?cluster a orth:OrthologsCluster. | ||
| ?cluster orth:hasHomologousMember ?node1. | ||
| ?cluster orth:hasHomologousMember ?node2. | ||
| ?node2 orth:hasHomologousMember* ?protein2. | ||
| ?node1 orth:hasHomologousMember* ?protein1. | ||
| ######## | ||
|
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| #Specify the protein to look for its orthologs | ||
| ?protein1 sio:SIO_010079/lscr:xrefEnsemblGene ensembl:ENSLACG00000002497. | ||
| ######## | ||
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| #The OMA link to the second protein | ||
| ?protein2 rdfs:seeAlso ?OMA_LINK. | ||
| ######## | ||
|
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| filter(?node1 != ?node2) | ||
| }""" . | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:5 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all genes that are paralogous to ENSG00000244734 Ensembl gene (identifier).""" ; | ||
| sh:select """select ?protein2 ?OMA_LINK | ||
| where { | ||
| #The three that contains paralogs. The leafs are proteins. | ||
| #This graph pattern defines the relationship protein1 is paralogous to protein2 | ||
| ?cluster a orth:ParalogsCluster. | ||
| ?cluster orth:hasHomologousMember ?node1. | ||
| ?cluster orth:hasHomologousMember ?node2. | ||
| ?node2 orth:hasHomologousMember* ?protein2. | ||
| ?node1 orth:hasHomologousMember* ?protein1. | ||
| ######## | ||
|
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| #Specify the protein to look for its paralogs | ||
| ?protein1 sio:SIO_010079/lscr:xrefEnsemblGene ensembl:ENSG00000244734. | ||
| ######## | ||
|
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| #The OMA link to the second protein | ||
| ?protein2 rdfs:seeAlso ?OMA_LINK. | ||
| ######## | ||
|
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| filter(?node1 != ?node2) | ||
| }""" . | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:6 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all genes that are paralogous to HUMAN00529 OMA protein (identifier) and their cross-reference links to OMA and Uniprot.""" ; | ||
| sh:select """select ?protein2 ?Uniprot_link | ||
| where { | ||
| ?cluster a orth:ParalogsCluster. | ||
| ?cluster orth:hasHomologousMember ?node1. | ||
| ?cluster orth:hasHomologousMember ?node2. | ||
| ?node2 orth:hasHomologousMember* ?protein2. | ||
| ?node1 orth:hasHomologousMember* ?protein1. | ||
| ?protein1 a orth:Protein. | ||
| ?protein1 dc:identifier 'HUMAN00529'. | ||
| ?protein2 a orth:Protein. | ||
| ?protein2 lscr:xrefUniprot ?Uniprot_link. | ||
| filter(?node1 != ?node2) | ||
| }""" . | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:7 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all genes that are orthologous to HUMAN22169 OMA protein (identifier) and their cross-reference links to OMA and Uniprot.""" ; | ||
| sh:select """select ?protein2 ?Uniprot_link | ||
| where { | ||
| ?cluster a orth:OrthologsCluster. | ||
| ?cluster orth:hasHomologousMember ?node1. | ||
| ?cluster orth:hasHomologousMember ?node2. | ||
| ?node2 orth:hasHomologousMember* ?protein2. | ||
| ?node1 orth:hasHomologousMember* ?protein1. | ||
| ?protein1 a orth:Protein. | ||
| ?protein1 dc:identifier 'HUMAN22169'. | ||
| ?protein2 a orth:Protein. | ||
| ?protein2 lscr:xrefUniprot ?Uniprot_link. | ||
| filter(?node1 != ?node2) | ||
| }""" . | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:8 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all genes per species that are orthologous to Rabbit's APOCI or APOC1 gene and their cross-reference links to OMA and Uniprot including the corresponding Ensembl gene identifier.""" ; | ||
| sh:select """select ?protein1 ?protein2 ?geneName2 ?species2 ?Prot2_uniprot ?prot2_ensemblGeneId | ||
| where { | ||
| ?cluster a orth:OrthologsCluster. | ||
| ?cluster orth:hasHomologousMember ?node1. | ||
| ?cluster orth:hasHomologousMember ?node2. | ||
| ?node2 orth:hasHomologousMember* ?protein2. | ||
| ?node1 orth:hasHomologousMember* ?protein1. | ||
| ?protein1 a orth:Protein; | ||
| orth:organism/obo:RO_0002162/up:scientificName 'Oryctolagus cuniculus'; | ||
| rdfs:label 'APOCI'. | ||
| ?protein2 a orth:Protein; | ||
| lscr:xrefUniprot ?Prot2_uniprot; | ||
| sio:SIO_010079/lscr:xrefEnsemblGene/dc:identifier ?prot2_ensemblGeneId; | ||
| rdfs:label ?geneName2; | ||
| orth:organism/obo:RO_0002162/up:scientificName ?species2. | ||
| filter(?node1 != ?node2) | ||
| }""" . |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:9 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all Rabbit's proteins encoded by genes that are orthologous to Mouses's hemoglobin Y gene and their cross-reference links to Uniprot.""" ; | ||
| sh:select """select distinct ?MOUSE_PROTEIN ?RABIT_PROTEIN ?MOUSE_UNIPROT_XREF ?RABIT_UNIPROT_XREF | ||
| where { | ||
| ?cluster a orth:OrthologsCluster. | ||
| ?cluster orth:hasHomologousMember ?node1. | ||
| ?cluster orth:hasHomologousMember ?node2. | ||
| ?node2 orth:hasHomologousMember* ?RABIT_PROTEIN. | ||
| ?node1 orth:hasHomologousMember* ?MOUSE_PROTEIN. | ||
| ?MOUSE_PROTEIN a orth:Protein. | ||
| ?MOUSE_PROTEIN orth:organism/obo:RO_0002162/up:scientificName 'Mus musculus'; | ||
| rdfs:label 'HBB-Y'; | ||
| lscr:xrefUniprot ?MOUSE_UNIPROT_XREF. | ||
| ?RABIT_PROTEIN a orth:Protein. | ||
| ?RABIT_PROTEIN orth:organism/obo:RO_0002162/up:scientificName 'Oryctolagus cuniculus' . | ||
| ?RABIT_PROTEIN lscr:xrefUniprot ?RABIT_UNIPROT_XREF. | ||
| filter(?node1 != ?node2) | ||
| }""" . |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:10 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all human proteins that are paralogous to the HBB gene and their UniProt cross-references.""" ; | ||
| sh:select """select distinct ?PROTEIN_HBB ?IS_PARALOGOUS_TO_PROTEIN ?PARALOG_GENE_LABEL ?HBB_UNIPROT_XREF ?PARALOG_UNIPROT_XREF | ||
| where { | ||
| ?cluster a orth:OrthologsCluster. | ||
| ?cluster orth:hasHomologousMember ?node1. | ||
| ?cluster orth:hasHomologousMember ?node2. | ||
| ?node2 orth:hasHomologousMember* ?PROTEIN_HBB. | ||
| ?node1 orth:hasHomologousMember* ?IS_PARALOGOUS_TO_PROTEIN. | ||
| ?PROTEIN_HBB a orth:Protein ; | ||
| orth:organism/obo:RO_0002162/up:scientificName 'Homo sapiens'; | ||
| rdfs:label 'HBB'; | ||
| lscr:xrefUniprot ?HBB_UNIPROT_XREF . | ||
| ?IS_PARALOGOUS_TO_PROTEIN a orth:Protein; | ||
| orth:organism/obo:RO_0002162/up:scientificName 'Homo sapiens' ; | ||
| lscr:xrefUniprot ?PARALOG_UNIPROT_XREF ; | ||
| rdfs:label ?PARALOG_GENE_LABEL . | ||
| filter(?node1 != ?node2) | ||
| }""" . |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:11 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """The percentage of proteins in Drosophila melanogaster that has at least one paralogous sequence (protein).""" ; | ||
| sh:select """select (((xsd:float(?num_paralogy)*100)/xsd:float(?total)) as ?result) | ||
| where { | ||
| { | ||
| select (count(distinct ?PROTEIN) as ?num_paralogy ) | ||
| where { | ||
| ?cluster a orth:ParalogsCluster. | ||
| ?cluster orth:hasHomologousMember ?node1. | ||
| ?cluster orth:hasHomologousMember ?node2. | ||
| ?node2 orth:hasHomologousMember* ?PROTEIN. | ||
| ?node1 orth:hasHomologousMember* ?IS_PARALOGOUS_TO_PROTEIN. | ||
| ?PROTEIN a orth:Protein. | ||
| ?PROTEIN orth:organism/obo:RO_0002162/up:scientificName ?species. | ||
| ?IS_PARALOGOUS_TO_PROTEIN a orth:Protein. | ||
| ?IS_PARALOGOUS_TO_PROTEIN orth:organism/obo:RO_0002162/up:scientificName ?species . | ||
| values(?species ){( 'Drosophila melanogaster' )} | ||
| filter(?node1 != ?node2) | ||
| } | ||
| } | ||
| { | ||
| select (count(distinct ?protein_total) as ?total) | ||
| where { | ||
| ?protein_total a orth:Protein . | ||
| ?protein_total orth:organism/obo:RO_0002162/up:scientificName ?species . | ||
| values(?species ){( 'Drosophila melanogaster' )} | ||
| } | ||
| } | ||
| }""" . |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:12 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all orthologs between mouse and rabbit, together with their HOG id""" ; | ||
| sh:select """select distinct ?MOUSE_PROTEIN ?RABIT_PROTEIN ?HOG | ||
| where { | ||
| ?HOG a orth:OrthologsCluster ; | ||
| orth:hasHomologousMember ?node1 ; | ||
| orth:hasHomologousMember ?node2 . | ||
| ?node2 orth:hasHomologousMember* ?RABIT_PROTEIN. | ||
| ?node1 orth:hasHomologousMember* ?MOUSE_PROTEIN. | ||
| ?MOUSE_PROTEIN a orth:Protein ; | ||
| orth:organism/obo:RO_0002162/up:scientificName 'Mus musculus'. | ||
| ?RABIT_PROTEIN a orth:Protein ; | ||
| orth:organism/obo:RO_0002162/up:scientificName 'Oryctolagus cuniculus' . | ||
| filter(?node1 != ?node2) | ||
| }""" . |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/> | ||
| prefix sh: <http://www.w3.org/ns/shacl#> | ||
| prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> | ||
| prefix schema:<https://schema.org/> | ||
| ex:13 | ||
| a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ; | ||
| sh:prefixes _:sparql_examples_prefixes ; | ||
| schema:target <https://sparql.omabrowser.org/sparql/> ; | ||
| rdfs:comment """Retrieve all proteins belongong to the Hierarchical Orthologous Group (HOG) at the level 'Vertebrata' to which humans' CDIN1 gene belong, together with their gene name symbol if available.""" ; | ||
| sh:select """select distinct ?HOG ?MEMBER ?GENE_LABEL | ||
| where { | ||
| ?HOG a orth:OrthologsCluster ; | ||
| orth:hasHomologousMember ?node1 ; | ||
| orth:hasTaxonomicRange ?taxRange . | ||
| ?taxRange orth:taxRange 'Vertebrata' . | ||
| ?node1 orth:hasHomologousMember* ?query ; | ||
| orth:hasHomologousMember* ?MEMBER . | ||
| ?MEMBER a orth:Protein . | ||
| OPTIONAL { | ||
| ?MEMBER rdfs:label ?GENE_LABEL . | ||
| } | ||
| ?query a orth:Protein ; | ||
| orth:organism/obo:RO_0002162/up:scientificName 'Homo sapiens'; | ||
| rdfs:label 'CDIN1'. | ||
| }""" . |
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you don't have to use numbers. You can name them e.g. ex:rat-proteins.