human gene (E37)
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language code | label | description | aliases | edit |
---|---|---|---|---|
en | human gene | schema of a human gene according to Gene Wiki | edit | |
da | menneske-gen | edit | ||
de | menschliches Gen | Schema für ein menschliches Gen | edit | |
eo | homa geno | edit | ||
es | gen humano | esquema de gen humano de acuerdo al proyecto Gene Wiki | edit | |
fr | gène humain | schema d'un gène humain selon Gene Wiki | edit | |
it | gene umano | schema per descrivere un gene umano | edit | |
ja | ヒトの遺伝子 | Gene Wikiにおいてヒトの遺伝子を記述するためのスキーマ | edit | |
nl | menselijk gen | basis schema voor een menselijk gen in Wikidata volgens gene wiki | edit | |
pl | ludzki gen | edit | ||
pt | gene humano | edit |
# E108: genome_assembly
IMPORT <https://www.wikidata.org/wiki/Special:EntitySchemaText/E108>
PREFIX E108: <https://www.wikidata.org/wiki/Special:EntitySchemaText/E108#>
# E109: human chromosome
IMPORT <https://www.wikidata.org/wiki/Special:EntitySchemaText/E109>
PREFIX E109: <https://www.wikidata.org/wiki/Special:EntitySchemaText/E109#>
# Shape Expression for Human genes in Wikidata
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX prv: <http://www.wikidata.org/prop/reference/value/>
PREFIX pr: <http://www.wikidata.org/prop/reference/>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
BASE <http://www.wikidata.org/entity/>
start = @<#wikidata-human-gene>
# Query with results
# SELECT * WHERE {?item wdt:P31 wd:Q7187 ; wdt:P703 wd:Q15978631 .} LIMIT 10
# Indicates which shape to use to start iterating over the graph if none is provided.
# wikidata-human gene is the main shape for a human gene data model in Wikidata. Each line between the brackets
# represents the structure than can be enforced to validate human gene annotations in Wikidata
#
# We distinguish between value statements, identifier statements, and erroneous statements.
# Value statements contain either actual values, or pointers to other Wikidata items. Identifier statements capture
# external identifiers, erroneous statements are those that are errors.
#
<#wikidata-human-gene> EXTRA p:P31 {
# below is a special shape used to express that both the genomic start and genomic end properties are not mandatory
# however if one does exist, the other one is required. The * behind the brackets indicates the 0 or more cardinality
# that expresses the requirement that both properties are not mandatory.
p:P31 @<#P31_instance_of_gene> ;
(
p:P644 @<#P644_genomic_start> ; # Its genomic start location
p:P645 @<#P645_genomic_end> ; # Its genomic end location
)* ; # Zero or more start and end locations.
p:P684 @<#P684_ortholog>* ; # Zero or more known orthologs.
p:P688 @<#P688_encodes>* ; # Zero or more known geneproducts.
p:P703 @<#P703_found_in_taxon_human> ; # In which taxonomy and where in that taxonomy this gene is found
p:P1057 @<#P1057_chromosome>* ; # Zero or more known chromosomes the gene is located on.
p:P2888 . ; # @<#P2888_exact_match>+ ; # One or more external Internationalized Resource Identifiers of a node on the
# semantic web, describing the same concept as linked data.
p:P2548 @<#P2548_strand_orientation> ; # Its strand orrientation
# IDENTIFIER STATEMENTS
p:P351 @<#P351_ncbi_gene_id> ; # Exactly one ncbi gene identifier
p:P353 @<#P353_hgnc_gene_symbol> ; # Exactly one hgnc gene symbol
p:P354 @<#P354_hgnc_gene_id> ; # Exactly one hgnc gene identifier
p:P594 @<#P594_ensembl_gene_id>* ; # Zero or more Ensembl gene identifier
p:P639 @<#P639_refseq_rna_id>* ; # Zero or more RefSeq RNA identifiers
p:P704 @<#P704_ensembl_transcript_id>* ; # Zero or more Ensembl Transcript identifiers.
p:P593 @<#P593_homologene_id> ; # Exactly one homologene identifier
# Negative shapes
p:P352 @<#P352_uniprot_id_wor>{0} ; # A gene can't have a uniprot identifier.
}
# Detailed ShExs for Wikidata statements
# Wikidata captures a statement in the following graph pattern:
####################
# wd:Pxx wikibase:directClaim wdt:Pxx ;
# wikibase:claim p:Pxx .
# <item> wdt:Pxx "value" or <other_item> .
# <item> p:Pxx <node> .
# <node> ps:Pxx "value" or <other_item> ;
# pq:Pxx "qualifier value" or <qualifier_item> ;
# pr:Pxx "reference value" or <reference_item> .
####################
<#P31_instance_of_gene> {
ps:P31 @<#gene_types> ; # Instance of [P31] gene types
prov:wasDerivedFrom @<#ncbi-gene-reference> OR @<#ensembl-gene-reference> ;
}
<#P279_subclass_of_gene> {
ps:P279 @<#gene_types> ; # Subclass of [P279] gene types <gene_types>
prov:wasDerivedFrom @<#ncbi-gene-reference> OR @<#ensembl-gene-reference> ;
}
<#P644_genomic_start> {
ps:P644 LITERAL ; # genomic start [P644] value
pq:P1057 @E109:humanChromosome+ ; # Qualifier indicating the applicable chromosome [P1057] from a set of
# list Wikidata on chromosomes described below.
pq:P659 @E108:sequence_assembly+ ; # Qualifier indicating the applicable genomic assembly versions.
prov:wasDerivedFrom @<#ensembl-gene-reference> ;
}
<#P645_genomic_end> {
ps:P645 LITERAL ; # genomic start [P645] value
pq:P1057 @E109:humanChromosome+ ; # Qualifier indicating the applicable chromosome [P1057] from a set of
# list Wikidata on chromosomes described below.
pq:P659 @E108:sequence_assembly+ ; # Qualifier indicating the applicable genomic assembly versions.
prov:wasDerivedFrom @<#ensembl-gene-reference> ;
}
<#P684_ortholog> {
ps:P684 IRI ; # Known orthologs [P684].
pq:P703 IRI ; # Qualifier indicating in which taxon the ortholog is found [P703].
prov:wasDerivedFrom @<#homologene-reference> ;
}
<#P688_encodes> {
ps:P688 IRI ; # gene encodes [688] for a gene product.
prov:wasDerivedFrom @<#uniprot-reference>;
}
<#P703_found_in_taxon_human> {
ps:P703 [wd:Q15978631] ; # the gene is found in taxon [P703] human [Q15978631]
prov:wasDerivedFrom @<#ncbi-gene-reference> OR @<#ensembl-gene-reference> ;
}
<#P1057_chromosome> {
ps:P1057 @E109:humanChromosome ; # gene is found on chromosome [P1057]
pq:P659 @E108:sequence_assembly+ ; # Qualifier indicating the one or more applicable genomic assembly
prov:wasDerivedFrom @<#ensembl-gene-reference> ;
}
<#P2888_exact_match> {
ps:P2888 IRI ; # External IRI which describe the exact same concept [P2888]
prov:wasDerivedFrom @<#miriam_reference> OR @<#ncbi-gene-reference> ;
}
<#P2548_strand_orientation> {
ps:P2548 @<#strand-orientation> ; # Strand orientation [P2548] of the gene
pq:P659 @E108:sequence_assembly+ ; # Qualifier indicating the one or more applicable genomic assembly
prov:wasDerivedFrom @<#ensembl-gene-reference> ;
}
<#strand-orientation> [ # list of wikidata items for both the reverse and forward strand
wd:Q22809711 # reverse strand
wd:Q22809680 # forward strand
]
## IDENTIFIERS
<#P351_ncbi_gene_id> {
ps:P351 LITERAL ; # The NCBI gene identifier [P351] for the applicable gene item.
prov:wasDerivedFrom @<#ncbi-gene-reference> ;
}
<#P352_uniprot_id_wor> { # The (non-existent) uniprot identifier [P352] for the applicable gene item.
ps:P352 LITERAL ;
}
<#P353_hgnc_gene_symbol> {
ps:P353 LITERAL ; # The gene symbol [P353] for the applicable gene item.
prov:wasDerivedFrom @<#ncbi-gene-reference> ;
}
<#P354_hgnc_gene_id> {
ps:P354 LITERAL ; # The HGNC gene identifier [P354] for the applicable gene item.
prov:wasDerivedFrom @<#ncbi-gene-reference> ;
}
<#P593_homologene_id> {
ps:P593 LITERAL ; # The homologene identifier [P593] for the applicable gene item.
prov:wasDerivedFrom @<#ncbi-gene-reference> ;
}
<#P594_ensembl_gene_id> {
ps:P594 LITERAL ; # The Ensembl gene identifier [P594] for the applicable gene item.
prov:wasDerivedFrom @<#ensembl-gene-reference> ;
}
<#P639_refseq_rna_id> {
ps:P639 LITERAL ; # The RefSeq RNA identifier [P351] for the applicable gene item.
prov:wasDerivedFrom @<#ncbi-gene-reference> ;
}
<#P704_ensembl_transcript_id> {
ps:P704 LITERAL ; # The Ensembl transcript identifier [P704] for the applicable gene item
prov:wasDerivedFrom @<#ensembl-gene-reference> OR <#ncbi-gene-reference> ;
}
## REFERENCES
<#ncbi-gene-reference> { # reference to a NCBI gene record
pr:P248 [ wd:Q20641742 ] ; # stated in [P248] NCBI gene [Q20641742]
pr:P351 LITERAL ; # NCBI gene identifier
pr:P813 xsd:dateTime ; # Date of retrieval
}
<#ensembl-gene-reference> {
pr:P248 [
wd:Q30227110 # stated in [P248] Ensembl Release 89 [Q30227110]
wd:Q46401024 # stated in [P248] Ensembl Release 91 [Q30227110]
wd:Q57339524 # stated in [P248] Ensembl Release 94 [Q57339524]
wd:Q63170780 # stated in [P248] Ensembl Release 96 [Q63170780]
wd:Q67600000 # stated in [P248] Ensembl Release 97 [Q67600000]
wd:Q71033229 # stated in [P248] Ensembl Release 98 [Q71033229]
wd:Q83867711 # stated in [P248] Ensembl Release 99 [Q83867711]
wd:Q110249889 # stated in [P248] Ensembl Release 105 [Q83867711]
] ;
pr:P594 LITERAL ; # Ensembl Gene ID [P594]
}
<#homologene-reference> {
pr:P248 [wd:Q20976936]; # Stated in [P248] homologene build68 [Q20976936]
pr:P593 LITERAL; # Homologene identifier
}
<#miriam_reference> {
pr:P248 [wd:Q16335166] ; # Stated in [P248] MIRIAM registry
pr:P854 IRI ; # Reference URL [P854] to a IRI
}
<#uniprot-reference> {
pr:P248 [wd:Q905695] ;
pr:P352 LITERAL ;
pr:P813 xsd:dateTime ;
}
## Lists with Wikidata items
<#gene_types> [
wd:Q7187 # gene
wd:Q20747295 # protein-coding gene
wd:Q284578 # snRNA
wd:Q284416 # snoRNA
wd:Q215980 # rRNA
wd:Q201448 # tRNA
wd:Q277338 # pseudo
wd:Q11053 # miscRNA
wd:Q25323710 # scRNA
]