SARS-CoV-2-Queries

virusGenesAll.rq

Code examples: curl

SPARQL

SELECT ?virus ?virusLabel ?gene ?geneLabel ?ncbigene WHERE {
  VALUES ?virus {
    wd:Q82069695 # SARS-CoV-2
    wd:Q16983360 # HKU1
    wd:Q16991954 # OC43
    wd:Q8351095  # NL63 
    wd:Q16983356 # 229E
    wd:Q4902157  # MERS-CoV
    wd:Q278567   # SARS-CoV
  }
  ?gene wdt:P703 ?virus ; wdt:P31 wd:Q7187 .
  OPTIONAL { ?gene wdt:P351 ?ncbigene }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} ORDER BY ?virus ?ncbigene ?gene

run or edit

Output

virus	gene	ncbigene
Human coronavirus 229E (edit)	Record to support submission of GeneRIFs for a gene not in Gene (Coronavirus 229E; Human coronavirus (STRAIN 229E); Human coronavirus serogroup 229E; Human coronavirus strain 229E). (edit)	2828637
Human coronavirus 229E (edit)	surface glycoprotein (edit)	918758
Human coronavirus 229E (edit)	4a protein (edit)	918759
Human coronavirus 229E (edit)	4b protein (edit)	918760
Human coronavirus 229E (edit)	envelope protein (edit)	918761
Human coronavirus 229E (edit)	membrane protein (edit)	918762
Human coronavirus 229E (edit)	nucleocapsid protein (edit)	918763
Human coronavirus 229E (edit)	replicase polyprotein 1a;replicase polyprotein 1ab (edit)	918764
Human coronavirus HKU1 (edit)	nucleocapsid phosphoprotein (edit)	3200423
Human coronavirus HKU1 (edit)	ORF8 (edit)	3200424
Human coronavirus HKU1 (edit)	hemagglutinin-esterase glycoprotein (edit)	3200425
Human coronavirus HKU1 (edit)	spike glycoprotein (edit)	3200426
Human coronavirus HKU1 (edit)	non-structural protein (edit)	3200427
Human coronavirus HKU1 (edit)	membrane glycoprotein (edit)	3200428
Human coronavirus HKU1 (edit)	ORF1a polyprotein;ORF1ab polyprotein (edit)	3200429
Human coronavirus HKU1 (edit)	envelope protein (edit)	3200430
Human coronavirus HKU1 (edit)	Record to support submission of GeneRIFs for a gene not in Gene (CoV-HKU1; Human CoV/HKU1). (edit)	3293713
Human coronavirus OC43 (edit)	Record to support submission of GeneRIFs for a gene not in Gene (Human coronavirus (strain OC43); Human coronavirus strain OC43). (edit)	2829172
Human coronavirus OC43 (edit)	ns2 (edit)	39105215
Human coronavirus OC43 (edit)	hemagglutinin-esterase (edit)	39105216
Human coronavirus OC43 (edit)	envelope protein (edit)	39105217
Human coronavirus OC43 (edit)	spike surface glycoprotein (edit)	39105218
Human coronavirus OC43 (edit)	ns12.9 (edit)	39105219
Human coronavirus OC43 (edit)	membrane protein (edit)	39105220
Human coronavirus OC43 (edit)	I protein;nucleocapsid protein (edit)	39105221
Human coronavirus OC43 (edit)	ORF1a polyprotein;ORF1ab polyprotein (edit)	39105222
SARSr-CoV (edit)	E2 glycoprotein precursor (edit)	1489668
SARSr-CoV (edit)	hypothetical protein sars3a (edit)	1489669
SARSr-CoV (edit)	hypothetical protein sars3b (edit)	1489670
SARSr-CoV (edit)	protein E (edit)	1489671
SARSr-CoV (edit)	matrix protein (edit)	1489672
SARSr-CoV (edit)	hypothetical protein sars6 (edit)	1489673
SARSr-CoV (edit)	hypothetical protein sars7a (edit)	1489674
SARSr-CoV (edit)	hypothetical protein sars7b (edit)	1489675
SARSr-CoV (edit)	hypothetical protein sars8a (edit)	1489676
SARSr-CoV (edit)	hypothetical protein sars8b (edit)	1489677
SARSr-CoV (edit)	nucleocapsid protein (edit)	1489678
SARSr-CoV (edit)	hypothetical protein sars9b (edit)	1489679
SARSr-CoV (edit)	orf1a polyprotein (pp1a);orf1ab polyprotein (pp1ab) (edit)	1489680
SARSr-CoV (edit)	Record to support submission of GeneRIFs for a gene not in Gene (Human coronavirus (strain SARS); SARS-like coronavirus; SARS-related coronavirus). (edit)	8673700
Middle East respiratory syndrome coronavirus (edit)	spike protein (edit)	14254594
Middle East respiratory syndrome coronavirus (edit)	NS3 protein (edit)	14254595
Middle East respiratory syndrome coronavirus (edit)	NS4A protein (edit)	14254596
Middle East respiratory syndrome coronavirus (edit)	NS4B protein (edit)	14254597
Middle East respiratory syndrome coronavirus (edit)	NS5 protein (edit)	14254598
Middle East respiratory syndrome coronavirus (edit)	envelope protein (edit)	14254599
Middle East respiratory syndrome coronavirus (edit)	membrane protein (edit)	14254600
Middle East respiratory syndrome coronavirus (edit)	nucleocapsid protein (edit)	14254601
Middle East respiratory syndrome coronavirus (edit)	1A polyprotein;1AB polyprotein (edit)	14254602
Middle East respiratory syndrome coronavirus (edit)	Record to support submission of GeneRIFs for a gene not in Gene (MERS coronavirus; MERS virus; Middle East Respiratory Syndrome Coronavirus (MERS-CoV); Middle East respiratory syndrome coronavirus). (edit)	18938949
Middle East respiratory syndrome coronavirus (edit)	ORF8b protein (edit)	19910005
SARS-CoV-2 (edit)	ORF3d (edit)
SARS-CoV-2 (edit)	Record to support submission of GeneRIFs for a gene not in Gene (COVID-19 virus; HCoV-19; Human coronavirus 2019; SARS-2; SARS-CoV2; SARS2). (edit)	43562271
SARS-CoV-2 (edit)	surface glycoprotein (edit)	43740568
SARS-CoV-2 (edit)	ORF3a protein-encoding gene (edit)	43740569
SARS-CoV-2 (edit)	envelope protein (edit)	43740570
SARS-CoV-2 (edit)	membrane glycoprotein (edit)	43740571
SARS-CoV-2 (edit)	ORF6 protein (edit)	43740572
SARS-CoV-2 (edit)	ORF7a protein (edit)	43740573
SARS-CoV-2 (edit)	ORF7b (edit)	43740574
SARS-CoV-2 (edit)	nucleocapsid phosphoprotein (edit)	43740575
SARS-CoV-2 (edit)	ORF10 protein (edit)	43740576
SARS-CoV-2 (edit)	ORF8 protein (edit)	43740577
SARS-CoV-2 (edit)	ORF1a polyprotein;ORF1ab polyprotein (edit)	43740578
human Coronavirus NL63 (edit)	spike protein (edit)	2943499
human Coronavirus NL63 (edit)	protein 3 (edit)	2943500
human Coronavirus NL63 (edit)	ORF1a polyprotein;ORF1ab polyprotein (edit)	2943501
human Coronavirus NL63 (edit)	envelope protein (edit)	2943502
human Coronavirus NL63 (edit)	membrane protein (edit)	2943503
human Coronavirus NL63 (edit)	nucleocapsid protein (edit)	2943504
human Coronavirus NL63 (edit)	Record to support submission of GeneRIFs for a gene not in Gene (Coronavirus NL63; Human coronavirus NL). (edit)	3293659

Code examples

curl

curl -s https://raw.githubusercontent.com/egonw/SARS-CoV-2-Queries/master/sparql/virusGenesAll.rq | sed 's+<lang/>+en+' > virusGenesAll.rq

curl -H "Accept: text/tab-separated-values" -G https://query.wikidata.org/bigdata/namespace/wdq/sparql --data-urlencode query@virusGenesAll.rq

This SPARQL query is available under CCZero.

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