SARS-CoV-2-Queries

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Genomas, Genes e Proteínas

Genomas

Talvez a primeira pergunta sobre esse tema possa ser: quais genomas foram já analisados para o SARS-CoV-2:

SPARQL sparql/genomes.rq (run, edit)

SELECT ?genome WHERE {
  wd:Q82069695 wdt:P527/wdt:P6800 ?genome .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "pt,en". }
}

Que lista as URLs de genoma:

genome
https://gisaid.org/CoV2020
https://www.ncbi.nlm.nih.gov/assembly/GCF_009858895.2
https://www.ncbi.nlm.nih.gov/genome/86693
https://www.ncbi.nlm.nih.gov/nuccore/1798174254

SARS-CoV-2

Genes

O RNA do SARS-CoV-2 já foi sequenciado. Dessa forma, os quadros abertos de leitura (ORFs) são conhecidos e identificados. Podemos consultar a informação sobre genes na Wikidata com essa busca:

SPARQL sparql/virusGenes.rq (run, edit)

SELECT ?gene ?geneLabel ?ncbigene WHERE {
  ?gene wdt:P703 wd:Q82069695 ; wdt:P31 wd:Q7187 .
  OPTIONAL { ?gene wdt:P351 ?ncbigene }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "pt,en". }
}

O que nos dá esses genes:

gene ncbigene
surface glycoprotein (edit) 43740568
ORF1a polyprotein;ORF1ab polyprotein (edit) 43740578
ORF3a protein (edit) 43740569
envelope protein (edit) 43740570
membrane glycoprotein (edit) 43740571
ORF6 protein (edit) 43740572
ORF7a protein (edit) 43740573
ORF7b (edit) 43740574
ORF8 protein (edit) 43740577
nucleocapsid phosphoprotein (edit) 43740575
ORF10 protein (edit) 43740576
Record to support submission of GeneRIFs for a gene not in Gene (COVID-19; COVID-19 virus; COVID19; HCoV-19; Human coronavirus 2019; SARS-2; SARS-CoV2; SARS2; Wuhan coronavirus; Wuhan seafood market pneumonia virus). (edit) 43562271

Proteínas

Alternativamente, podemos estar interessados nas proteínas dos coronavirus. Podemos obtê-las com essa busca:

SPARQL sparql/virusProteins.rq (run, edit)

SELECT ?protein ?proteinLabel ?short ?refseq ?uniprot ?guideToPharma WHERE {
  ?protein wdt:P703 wd:Q82069695 ; wdt:P31 wd:Q8054 .
  OPTIONAL { ?protein wdt:P637 ?refseq }
  OPTIONAL { ?protein wdt:P352 ?uniprot }
  OPTIONAL { ?protein wdt:P5458 ?guideToPharma }
  OPTIONAL { ?protein wdt:P1813 ?short }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} ORDER BY ASC(?protein) ASC(?uniprot)

O que nos dá essas proteínas:

protein short refseq uniprot guideToPharma
putative protein ORF3c (edit) P0DTG1
Non-structural protein 11 [SARS CoV-2] (edit) nsp11
ORF3b protein [SARS-CoV-2] (edit) P0DTF1
ORF9c protein [SARS CoV-2] (edit) P0DTD3
Non-structural protein 10 [SARS CoV-2] (edit) nsp10
non-structural protein 15 [SARS-CoV-2] (edit) nsp15
non-structural protein 16 [SARS-CoV-2] (edit) nsp16 P0DTD1-PRO_0000449633
Papain-like proteinase [SARS-CoV-2] (edit) nsp3 YP_009725299.1 P0DTC1-PRO_0000449637
Papain-like proteinase [SARS-CoV-2] (edit) nsp3 YP_009725299.1 P0DTD1-PRO_0000449621
non-structural protein 5 [SARS-CoV-2] (edit) nsp5 YP_009725301 P0DTC1-PRO_0000449639 3111
non-structural protein 5 [SARS-CoV-2] (edit) nsp5 YP_009725301 P0DTD1-PRO_0000449623 3111
nucleocapsid protein [SARS-CoV-2] (edit) N YP_009724397.2 P0DTC9 3121
spike glycoprotein [SARS-CoV-2] (edit) S YP_009724390.1 P0DTC2 3114
orf1ab polyprotein [SARS-Cov 2] (edit) QHD43415 P0DTD1 3125
Viroporin 3a [SARS-CoV-2] (edit) YP_009724391.1 P0DTC3 3115
envelope protein [SARS-CoV-2] (edit) YP_009724392.1 P0DTC4 3116
membrane protein [SARS-CoV-2] (edit) YP_009724393.1 P0DTC5 3117
non-structural protein 6 [SARS-CoV-2] (edit) nsp6 P0DTC1-PRO_0000449640 3118
non-structural protein 6 [SARS-CoV-2] (edit) nsp6 P0DTD1-PRO_0000449624 3118
ORF1a polyprotein (edit) P0DTC1 3124
Protein 7a [SARS-CoV-2] (edit) YP_009724395.1 P0DTC7 3119
Protein non-structural 7b [SARS-CoV-2] (edit) YP_009725318.1 P0DTD8 3123
ORF8 protein [SARS-CoV-2] (edit) YP_009724396.1 P0DTC8 3120
Non-structural protein 2 [SARS CoV-2] (edit) nsp2 P0DTC1-PRO_0000449636
Non-structural protein 2 [SARS CoV-2] (edit) nsp2 P0DTD1-PRO_0000449620
ORF6 protein [SARS-CoV-2] (edit) YP_009724394.1 P0DTC6
ORF10 protein [SARS-CoV-2] (edit) YP_009725255.1 A0A663DJA2
Protein ORF9b [SARS-CoV-2] (edit) P0DTD2 3122
Non-structural protein 9 [SARS-CoV-2] (edit) nsp9 P0DTC1-PRO_0000449643
Non-structural protein 9 [SARS-CoV-2] (edit) nsp9 P0DTD1-PRO_0000449627
Host translation inhibitor nsp1 [SARS-CoV-2] (edit) nsp1 P0DTC1-PRO_0000449635
Host translation inhibitor nsp1 [SARS-CoV-2] (edit) nsp1 P0DTD1-PRO_0000449619
Non-structural protein 4 [SARS-CoV-2] (edit) nsp4 P0DTC1-PRO_0000449638
Non-structural protein 4 [SARS-CoV-2] (edit) nsp4 P0DTD1-PRO_0000449622
Non-structural protein 7 [SARS-CoV-2] (edit) nsp7 P0DTC1-PRO_0000449641
Non-structural protein 7 [SARS-CoV-2] (edit) nsp7 P0DTD1-PRO_0000449625
RNA-directed RNA polymerase [SARS-CoV-2] (edit) nsp12 P0DTD1-PRO_0000449629
Non-structural protein 14 [SARS-CoV-2] (edit) nsp14 P0DTD1-PRO_0000449631
Helicase [SARS-CoV-2] (edit) nsp13
Uncharacterized protein 14 (edit) P0DTD3
Non-structural protein nsp8 [SARS-CoV-2] (edit) nsp8 P0DTC1-PRO_0000449642
Non-structural protein nsp8 [SARS-CoV-2] (edit) nsp8 P0DTD1-PRO_0000449626

Complejos proteicos

Graças ao trabalho realizado por uma equipe no BioHackathon online em April 2020, as estruturas macromoleculares do Complex Portal [1] foram inseridas no Wikidata:

SPARQL sparql/complexes.rq (run, edit)

SELECT ?cpx ?complex ?complexLabel WHERE {
  ?complex wdt:P7718 ?cpx ;
           wdt:P703 wd:Q82069695
  SERVICE wikibase:label { bd:serviceParam wikibase:language "pt,en". }
}

Lista destes complexos:

cpx complex
CPX-5687 SARS-CoV-2 NSP9 complex (edit)
CPX-5683 SARS-CoV-2 Spike - human ACE2 receptor complex (edit)
CPX-5684 SARS-CoV-2 Spike - human ACE2-SLC6A19 complex (edit)
CPX-5682 SARS-CoV-2 Spike protein complex (edit)
CPX-5685 SARS-CoV-2 main protease complex (edit)
CPX-5686 SARS-CoV-2 nucleocapsid complex (edit)
CPX-5688 SARS-CoV-2 NSP10-NSP16 complex (edit)
CPX-5689 SARS-CoV-2 NSP15 complex (edit)
CPX-5690 SARS-CoV-2 primase complex (edit)
CPX-5691 SARS-CoV-2 NSP3-NSP4-NSP6 complex (edit)
CPX-5692 SARS-CoV-2 Guanine-N7 methyltransferase complex (edit)
CPX-5742 SARS-CoV-2 polymerase complex (edit)

Estruturas do PDB

Para as proteínas, podemos consultar as estruturas do PDB [2]:

SPARQL sparql/virusProteinsPDB.rq (run, edit)

SELECT ?protein ?proteinLabel ?refseq ?uniprot ?pdb WHERE {
  ?protein wdt:P703 wd:Q82069695 ; wdt:P31 wd:Q8054 .
  ?protein wdt:P638 ?pdb .
  OPTIONAL { ?protein wdt:P637 ?refseq }
  OPTIONAL { ?protein wdt:P352 ?uniprot }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "pt,en". }
}

O que nos dá:

protein refseq uniprot pdb
Non-structural protein 10 [SARS CoV-2] (edit) 6W4H
non-structural protein 15 [SARS-CoV-2] (edit) 6VWW
non-structural protein 15 [SARS-CoV-2] (edit) 6W01
non-structural protein 16 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449633 6W4H
Papain-like proteinase [SARS-CoV-2] (edit) YP_009725299.1 P0DTD1-PRO_0000449621 6VXS
Papain-like proteinase [SARS-CoV-2] (edit) YP_009725299.1 P0DTD1-PRO_0000449621 6W02
Papain-like proteinase [SARS-CoV-2] (edit) YP_009725299.1 P0DTC1-PRO_0000449637 6VXS
Papain-like proteinase [SARS-CoV-2] (edit) YP_009725299.1 P0DTC1-PRO_0000449637 6W02
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639 5R81
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639 5R82
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639 5R83
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639 6M03
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639 6Y2E
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639 6Y2F
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639 6Y84
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639 6LU7
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623 5R81
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623 5R82
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623 5R83
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623 6M03
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623 6Y2E
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623 6Y2F
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623 6Y84
non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623 6LU7
nucleocapsid protein [SARS-CoV-2] (edit) YP_009724397.2 P0DTC9 6M3M
spike glycoprotein [SARS-CoV-2] (edit) YP_009724390.1 P0DTC2 6VXX
spike glycoprotein [SARS-CoV-2] (edit) YP_009724390.1 P0DTC2 6VYB
orf1ab polyprotein [SARS-Cov 2] (edit) QHD43415 P0DTD1 6Y2E
orf1ab polyprotein [SARS-Cov 2] (edit) QHD43415 P0DTD1 6Y2F
orf1ab polyprotein [SARS-Cov 2] (edit) QHD43415 P0DTD1 6Y2G

Todos os virus relacionados com o SARS

Assim comoa a consulta anterior, também podemos buscar todos os genes e proteínas de todos os vírus relacionados com o SARS. Isso se faz com as seguintes consultas:

Todos os genes relacionados com o SARS

Todos os genes que obtemos com:

SPARQL sparql/virusGenesSARSr.rq (run, edit)

SELECT ?virus ?virusLabel ?gene ?geneLabel ?ncbigene WHERE {
  VALUES ?virus {
    wd:Q16000326 # SL-CoV-WIV1
    wd:Q88162038 # Bat SARS coronavirus Rp1
    wd:Q85939995 # SHC014-CoV
    wd:Q82069695 # SARS-CoV-2
    wd:Q34967815 # SARS coronavirus
    wd:Q85438966 # severe acute respiratory syndrome coronavirus
    wd:Q278567   # SARSr-CoV / SARS-CoV
  }
  ?gene wdt:P703 ?virus ; wdt:P31 wd:Q7187 .
  OPTIONAL { ?gene wdt:P351 ?ncbigene }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "pt,en". }
}

Que devolve:

virus gene ncbigene
coronavírus da síndrome respiratória aguda grave 2 (edit) surface glycoprotein (edit) 43740568
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF1a polyprotein;ORF1ab polyprotein (edit) 43740578
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF3a protein (edit) 43740569
coronavírus da síndrome respiratória aguda grave 2 (edit) envelope protein (edit) 43740570
coronavírus da síndrome respiratória aguda grave 2 (edit) membrane glycoprotein (edit) 43740571
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF6 protein (edit) 43740572
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF7a protein (edit) 43740573
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF7b (edit) 43740574
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF8 protein (edit) 43740577
coronavírus da síndrome respiratória aguda grave 2 (edit) nucleocapsid phosphoprotein (edit) 43740575
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF10 protein (edit) 43740576
coronavírus da síndrome respiratória aguda grave 2 (edit) Record to support submission of GeneRIFs for a gene not in Gene (COVID-19; COVID-19 virus; COVID19; HCoV-19; Human coronavirus 2019; SARS-2; SARS-CoV2; SARS2; Wuhan coronavirus; Wuhan seafood market pneumonia virus). (edit) 43562271
SARS-CoV (edit) protein E (edit) 1489671
SARS-CoV (edit) hypothetical protein sars6 (edit) 1489673
SARS-CoV (edit) hypothetical protein sars9b (edit) 1489679
SARS-CoV (edit) Record to support submission of GeneRIFs for a gene not in Gene (Human coronavirus (strain SARS); SARS coronavirus; SARS virus; SARS-like coronavirus; SARS-related coronavirus; Severe acute respiratory syndrome coronavirus). (edit) 8673700
SARS-CoV (edit) hypothetical protein sars7a (edit) 1489674
SARS-CoV (edit) hypothetical protein sars7a (edit) 1489674
SARS-CoV (edit) hypothetical protein sars7b (edit) 1489675
SARS-CoV (edit) hypothetical protein sars3a (edit) 1489669
SARS-CoV (edit) matrix protein (edit) 1489672
SARS-CoV (edit) orf1a polyprotein (pp1a);orf1ab polyprotein (pp1ab) (edit) 1489680
SARS-CoV (edit) hypothetical protein sars3b (edit) 1489670
SARS-CoV (edit) hypothetical protein sars8a (edit) 1489676
SARS-CoV (edit) E2 glycoprotein precursor (edit) 1489668
SARS-CoV (edit) hypothetical protein sars8b (edit) 1489677
SARS-CoV (edit) nucleocapsid protein (edit) 1489678

Todas as proteínas relacionadas com o SARS

E todas as proteínas que obtemos com:

SPARQL sparql/virusProteinsSARSr.rq (run, edit)

SELECT ?virus ?virusLabel ?protein ?proteinLabel ?refseq ?uniprot WHERE {
  VALUES ?virus {
    wd:Q16000326 # SL-CoV-WIV1
    wd:Q88162038 # Bat SARS coronavirus Rp1
    wd:Q85939995 # SHC014-CoV
    wd:Q82069695 # SARS-CoV-2
    wd:Q34967815 # SARS coronavirus
    wd:Q85438966 # severe acute respiratory syndrome coronavirus
    wd:Q278567   # SARSr-CoV / SARS-CoV
  }
  ?protein wdt:P703 ?virus ; wdt:P31 wd:Q8054 .
  OPTIONAL { ?protein wdt:P637 ?refseq }
  OPTIONAL { ?protein wdt:P352 ?uniprot }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "pt,en". }
} ORDER BY ASC(?virus) ASC(?protein)

Que devolve:

virus protein refseq uniprot
SARS-CoV (edit) Protein 3a [SARS-Cov] (edit) NP_828852.2 P59632
SARS-CoV (edit) Replicase polyprotein 1a (edit) P0C6U8
coronavírus da síndrome respiratória aguda grave 2 (edit) putative protein ORF3c (edit) P0DTG1
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 11 [SARS CoV-2] (edit)
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF3b protein [SARS-CoV-2] (edit) P0DTF1
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF9c protein [SARS CoV-2] (edit) P0DTD3
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 10 [SARS CoV-2] (edit)
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 15 [SARS-CoV-2] (edit)
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 16 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449633
coronavírus da síndrome respiratória aguda grave 2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) YP_009725299.1 P0DTD1-PRO_0000449621
coronavírus da síndrome respiratória aguda grave 2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) YP_009725299.1 P0DTC1-PRO_0000449637
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623
coronavírus da síndrome respiratória aguda grave 2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) YP_009724397.2 P0DTC9
coronavírus da síndrome respiratória aguda grave 2 (edit) spike glycoprotein [SARS-CoV-2] (edit) YP_009724390.1 P0DTC2
coronavírus da síndrome respiratória aguda grave 2 (edit) orf1ab polyprotein [SARS-Cov 2] (edit) QHD43415 P0DTD1
coronavírus da síndrome respiratória aguda grave 2 (edit) Viroporin 3a [SARS-CoV-2] (edit) YP_009724391.1 P0DTC3
coronavírus da síndrome respiratória aguda grave 2 (edit) envelope protein [SARS-CoV-2] (edit) YP_009724392.1 P0DTC4
coronavírus da síndrome respiratória aguda grave 2 (edit) membrane protein [SARS-CoV-2] (edit) YP_009724393.1 P0DTC5
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 6 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449640
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 6 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449624
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF1a polyprotein (edit) P0DTC1
coronavírus da síndrome respiratória aguda grave 2 (edit) Protein 7a [SARS-CoV-2] (edit) YP_009724395.1 P0DTC7
coronavírus da síndrome respiratória aguda grave 2 (edit) Protein non-structural 7b [SARS-CoV-2] (edit) YP_009725318.1 P0DTD8
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF8 protein [SARS-CoV-2] (edit) YP_009724396.1 P0DTC8
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 2 [SARS CoV-2] (edit) P0DTD1-PRO_0000449620
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 2 [SARS CoV-2] (edit) P0DTC1-PRO_0000449636
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF6 protein [SARS-CoV-2] (edit) YP_009724394.1 P0DTC6
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF10 protein [SARS-CoV-2] (edit) YP_009725255.1 A0A663DJA2
coronavírus da síndrome respiratória aguda grave 2 (edit) Protein ORF9b [SARS-CoV-2] (edit) P0DTD2
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449643
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449627
coronavírus da síndrome respiratória aguda grave 2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449635
coronavírus da síndrome respiratória aguda grave 2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449619
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 4 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449638
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 4 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449622
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 7 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449641
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 7 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449625
coronavírus da síndrome respiratória aguda grave 2 (edit) RNA-directed RNA polymerase [SARS-CoV-2] (edit) P0DTD1-PRO_0000449629
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 14 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449631
coronavírus da síndrome respiratória aguda grave 2 (edit) Helicase [SARS-CoV-2] (edit)
coronavírus da síndrome respiratória aguda grave 2 (edit) Uncharacterized protein 14 (edit) P0DTD3
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein nsp8 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449642
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein nsp8 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449626
SARS-CoV (edit) Envelope small membrane protein [SARS-Cov] (edit) NP_828854.1 P59637
SARS-CoV (edit) Non-structural protein NS6 [SARS-Cov] (edit) NP_828856.1 P59634
SARS-CoV (edit) Protein 9b [SARS-Cov] (edit) NP_828859.1 P59636
SARS-CoV (edit) Protein 7a [SARS-Cov] (edit) NP_828857.1 P59635
SARS-CoV (edit) Protein non-structural 7b [SARS-Cov] (edit) NP_849175.1 Q7TFA1
SARS-CoV (edit) Protein 3a [SARS-Cov] (edit) NP_828852.2 P59632
SARS-CoV (edit) Membrane protein [SARS-Cov] (edit) NP_828855.1 P59596
SARS-CoV (edit) Non-structural protein 3b [SARS-Cov] (edit) NP_828853.1 P59633
SARS-CoV (edit) replicase polyprotein 1ab [SARS-Cov] (edit) P0C6X7
SARS-CoV (edit) 2'-O-methyltransferase [SARS-Cov] (edit)
SARS-CoV (edit) 3C-like proteinase [SARS-Cov] (edit)
SARS-CoV (edit) non-structural protein 9 [SARS-Cov] (edit)
SARS-CoV (edit) nucleoprotein [SARS-Cov] (edit) P59595
SARS-CoV (edit) spike glycoprotein [SARS-Cov] (edit) NP_828851.1 P59594
SARS-CoV (edit) spike protein S2 [SARS-Cov] (edit)
SARS-CoV (edit) non-structural protein 7 [SARS-Cov] (edit)
SARS-CoV (edit) uridylate-specific endoribonuclease [SARS-Cov] (edit)
SARS-CoV (edit) non-structural protein 8 [SARS-Cov] (edit)
SARS-CoV (edit) papain-like proteinase [SARS-Cov] (edit)
SARS-CoV (edit) host translation inhibitor nsp1 [SARS-Cov] (edit)
SARS-CoV (edit) non-structural protein 10 [SARS-Cov] (edit)
SARS-CoV (edit) Guanine-N7 methyltransferase [SARS-Cov] (edit)
SARS-CoV (edit) RNA-directed RNA polymerase [SARS-Cov] (edit)
SARS-CoV (edit) helicase [SARS-Cov] (edit)
SARS-CoV (edit) non-structural protein 4 [SARS-Cov] (edit)
SARS-CoV (edit) non-structural protein 6 [SARS-Cov] (edit)
SARS-CoV (edit) non-structural protein 2 [SARS-Cov] (edit)
SARS-CoV (edit) non-structural protein 11 [SARS-Cov] (edit)
SARS-CoV (edit) protein non-structural 8a [SARS-Cov] (edit) NP_849176.1 Q7TFA0
SARS-CoV (edit) protein non-structural 8b [SARS-Cov] (edit) NP_849177.1 Q80H93

Todos os coronavirus humanos

Como na busca anterior, também podemos pedir por todos os genes e proteínas. Isso se faz com as seguintes buscas:

Todos os genes de coronavirus humano

Todos os genes que obtemos são:

SPARQL sparql/virusGenesAll.rq (run, edit)

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 "pt,en". }
} ORDER BY ?virus ?ncbigene ?gene

Que devolve:

virus gene ncbigene
Coronavírus humano 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
Coronavírus humano 229E (edit) surface glycoprotein (edit) 918758
Coronavírus humano 229E (edit) 4a protein (edit) 918759
Coronavírus humano 229E (edit) 4b protein (edit) 918760
Coronavírus humano 229E (edit) envelope protein (edit) 918761
Coronavírus humano 229E (edit) membrane protein (edit) 918762
Coronavírus humano 229E (edit) nucleocapsid protein (edit) 918763
Coronavírus humano 229E (edit) replicase polyprotein 1a;replicase polyprotein 1ab (edit) 918764
Coronavírus humano HKU1 (edit) nucleocapsid phosphoprotein (edit) 3200423
Coronavírus humano HKU1 (edit) nucleocapsid phosphoprotein 2 (edit) 3200424
Coronavírus humano HKU1 (edit) hemagglutinin-esterase glycoprotein (edit) 3200425
Coronavírus humano HKU1 (edit) spike glycoprotein (edit) 3200426
Coronavírus humano HKU1 (edit) non-structural protein (edit) 3200427
Coronavírus humano HKU1 (edit) membrane glycoprotein (edit) 3200428
Coronavírus humano HKU1 (edit) orf1ab polyprotein (edit) 3200429
Coronavírus humano HKU1 (edit) small membrane protein (edit) 3200430
Coronavírus humano HKU1 (edit) Record to support submission of GeneRIFs for a gene not in Gene (CoV-HKU1; Human CoV/HKU1). (edit) 3293713
Coronavírus humano OC43 (edit) Record to support submission of GeneRIFs for a gene not in Gene (Human coronavirus (strain OC43); Human coronavirus strain OC43). (edit) 2829172
Coronavírus humano OC43 (edit) ns2 (edit) 39105215
Coronavírus humano OC43 (edit) hemagglutinin-esterase (edit) 39105216
Coronavírus humano OC43 (edit) envelope protein (edit) 39105217
Coronavírus humano OC43 (edit) spike surface glycoprotein (edit) 39105218
Coronavírus humano OC43 (edit) ns12.9 (edit) 39105219
Coronavírus humano OC43 (edit) membrane protein (edit) 39105220
Coronavírus humano OC43 (edit) nucleocapsid protein (edit) 39105221
Coronavírus humano OC43 (edit) Orf1ab (edit) 39105222
SARS-CoV (edit) E2 glycoprotein precursor (edit) 1489668
SARS-CoV (edit) hypothetical protein sars3a (edit) 1489669
SARS-CoV (edit) hypothetical protein sars3b (edit) 1489670
SARS-CoV (edit) protein E (edit) 1489671
SARS-CoV (edit) matrix protein (edit) 1489672
SARS-CoV (edit) hypothetical protein sars6 (edit) 1489673
SARS-CoV (edit) hypothetical protein sars7a (edit) 1489674
SARS-CoV (edit) hypothetical protein sars7b (edit) 1489675
SARS-CoV (edit) hypothetical protein sars8a (edit) 1489676
SARS-CoV (edit) hypothetical protein sars8b (edit) 1489677
SARS-CoV (edit) nucleocapsid protein (edit) 1489678
SARS-CoV (edit) hypothetical protein sars9b (edit) 1489679
SARS-CoV (edit) orf1a polyprotein (pp1a);orf1ab polyprotein (pp1ab) (edit) 1489680
SARS-CoV (edit) Record to support submission of GeneRIFs for a gene not in Gene (Human coronavirus (strain SARS); SARS coronavirus; SARS virus; SARS-like coronavirus; SARS-related coronavirus; Severe acute respiratory syndrome coronavirus). (edit) 8673700
Síndrome respiratória por coronavírus do Oriente Médio (edit) spike glycoprotein (edit) 14254594
Síndrome respiratória por coronavírus do Oriente Médio (edit) NS3 protein (edit) 14254595
Síndrome respiratória por coronavírus do Oriente Médio (edit) NS4A protein (edit) 14254596
Síndrome respiratória por coronavírus do Oriente Médio (edit) NS4B protein (edit) 14254597
Síndrome respiratória por coronavírus do Oriente Médio (edit) NS5 protein (edit) 14254598
Síndrome respiratória por coronavírus do Oriente Médio (edit) envelope protein (edit) 14254599
Síndrome respiratória por coronavírus do Oriente Médio (edit) membrane protein (edit) 14254600
Síndrome respiratória por coronavírus do Oriente Médio (edit) nucleoprotein (edit) 14254601
Síndrome respiratória por coronavírus do Oriente Médio (edit) 1A polyprotein;1AB polyprotein (edit) 14254602
Síndrome respiratória por coronavírus do Oriente Médio (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
Síndrome respiratória por coronavírus do Oriente Médio (edit) ORF8b protein (edit) 19910005
coronavírus da síndrome respiratória aguda grave 2 (edit) Record to support submission of GeneRIFs for a gene not in Gene (COVID-19; COVID-19 virus; COVID19; HCoV-19; Human coronavirus 2019; SARS-2; SARS-CoV2; SARS2; Wuhan coronavirus; Wuhan seafood market pneumonia virus). (edit) 43562271
coronavírus da síndrome respiratória aguda grave 2 (edit) surface glycoprotein (edit) 43740568
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF3a protein (edit) 43740569
coronavírus da síndrome respiratória aguda grave 2 (edit) envelope protein (edit) 43740570
coronavírus da síndrome respiratória aguda grave 2 (edit) membrane glycoprotein (edit) 43740571
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF6 protein (edit) 43740572
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF7a protein (edit) 43740573
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF7b (edit) 43740574
coronavírus da síndrome respiratória aguda grave 2 (edit) nucleocapsid phosphoprotein (edit) 43740575
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF10 protein (edit) 43740576
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF8 protein (edit) 43740577
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF1a polyprotein;ORF1ab polyprotein (edit) 43740578
Coronavírus humano NL63 (edit) spike protein (edit) 2943499
Coronavírus humano NL63 (edit) protein 3 (edit) 2943500
Coronavírus humano NL63 (edit) replicase polyprotein 1ab (edit) 2943501
Coronavírus humano NL63 (edit) envelope protein (edit) 2943502
Coronavírus humano NL63 (edit) membrane protein (edit) 2943503
Coronavírus humano NL63 (edit) nucleocapsid protein (edit) 2943504
Coronavírus humano NL63 (edit) Record to support submission of GeneRIFs for a gene not in Gene (Coronavirus NL63; Human coronavirus NL). (edit) 3293659

Todas as proteínas de coronavirus humanos

E todas as proteínas que obtemos com:

SPARQL sparql/virusProteinsAll.rq (run, edit)

SELECT ?virus ?virusLabel ?protein ?proteinLabel ?refseq ?uniprot 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
  }
  ?protein wdt:P703 ?virus ; wdt:P31 wd:Q8054 .
  OPTIONAL { ?protein wdt:P637 ?refseq }
  OPTIONAL { ?protein wdt:P352 ?uniprot }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "pt,en". }
} ORDER BY ?virus

Que retorna:

virus protein refseq uniprot
Coronavírus humano 229E (edit) Non-structural protein 4a (edit) NP_073552.1 P19739
Coronavírus humano 229E (edit) Non-structural protein 4b (edit) NP_073553.1 P19740
Coronavírus humano 229E (edit) Spike glycoprotein (edit) NP_073551.1 P15423
Coronavírus humano 229E (edit) Membrane protein (edit) NP_073555.1 P15422
Coronavírus humano 229E (edit) Nucleoprotein (edit) NP_073556.1 P15130
Coronavírus humano 229E (edit) Envelope small membrane protein (edit) NP_073554.1 P19741
Coronavírus humano 229E (edit) Replicase polyprotein 1a (edit) NP_073550.1 P0C6U2
Coronavírus humano 229E (edit) Replicase polyprotein 1ab (edit) NP_073549.1 P0C6X1
Coronavírus humano HKU1 (edit) Protein I (edit) YP_173243.1 Q5MQC5
Coronavírus humano HKU1 (edit) Spike glycoprotein (edit) E0YJ44
Coronavírus humano HKU1 (edit) Non-structural protein 4 (edit) YP_173239.1 Q5MQC9
Coronavírus humano HKU1 (edit) Spike glycoprotein (edit) YP_173238.1 Q5MQD0
Coronavírus humano HKU1 (edit) Envelope small membrane protein (edit) YP_173240.1 Q5MQC8
Coronavírus humano HKU1 (edit) Nucleoprotein (edit) YP_173242.1 Q5MQC6
Coronavírus humano HKU1 (edit) Replicase polyprotein 1ab (edit) YP_173236.1 P0C6X2
Coronavírus humano HKU1 (edit) Hemagglutinin-esterase (edit) YP_173237.1 Q5MQD1
Coronavírus humano HKU1 (edit) Membrane protein (edit) YP_173241.1 Q5MQC7
Coronavírus humano OC43 (edit) hemagglutinin-esterase (edit) YP_009555240.1 P30215
Coronavírus humano OC43 (edit) envelope protein (edit) YP_009555243.1
Coronavírus humano OC43 (edit) ns2 (edit) YP_009555239.1
Coronavírus humano OC43 (edit) ns12.9 (edit) YP_009555242.1
Coronavírus humano OC43 (edit) nucleocapsid protein (edit) YP_009555245.1
Coronavírus humano OC43 (edit) spike surface glycoprotein (edit) YP_009555241.1
Coronavírus humano OC43 (edit) Orf1ab (edit) YP_009555238.1
Coronavírus humano OC43 (edit) membrane protein (edit) YP_009555244.1
SARS-CoV (edit) Protein 3a [SARS-Cov] (edit) NP_828852.2 P59632
SARS-CoV (edit) Replicase polyprotein 1a (edit) P0C6U8
Síndrome respiratória por coronavírus do Oriente Médio (edit) spike glycoprotein (edit) YP_009047204.1 K9N5Q8
Síndrome respiratória por coronavírus do Oriente Médio (edit) nucleoprotein (edit) YP_009047211.1 K9N4V7
Síndrome respiratória por coronavírus do Oriente Médio (edit) NS3 protein (edit) YP_009047205.1 K9N796
Síndrome respiratória por coronavírus do Oriente Médio (edit) NS4B protein (edit) YP_009047207.1 K9N643
Síndrome respiratória por coronavírus do Oriente Médio (edit) Envelope small membrane protein (edit) K9N5R3
Síndrome respiratória por coronavírus do Oriente Médio (edit) Replicase polyprotein 1ab (edit) K9N7C7
Síndrome respiratória por coronavírus do Oriente Médio (edit) Non-structural protein ORF5 (edit) K9N7D2
Síndrome respiratória por coronavírus do Oriente Médio (edit) Replicase polyprotein 1a (edit) K9N638
Síndrome respiratória por coronavírus do Oriente Médio (edit) Membrane protein (edit) K9N7A1
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 10 [SARS CoV-2] (edit)
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 15 [SARS-CoV-2] (edit)
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 16 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449633
coronavírus da síndrome respiratória aguda grave 2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) YP_009725299.1 P0DTD1-PRO_0000449621
coronavírus da síndrome respiratória aguda grave 2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) YP_009725299.1 P0DTC1-PRO_0000449637
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTC1-PRO_0000449639
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 5 [SARS-CoV-2] (edit) YP_009725301 P0DTD1-PRO_0000449623
coronavírus da síndrome respiratória aguda grave 2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) YP_009724397.2 P0DTC9
coronavírus da síndrome respiratória aguda grave 2 (edit) spike glycoprotein [SARS-CoV-2] (edit) YP_009724390.1 P0DTC2
coronavírus da síndrome respiratória aguda grave 2 (edit) orf1ab polyprotein [SARS-Cov 2] (edit) QHD43415 P0DTD1
coronavírus da síndrome respiratória aguda grave 2 (edit) Viroporin 3a [SARS-CoV-2] (edit) YP_009724391.1 P0DTC3
coronavírus da síndrome respiratória aguda grave 2 (edit) envelope protein [SARS-CoV-2] (edit) YP_009724392.1 P0DTC4
coronavírus da síndrome respiratória aguda grave 2 (edit) membrane protein [SARS-CoV-2] (edit) YP_009724393.1 P0DTC5
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 6 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449640
coronavírus da síndrome respiratória aguda grave 2 (edit) non-structural protein 6 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449624
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF1a polyprotein (edit) P0DTC1
coronavírus da síndrome respiratória aguda grave 2 (edit) Protein 7a [SARS-CoV-2] (edit) YP_009724395.1 P0DTC7
coronavírus da síndrome respiratória aguda grave 2 (edit) Protein non-structural 7b [SARS-CoV-2] (edit) YP_009725318.1 P0DTD8
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF8 protein [SARS-CoV-2] (edit) YP_009724396.1 P0DTC8
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 2 [SARS CoV-2] (edit) P0DTD1-PRO_0000449620
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 2 [SARS CoV-2] (edit) P0DTC1-PRO_0000449636
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF6 protein [SARS-CoV-2] (edit) YP_009724394.1 P0DTC6
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF10 protein [SARS-CoV-2] (edit) YP_009725255.1 A0A663DJA2
coronavírus da síndrome respiratória aguda grave 2 (edit) Protein ORF9b [SARS-CoV-2] (edit) P0DTD2
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449643
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449627
coronavírus da síndrome respiratória aguda grave 2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449635
coronavírus da síndrome respiratória aguda grave 2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449619
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 4 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449638
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 4 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449622
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 7 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449641
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 7 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449625
coronavírus da síndrome respiratória aguda grave 2 (edit) RNA-directed RNA polymerase [SARS-CoV-2] (edit) P0DTD1-PRO_0000449629
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 14 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449631
coronavírus da síndrome respiratória aguda grave 2 (edit) Helicase [SARS-CoV-2] (edit)
coronavírus da síndrome respiratória aguda grave 2 (edit) Uncharacterized protein 14 (edit) P0DTD3
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein nsp8 [SARS-CoV-2] (edit) P0DTC1-PRO_0000449642
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein nsp8 [SARS-CoV-2] (edit) P0DTD1-PRO_0000449626
coronavírus da síndrome respiratória aguda grave 2 (edit) putative protein ORF3c (edit) P0DTG1
coronavírus da síndrome respiratória aguda grave 2 (edit) Non-structural protein 11 [SARS CoV-2] (edit)
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF3b protein [SARS-CoV-2] (edit) P0DTF1
coronavírus da síndrome respiratória aguda grave 2 (edit) ORF9c protein [SARS CoV-2] (edit) P0DTD3
Coronavírus humano NL63 (edit) Spike glycoprotein [NL63] (edit) YP_003767.1 Q6Q1S2
Coronavírus humano NL63 (edit) Non-structural protein 3 (edit) YP_003768.1 Q6Q1S1
Coronavírus humano NL63 (edit) Envelope small membrane protein (edit) YP_003769.1 Q6Q1S0
Coronavírus humano NL63 (edit) Nucleoprotein (edit) YP_003771.1 Q6Q1R8
Coronavírus humano NL63 (edit) Membrane protein (edit) YP_003770.1 Q6Q1R9
Coronavírus humano NL63 (edit) Replicase polyprotein 1ab (edit) YP_003766.2 P0C6X5

Referências

  1. Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, et al. Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. NAR. 2019 Jan 1;47(D1):D550–8. doi:10.1093/NAR/GKY1001 (Scholia)
  2. Burley SK, Berman HM, Kleywegt G, Markley JL, Nakamura H, Velankar S. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. Methods in Molecular Biology. 2017 Jan 1;1607:627–41. doi:10.1007/978-1-4939-7000-1_26 (Scholia)