SARS-CoV-2-Queries

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Literature

These queries list the latest 10 articles about a number of topics. It is no replacement for Scholia [1], which has a much richer overview of literature on the topic. Each section includes a link to the Scholia page for that topic. The queries used here are very basic, and only use the ‘main subject’ property. This tutorial explains how to annotation literature with main subjects in Wikidata.

about SARS-CoV-2

SARS-CoV-2 is the name of the virus.

SPARQL sparql/litSARSCoV2.rq (run, edit)

SELECT (MAX(?dates) as ?date) ?work ?workLabel ?doi WHERE {
  ?work wdt:P921 wd:Q82069695 .
  OPTIONAL { ?work wdt:P577 ?dates . }
  OPTIONAL { ?work wdt:P356 ?doi . }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} GROUP BY ?work ?workLabel ?doi ORDER BY DESC(?date) ?work

This gives these 10 papers:

date work doi
2021-06-01 The fate of SARS-COV-2 in WWTPS points out the sludge line as a suitable spot for detection of COVID-19 (edit) 10.1016/J.SCITOTENV.2021.145268
2021-06-01 Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution (edit) 10.1016/J.VIROL.2021.02.013
2021-06-01 Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes (edit) 10.1016/J.MGENE.2021.100873
2021-06-01 Mutational analysis of SARS-CoV-2 during six months of COVID-19 pandemic (edit) 10.1016/J.GENREP.2021.101024
2021-04-23 ORF8 contributes to cytokine storm during SARS-CoV-2 infection by activating IL-17 pathway (edit) 10.1016/J.ISCI.2021.102293
2021-04-23 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring (edit) 10.1016/J.BBRC.2021.02.080
2021-04-16 The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins (edit) 10.1016/J.JMB.2021.166875
2021-04-01 Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8 (edit) 10.1002/PRO.4050
This table is truncated. See the full table at sparql/litSARSCoV2.rq

about SARS-CoV-2 genes

We can also query for articles about the genes. It breaks down like this:

We get that bar chart with this query:

SPARQL sparql/articleCountPerGene.rq (run, edit)

#defaultView:BarChart
SELECT ?gene ?geneLabel (COUNT(?work) AS ?count) WHERE {
  ?gene wdt:P703 wd:Q82069695 ; wdt:P31 wd:Q7187 .
  ?work wdt:P921 ?gene .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} GROUP BY ?gene ?geneLabel
  ORDER BY ASC(?geneLabel)

The articles themselves we can list with this query:

SPARQL sparql/litSARSCoV2Genes.rq (run, edit)

SELECT (MAX(?dates) as ?date) ?work ?workLabel ?doi WHERE {
  ?gene wdt:P703 wd:Q82069695 ; wdt:P31 wd:Q7187 .
  ?work wdt:P921 ?gene .
  OPTIONAL { ?work wdt:P577 ?dates . }
  OPTIONAL { ?work wdt:P356 ?doi . }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} GROUP BY ?work ?workLabel ?doi ORDER BY DESC(?date)

Which currently returns:

date work doi
2020-08-18 Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study (edit) 10.1016/S0140-6736(20)31757-8
2020-07-21 Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 (edit) 10.1128/MBIO.01610-20
2020-06-22 A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2 (edit) 10.1126/SCIENCE.ABC6952
2020-06-16 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East (edit) 10.1080/22221751.2020.1782271
2020-05-25 Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a (edit) 10.1101/2020.05.22.20108498
2020-05-18 Molecular conservation and Differential mutation on ORF3a gene in Indian SARS-CoV2 genomes (edit) 10.1101/2020.05.14.096107
2020-04-30 A SARS-CoV-2 protein interaction map reveals targets for drug repurposing (edit) 10.1038/S41586-020-2286-9
2020-04-20 Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites (edit) 10.1016/J.APSB.2020.04.009
This table is truncated. See the full table at sparql/litSARSCoV2Genes.rq

about SARS-CoV-2 proteins

And about the virus proteins we have this distribution of articles:

We get that bar chart with this query:

SPARQL sparql/articleCountPerProtein.rq (run, edit)

#defaultView:BarChart
SELECT ?protein ?proteinLabel (COUNT(?work) AS ?count) WHERE {
  ?protein wdt:P703 wd:Q82069695 ; wdt:P31 wd:Q8054 .
  ?work wdt:P921 ?protein .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} GROUP BY ?protein ?proteinLabel
  ORDER BY ASC(?proteinLabel)

The articles themselves we can list with this query:

SPARQL sparql/litSARSCoV2Proteins.rq (run, edit)

SELECT (MAX(?dates) as ?date) ?work ?workLabel ?doi WHERE {
  ?protein wdt:P703 wd:Q82069695 ; wdt:P31 wd:Q8054 .
  ?work wdt:P921 ?protein .
  OPTIONAL { ?work wdt:P577 ?dates . }
  OPTIONAL { ?work wdt:P356 ?doi . }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} GROUP BY ?work ?workLabel ?doi ORDER BY DESC(?date)

Which currently returns:

date work doi
2021-04-23 ORF8 contributes to cytokine storm during SARS-CoV-2 infection by activating IL-17 pathway (edit) 10.1016/J.ISCI.2021.102293
2021-04-16 The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins (edit) 10.1016/J.JMB.2021.166875
2021-04-01 Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8 (edit) 10.1002/PRO.4050
2021-04-01 The ORF8 protein of SARS-CoV-2 induced endoplasmic reticulum stress and mediated immune evasion by antagonizing production of interferon beta (edit) 10.1016/J.VIRUSRES.2021.198350
2021-03-25 Characterization of SARS-CoV-2 proteins reveals Orf6 pathogenicity, subcellular localization, host interactions and attenuation by Selinexor (edit) 10.1186/S13578-021-00568-7
2021-03-24 Arginine Methylation Regulates SARS-CoV-2 Nucleocapsid Protein Function and Viral Replication (edit) 10.1101/2021.03.24.436822
2021-03-23 SARS-CoV-2 variants lacking ORF8 occurred in farmed mink and pangolin (edit) 10.1016/J.GENE.2021.145596
2021-03-15 SARS-CoV-2 Nsp8 N-terminal domain dimerizes and harbors autonomously folded elements (edit) 10.1101/2021.03.12.435186
This table is truncated. See the full table at sparql/litSARSCoV2Proteins.rq

about coronaviruses

As outlined in Chapter 2, SARS-Cov-2 is one of the coronaviruses that can infect humans.

SPARQL sparql/litCoronaviruses.rq (run, edit)

SELECT (MAX(?dates) as ?date) ?work ?workLabel ?doi WHERE {
  ?work wdt:P921 wd:Q57751738 .
  OPTIONAL { ?work wdt:P577 ?dates . }
  OPTIONAL { ?work wdt:P356 ?doi . }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} GROUP BY ?work ?workLabel ?doi ORDER BY DESC(?date)

This gives these 10 papers:

date work doi
2020-04-01 [Recommendations for critically ill patients with COVID-19] (edit) 10.1007/S00063-020-00674-3
2020-03-27 A new threat from an old enemy: Re‑emergence of coronavirus (Review) (edit) 10.3892/IJMM.2020.4555
2020-02-26 Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review (edit) 10.3390/JCM9030623
2020-02-14 The First Disease X is Caused by a Highly Transmissible Acute Respiratory Syndrome Coronavirus (edit) 10.1007/S12250-020-00206-5

about human coronaviruses

The seven human coronaviruses have more than 6000 thousand articles about them in Wikidata. The following query therefore is a bit tuned for performance and more complex. Also, the list is quite long, and not given on this page. To see the output, click below in the name of the litHumanCoronaviruses.rq file:

SPARQL sparql/litHumanCoronaviruses.rq (run, edit)

SELECT ?date ?work ?workLabel ?virus ?virusLabel ?doi ?pubmed WITH {
  SELECT (MAX(?dates) as ?date) ?work ?doi ?virus 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
    }
    ?work wdt:P577 ?dates ;
          wdt:P921 ?virus .
  } GROUP BY ?work ?doi ?virus
    ORDER BY DESC(?date)
    LIMIT 5000
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  OPTIONAL { ?work wdt:P356 ?doi . }
  OPTIONAL { ?work wdt:P698 ?pubmed . }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}
ORDER BY DESC(?date) ?doi ?pubmed ?virus

Moreover, the number of articles for each virus varies significantly, which can be visualized with this query:

SPARQL sparql/litHumanCoronavirusesCounts.rq (run, edit)

SELECT ?virus ?virusLabel ?count WITH {
  SELECT ?virus (COUNT(DISTINCT ?work) AS ?count) 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
    }
    ?work wdt:P921 ?virus .
  } GROUP BY ?virus
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}
ORDER BY DESC(?count)

Which tells us:

virus count
SARS-CoV-2 (edit) 18543
SARSr-CoV (edit) 2481
Middle East respiratory syndrome coronavirus (edit) 1042
Human coronavirus OC43 (edit) 91
Human coronavirus 229E (edit) 84
Human Coronavirus NL63 (edit) 79
Human coronavirus HKU1 (edit) 21

and their genes

SPARQL sparql/litHumanCoronavirusesGeneCounts.rq (run, edit)

SELECT ?virus ?virusLabel ?gene ?geneLabel ?count WITH {
  SELECT ?virus ?gene (COUNT(DISTINCT ?work) AS ?count) 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 .
    ?work wdt:P921 ?gene .
  } GROUP BY ?virus ?gene
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}
ORDER BY DESC(?count)

Which shows us:

virus gene count
SARS-CoV-2 (edit) ORF8 protein (edit) 6
Human Coronavirus NL63 (edit) membrane protein (edit) 3
Human Coronavirus NL63 (edit) nucleocapsid protein (edit) 3
Human Coronavirus NL63 (edit) envelope protein (edit) 3
Human Coronavirus NL63 (edit) spike protein (edit) 3
Human Coronavirus NL63 (edit) replicase polyprotein 1ab (edit) 2
Human Coronavirus NL63 (edit) protein 3 (edit) 2
Human coronavirus 229E (edit) nucleocapsid protein (edit) 2
Human coronavirus 229E (edit) surface glycoprotein (edit) 2
Human coronavirus OC43 (edit) spike surface glycoprotein (edit) 2
SARS-CoV-2 (edit) nucleocapsid phosphoprotein (edit) 2
SARS-CoV-2 (edit) ORF7b (edit) 2
SARS-CoV-2 (edit) ORF3a protein (edit) 2
SARS-CoV-2 (edit) surface glycoprotein (edit) 2
Human coronavirus 229E (edit) envelope protein (edit) 1
Human coronavirus 229E (edit) membrane protein (edit) 1
Human coronavirus 229E (edit) 4b protein (edit) 1
Human coronavirus 229E (edit) 4a protein (edit) 1
Human coronavirus OC43 (edit) membrane protein (edit) 1
Human coronavirus OC43 (edit) I protein;nucleocapsid protein (edit) 1
Human coronavirus OC43 (edit) ns2 (edit) 1
Human coronavirus HKU1 (edit) membrane glycoprotein (edit) 1
Human coronavirus HKU1 (edit) hemagglutinin-esterase glycoprotein (edit) 1
Human coronavirus HKU1 (edit) ORF1a polyprotein;ORF1ab polyprotein (edit) 1
Human coronavirus HKU1 (edit) nucleocapsid phosphoprotein (edit) 1
Human coronavirus HKU1 (edit) envelope protein (edit) 1
Human coronavirus HKU1 (edit) spike glycoprotein (edit) 1
SARS-CoV-2 (edit) ORF7a protein (edit) 1
SARS-CoV-2 (edit) membrane glycoprotein (edit) 1
SARS-CoV-2 (edit) envelope protein (edit) 1
SARS-CoV-2 (edit) ORF1a polyprotein;ORF1ab polyprotein (edit) 1

and their proteins

SPARQL sparql/litHumanCoronavirusesProteinCounts.rq (run, edit)

SELECT ?virus ?virusLabel ?protein ?proteinLabel ?count WITH {
  SELECT ?virus ?protein (COUNT(DISTINCT ?work) AS ?count) 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:P31 wd:Q8054 .
    { ?protein wdt:P703 ?virus }
    UNION
    { ?protein wdt:P702 | ^wdt:P688 ?gene . ?gene wdt:P703 ?virus }
    ?work wdt:P921 ?protein .
  } GROUP BY ?virus ?protein
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}
ORDER BY DESC(?count) ?virus ?protein

Where the counts are:

virus protein count
SARS-CoV-2 (edit) spike glycoprotein [SARS-CoV-2] (edit) 104
SARSr-CoV (edit) spike glycoprotein [SARS-Cov] (edit) 83
SARSr-CoV (edit) nucleoprotein [SARS-Cov] (edit) 60
SARSr-CoV (edit) 3C-like proteinase [SARS-Cov] (edit) 57
SARS-CoV-2 (edit) nucleocapsid protein [SARS-CoV-2] (edit) 48
SARSr-CoV (edit) Protein 3a [SARS-Cov] (edit) 39
SARSr-CoV (edit) papain-like proteinase [SARS-Cov] (edit) 38
SARSr-CoV (edit) Envelope small membrane protein [SARS-Cov] (edit) 36
SARS-CoV-2 (edit) Papain-like proteinase [SARS-CoV-2] (edit) 28
SARS-CoV-2 (edit) Host translation inhibitor nsp1 [SARS-CoV-2] (edit) 28
SARS-CoV-2 (edit) non-structural protein 16 [SARS-CoV-2] (edit) 26
SARS-CoV-2 (edit) Non-structural protein 10 [SARS CoV-2] (edit) 25
SARS-CoV-2 (edit) RNA-directed RNA polymerase [SARS-CoV-2] (edit) 25
SARS-CoV-2 (edit) non-structural protein 5 [SARS-CoV-2] (edit) 24
SARSr-CoV (edit) Membrane protein [SARS-Cov] (edit) 23
SARS-CoV-2 (edit) ORF8 protein [SARS-CoV-2] (edit) 20
SARS-CoV-2 (edit) Helicase [SARS-CoV-2] (edit) 17
SARSr-CoV (edit) Non-structural protein NS6 [SARS-Cov] (edit) 15
SARSr-CoV (edit) Protein 7a [SARS-Cov] (edit) 14
SARS-CoV-2 (edit) non-structural protein 15 [SARS-CoV-2] (edit) 14
SARS-CoV-2 (edit) Non-structural protein 14 [SARS-CoV-2] (edit) 13
SARS-CoV-2 (edit) Non-structural protein nsp8 [SARS-CoV-2] (edit) 13
SARSr-CoV (edit) host translation inhibitor nsp1 [SARS-Cov] (edit) 12
SARS-CoV-2 (edit) Non-structural protein 7 [SARS-CoV-2] (edit) 11
SARSr-CoV (edit) Guanine-N7 methyltransferase [SARS-Cov] (edit) 10
SARSr-CoV (edit) protein non-structural 8a [SARS-Cov] (edit) 10
Middle East respiratory syndrome coronavirus (edit) spike glycoprotein (edit) 10
SARSr-CoV (edit) Non-structural protein 3b [SARS-Cov] (edit) 9
SARSr-CoV (edit) 2'-O-methyltransferase [SARS-Cov] (edit) 9
SARS-CoV-2 (edit) envelope protein [SARS-CoV-2] (edit) 9
SARS-CoV-2 (edit) Protein 7a [SARS-CoV-2] (edit) 9
SARSr-CoV (edit) Protein 9b [SARS-Cov] (edit) 8
SARSr-CoV (edit) uridylate-specific endoribonuclease [SARS-Cov] (edit) 8
SARSr-CoV (edit) protein non-structural 8b [SARS-Cov] (edit) 8
SARS-CoV-2 (edit) membrane protein [SARS-CoV-2] (edit) 8
SARS-CoV-2 (edit) ORF6 protein [SARS-CoV-2] (edit) 8
SARS-CoV-2 (edit) Non-structural protein 9 [SARS-CoV-2] (edit) 8
SARSr-CoV (edit) non-structural protein 10 [SARS-Cov] (edit) 7
SARSr-CoV (edit) RNA-directed RNA polymerase [SARS-Cov] (edit) 7
SARSr-CoV (edit) helicase [SARS-Cov] (edit) 7
SARS-CoV-2 (edit) Viroporin 3a [SARS-CoV-2] (edit) 7
SARS-CoV-2 (edit) Non-structural protein 2 [SARS CoV-2] (edit) 7
SARSr-CoV (edit) replicase polyprotein 1ab [SARS-Cov] (edit) 6
SARSr-CoV (edit) non-structural protein 7 [SARS-Cov] (edit) 6
SARSr-CoV (edit) non-structural protein 8 [SARS-Cov] (edit) 6
Human coronavirus OC43 (edit) nucleocapsid protein (edit) 5
SARSr-CoV (edit) Protein non-structural 7b [SARS-Cov] (edit) 5
SARSr-CoV (edit) non-structural protein 9 [SARS-Cov] (edit) 5
SARS-CoV-2 (edit) ORF3b protein [SARS-CoV-2] (edit) 5
SARS-CoV-2 (edit) non-structural protein 6 [SARS-CoV-2] (edit) 5
SARS-CoV-2 (edit) Protein ORF9b [SARS-CoV-2] (edit) 5
Human Coronavirus NL63 (edit) Spike glycoprotein [NL63] (edit) 5
Human coronavirus OC43 (edit) spike surface glycoprotein (edit) 4
SARSr-CoV (edit) non-structural protein 4 [SARS-Cov] (edit) 4
SARS-CoV-2 (edit) ORF10 protein [SARS-CoV-2] (edit) 4
Human coronavirus HKU1 (edit) Spike glycoprotein (edit) 3
SARSr-CoV (edit) non-structural protein 6 [SARS-Cov] (edit) 3
Middle East respiratory syndrome coronavirus (edit) nucleoprotein (edit) 3
SARS-CoV-2 (edit) Protein non-structural 7b [SARS-CoV-2] (edit) 3
SARS-CoV-2 (edit) Non-structural protein 4 [SARS-CoV-2] (edit) 3
Human coronavirus 229E (edit) Non-structural protein 4b (edit) 2
Human coronavirus 229E (edit) Spike glycoprotein (edit) 2
Human coronavirus HKU1 (edit) Replicase polyprotein 1ab (edit) 2
Human coronavirus OC43 (edit) ns12.9 (edit) 2
Human coronavirus OC43 (edit) hemagglutinin-esterase (edit) 2
SARSr-CoV (edit) non-structural protein 2 [SARS-Cov] (edit) 2
SARS-CoV-2 (edit) orf1ab polyprotein [SARS-Cov 2] (edit) 2
Human Coronavirus NL63 (edit) Nucleoprotein (edit) 2
Human coronavirus 229E (edit) Non-structural protein 4a (edit) 1
Human coronavirus 229E (edit) Nucleoprotein (edit) 1
Human coronavirus 229E (edit) Replicase polyprotein 1ab (edit) 1
Human coronavirus HKU1 (edit) Spike glycoprotein (edit) 1
Human coronavirus HKU1 (edit) Membrane protein (edit) 1
Human coronavirus OC43 (edit) ns2 (edit) 1
Human coronavirus OC43 (edit) membrane protein (edit) 1
SARSr-CoV (edit) spike protein S2 [SARS-Cov] (edit) 1
SARSr-CoV (edit) Replicase polyprotein 1a (edit) 1
Middle East respiratory syndrome coronavirus (edit) NS4B protein (edit) 1
SARS-CoV-2 (edit) putative protein ORF3c (edit) 1
SARS-CoV-2 (edit) Non-structural protein 11 [SARS CoV-2] (edit) 1
SARS-CoV-2 (edit) ORF9c protein [SARS CoV-2] (edit) 1
Human Coronavirus NL63 (edit) Membrane protein (edit) 1

References

  1. Rasberry L, Willighagen E, Nielsen FÅ, Mietchen D. Robustifying Scholia: paving the way for knowledge discovery and research assessment through Wikidata. RIO Journal [Internet]. 2019 May 2;5. Available from: https://riojournal.com/article/35820/ doi:10.3897/RIO.5.E35820 (Scholia)