User:SCIdude/Rotavirus

Rotavirus A annotation

InterPro families

Rotavirus VP1 RNA-directed RNA polymerase, C-terminal domain, protein family (Q83133549)
Rotavirus VP2 (Q24745872)
Protein VP3, rotavirus (Q24770641)
Outer capsid protein VP4 (Q81490100)
VP5*, fragment of Outer capsid protein VP4 (Q81490100) (cleaved by trypsin)
Rotavirus A/C, major capsid protein VP6 (Q24774064)
Rotavirus major outer capsid VP7 (Q24773176)
VP8*, fragment of Outer capsid protein VP4 (Q81490100) (cleaved by trypsin)

Strains / generic groups used in experimental papers

Strains / generic groups in WD

Roughly sorted by usage.

simian rhesus rotavirus (Q112242067) --- G3 P[3] I2 R2 C3 M3 A9 N? T3 E3 H6
Simian rotavirus A/SA11 (Q112242768) --- G3 P[1/2] I2 R2 C5 M5 A5 N5/N2 T5 E2 H5
Bovine rotavirus strain RF (Q113380949) --- G6 P[1] I2 R2 C2 M2 A3 N2 T6 E2 H3
Bovine rotavirus strain UK (Q113433734) --- G6 P[5] I2 R2 C2 M2 A3 N2 T7 E2 H3
Bovine rotavirus strain NCDV (Q113434050) --- G6 P[1] I2 R2 C2 M2 N2 T6 E2
Bovine rotavirus strain WC3 (Q113451268) --- G6 P[5] I2 R2 C2 M2 A3 N2 T6 E2 H3
Porcine rotavirus OSU (Q112246255) --- G5 P[7] I5 R1 C1 M1 A1 N1 T1 E1 H1
Human rotavirus strain WA (Q112246336) --- G1 P[8] I1 R1 C1 M1 A1 N1 T1 E1 H1
Simian rotavirus A/SA11-4F (Q112242692)
Human rotavirus RV-5 (Q112252986) --- G2 P[4] N2 E2
Porcine rotavirus strain CRW-8 (Q112262674) --- G3 P[7] I5
human rotavirus HAL1166 (Q112242465) --- G8 P[14]
Human rotavirus DS1 (Q112252639) --- G2 P[4] I2 R2 C2 M2 A2 N2 T2 E2 H2
human rotavirus strain PA169 (Q112252484) --- G6 P[14] I2 R2 C2 M2 A3 N2 T6 E2 H3
Equine rotavirus strain H-2 (Q112252427) --- G3 P[12] I2 A10 E2
Equine rotavirus strain H-1 (Q112252150) --- G5 P[7] I5 A8 E1
human rotavirus strain KUN (Q112703025) --- G2 P[4] E2 H2
Porcine rotavirus strain YM (Q112252803) --- G11 P[7] I5 R1 C1 M1 A8 N1 T1 E1
Human rotavirus KU (Q112252774) --- G1 P[8] I1 R1 C1 M1 A1 N1 T1 E1 H1
Porcine rotavirus strain Gottfried (Q112252593) --- G4 P[6] I1 R1 C1 M1 A8 N1 T1 E1 H1
Murine rotavirus EDIM (Q112246056) --- G16 P[16] I7 A7 E7
Rabbit rotavirus strain Alabama (Q113380805) --- G3 P[14] A9 E5 H3
Bovine rotavirus strain C486 (Q113381814)
human rotavirus strain D (Q113396346) --- G1 P[8] I1 R1 C1 M1 A1 N1 T1 E1 H1
Simian rotavirus A/SA11-5N (Q113354635) --- G3 P[1] I2 R2 C5 M5 A5 N5 T5 E2 H5
Human rotavirus strain ST3 (Q113457173) --- G4 P[6] I1 R1 C1 M1 A1 N1 T1 E1 H1
Human rotavirus strain MO (Q113468985) --- G3 P[8] E1
human rotavirus K8 (Q113531324) --- G1 P[9] A1 H3
Human rotavirus RV-3 (Q113531390) --- G3 P[6] I1 E1
Human rotavirus WI-61 (Q113531550) --- G9 P[8] I1 R1 C1 M1 A1 N1 T1 E1 H1
bovine rotavirus (Q112246123)
porcine rotavirus (Q113469026)
Avian rotavirus (Q113469397)
human rotavirus (Q113531739)
Murine rotavirus (Q113562395)

Query

The following query uses these:

Items: scholarly article (Q13442814)   , Rotavirus (Q164778)

Properties: instance of (P31)   , main subject (P921)   , describes a project that uses (P4510)  
```
SELECT ?ditemLabel (COUNT(?item) AS ?count)
WHERE
{
  ?item wdt:P31 wd:Q13442814.
  ?item wdt:P921 wd:Q164778.
  ?item wdt:P4510 ?ditem.
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
GROUP BY ?ditemLabel
```

Try it!

Papers using many strains

The following query uses these:

Items: scholarly article (Q13442814)   , Rotavirus (Q164778)

Properties: instance of (P31)   , main subject (P921)   , describes a project that uses (P4510)  
```
SELECT ?item ?itemLabel ?cnt
{
  {
       SELECT ?item (COUNT(?value) AS ?cnt)
       {
          ?item wdt:P31 wd:Q13442814.
          ?item wdt:P921 wd:Q164778.
          ?item wdt:P4510 ?value
       }
       GROUP BY ?item ORDER BY DESC(?cnt) LIMIT 100
  }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
ORDER BY DESC(?cnt)
```

Try it!

Literature Queries

The following query uses these:

Items: Rotavirus (Q164778)   , pharmacology (Q128406)   , structural biology (Q908902)   , viral entry into host cell (Q4118894)   , viral genome replication (Q3933202)   , virion assembly (Q14916420)   , viral RNA (Q27108123)   , post-translational protein modification (Q898362)   , modulation by virus of host process (Q14818042)   , modulation by host of viral process (Q22244941)   , RNA (Q11053)   , Rotavirus VP1 RNA-directed RNA polymerase, C-terminal domain, protein family (Q83133549)   , Rotavirus VP2 (Q24745872)   , Protein VP3, rotavirus (Q24770641)   , Outer capsid protein VP4 (Q81490100)   , Rotavirus A/C, major capsid protein VP6 (Q24774064)   , Rotavirus major outer capsid VP7 (Q24773176)   , Rotavirus non-structural protein 1 (Q24724262)   , Rotavirus non-structural protein 2 (Q24719751)   , Rotavirus non-structural protein NSP3 (Q24785520)   , Rotavirus non-structural protein 4 (Q24726417)   , Rotavirus A/C, non-structural protein 5 (Q24739451)   , Rotavirus non-structural protein 6 (Q24782928)

Properties: cites work (P2860)   , publication date (P577)   , PMC publication ID (P932)   , DOI (P356)   , main subject (P921)  
```
SELECT DISTINCT ?label ?item ?pmcid ?doi ?date
{
  VALUES ?pw { wd:Q164778 }
  VALUES ?top { wd:Q128406 wd:Q908902 wd:Q4118894 wd:Q3933202 wd:Q14916420 wd:Q27108123 wd:Q898362 wd:Q14818042 wd:Q22244941 wd:Q11053 wd:Q83133549 wd:Q24745872 wd:Q24770641 wd:Q81490100 wd:Q24774064 wd:Q24773176 wd:Q24724262 wd:Q24719751 wd:Q24785520 wd:Q24726417 wd:Q24739451 wd:Q24782928 }
  ?item p:P921 [ ps:P921 ?pw].
  ?item p:P921 [ ps:P921 ?top].
  MINUS { ?item wdt:P2860 [] }
  ?item wdt:P577 ?date.
  OPTIONAL { 
    ?item wdt:P932 ?pmcid.
  }
  OPTIONAL { 
    ?item wdt:P356 ?doi.
  }
  ?item rdfs:label ?label.
  FILTER(lang(?label) = 'en' && !STRENDS(?doi, 'PDB'))
}
```

Try it!