Marmosets!

[cjcarlson]

> classification("marmosets", db = "ncbi")
==  1 queries  ===============

Retrieving data for taxon 'marmosets'

√  Found:  marmosets
==  Results  =================

* Total: 1 
* Found: 1 
* Not Found: 0
$marmosets
                    name         rank      id
1     cellular organisms      no rank  131567
2              Eukaryota superkingdom    2759
3           Opisthokonta        clade   33154
4                Metazoa      kingdom   33208
5              Eumetazoa        clade    6072
6              Bilateria        clade   33213
7          Deuterostomia        clade   33511
8               Chordata       phylum    7711
9               Craniata    subphylum   89593
10            Vertebrata        clade    7742
11         Gnathostomata        clade    7776
12            Teleostomi        clade  117570
13          Euteleostomi        clade  117571
14         Sarcopterygii   superclass    8287
15  Dipnotetrapodomorpha        clade 1338369
16             Tetrapoda        clade   32523
17               Amniota        clade   32524
18              Mammalia        class   40674
19                Theria        clade   32525
20              Eutheria        clade    9347
21         Boreoeutheria        clade 1437010
22      Euarchontoglires   superorder  314146
23              Primates        order    9443
24 unclassified Primates      no rank   57118
25             marmosets      species   38020

attr(,"class")
[1] "classification"
attr(,"db")
[1] "ncbi"

Because of this there's five records in virion with host sp as "marmosets", no genus except for one (GLOBI - the other four are from GenBank), and nothing else below primates. If nothing else, you could have that bind to Callitrichidae. But this seems like a case of potentially broken NCBI taxonomy? I'm not sure if this one is a bug or a feature and will pass it onto Ryan for his judgment

[cjcarlson]

how is this still in here!!!!!!

[cjcarlson]

But this makes me think the pipeline isn't updating well

> classification("marmosets", db = "ncbi")
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
══  1 queries  ═══════════════

Retrieving data for taxon 'marmosets'

✔  Found:  marmosets
══  Results  ═════════════════

• Total: 1 
• Found: 1 
• Not Found: 0
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
$marmosets
                          name         rank      id
1           cellular organisms      no rank  131567
2                    Eukaryota superkingdom    2759
3                 Opisthokonta        clade   33154
4                      Metazoa      kingdom   33208
5                    Eumetazoa        clade    6072
6                    Bilateria        clade   33213
7                Deuterostomia        clade   33511
8                     Chordata       phylum    7711
9                     Craniata    subphylum   89593
10                  Vertebrata        clade    7742
11               Gnathostomata        clade    7776
12                  Teleostomi        clade  117570
13                Euteleostomi        clade  117571
14               Sarcopterygii   superclass    8287
15        Dipnotetrapodomorpha        clade 1338369
16                   Tetrapoda        clade   32523
17                     Amniota        clade   32524
18                    Mammalia        class   40674
19                      Theria        clade   32525
20                    Eutheria        clade    9347
21               Boreoeutheria        clade 1437010
22            Euarchontoglires   superorder  314146
23                    Primates        order    9443
24                 Haplorrhini     suborder  376913
25                 Simiiformes   infraorder  314293
26                 Platyrrhini    parvorder    9479
27                     Cebidae       family    9498
28              Callitrichinae    subfamily    9480
29 unclassified Callitrichinae      no rank 3085340
30          Callitrichinae sp.      species   38020

attr(,"class")
[1] "classification"
attr(,"db")
[1] "ncbi"