viralemergence / virion

The Global Virome in One Network
https://viralemergence.github.io/virion
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Marmosets! #40

Open cjcarlson opened 3 years ago

cjcarlson commented 3 years ago

> 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