Handling Metadata in RNeXML

Carl Boettiger

Scott Chamberlain

Rutger Vos

Hilmar Lapp

Writing NeXML metadata

The add_basic_meta() function takes as input an existing nexml object (like the other add_ functions, if none is provided it will create one), and at the time of this writing any of the following parameters: title, description, creator, pubdate, rights, publisher, citation. Other metadata elements and corresponding parameters may be added in the future.

Load the packages and data:

library('RNeXML')
data(bird.orders)

Create an nexml object for the phylogeny bird.orders and add appropriate metadata:

birds <- add_trees(bird.orders)
birds <- add_basic_meta(
  title = "Phylogeny of the Orders of Birds From Sibley and Ahlquist",

  description = "This data set describes the phylogenetic relationships of the
     orders of birds as reported by Sibley and Ahlquist (1990). Sibley
     and Ahlquist inferred this phylogeny from an extensive number of
     DNA/DNA hybridization experiments. The ``tapestry'' reported by
     these two authors (more than 1000 species out of the ca. 9000
     extant bird species) generated a lot of debates.

     The present tree is based on the relationships among orders. The
     branch lengths were calculated from the values of Delta T50H as
     found in Sibley and Ahlquist (1990, fig. 353).",

  citation = "Sibley, C. G. and Ahlquist, J. E. (1990) Phylogeny and
     classification of birds: a study in molecular evolution. New
     Haven: Yale University Press.",

  creator = "Sibley, C. G. and Ahlquist, J. E.",
    nexml=birds)

Instead of a literal string, citations can also be provided in R’s bibentry type, which is the one in which R package citations are obtained:

birds <- add_basic_meta(citation = citation("ape"), nexml = birds)

Taxonomic identifiers

RNeXML now uses taxald for fast look-up of taxonomic information. If a unique match is found, a metadata annotation is added to the taxon providing the unique URI to the taxonomic unit.

birds <- taxize_nexml(birds, "NCBI")

If no perfect match is found, the user is warned to check for possible typographic errors in the taxonomic labels provided.

Custom metadata extensions

We can get a list of namespaces along with their prefixes from the nexml object:

prefixes <- get_namespaces(birds)
prefixes["dc"]
                                dc 
"http://purl.org/dc/elements/1.1/" 

We create a meta element containing this annotation using the meta function:

modified <- meta(property = "prism:modificationDate", content = "2013-10-04")

We can add this annotation to our existing birds NeXML file using the add_meta() function. Because we do not specify a level, it is added to the root node, referring to the NeXML file as a whole.

birds <- add_meta(modified, birds) 

The built-in vocabularies are just the tip of the iceberg of established vocabularies. Here we add an annotation from the skos namespace which describes the history of where the data comes from:

history <- meta(property = "skos:historyNote",
  content = "Mapped from the bird.orders data in the ape package using RNeXML")

Because skos is not in the current namespace list, we add it with a url when adding this meta element. We also specify that this annotation be placed at the level of the trees sub-node in the NeXML file.

birds <- add_meta(history, 
                birds, 
                level = "trees",
                namespaces = c(skos = "http://www.w3.org/2004/02/skos/core#"))

For finer control of the level at which a meta element is added, we will manipulate the nexml R object directly using S4 sub-setting, as shown in the supplement.

Much richer metadata annotation is possible. Later we illustrate how metadata annotation can be used to extend the base NeXML format to represent new forms of data while maintaining compatibility with any NeXML parser. The RNeXML package can be easily extended to support helper functions such as taxize_nexml to add additional metadata without imposing a large burden on the user.

Reading NeXML metadata

A call to the nexml object prints some metadata summarizing the data structure:

birds
A nexml object representing:
     1 phylogenetic tree block(s), where:
       block 1 contains 1 phylogenetic tree(s) 
     0 character block(s),  
     23 taxonomic units in 1 block(s) 
  Taxa:  Struthioniformes, Tinamiformes, Craciformes, Galliformes, Anseriformes, Turniciformes ...
  Metadata annotations: 
    18 at top level 
    0 in block 1 at otu level  

This data set describes the phylogenetic relationships of the
     orders of birds as reported by Sibley and Ahlquist (1990). Sibley
     and Ahlquist inferred this phylogeny from an extensive number of
     DNA/DNA hybridization experiments. The ``tapestry'' reported by
     these two authors (more than 1000 species out of the ca. 9000
     extant bird species) generated a lot of debates.

     The present tree is based on the relationships among orders. The
     branch lengths were calculated from the values of Delta T50H as
     found in Sibley and Ahlquist (1990, fig. 353).

Author(s): Sibley, C. G. and Ahlquist, J. E., cboettig

License: http://creativecommons.org/publicdomain/zero/1.0/

NeXML generated by RNeXML using schema version: 0.9 
Size: 358.3 Kb 

We can extract all metadata pertaining to the NeXML document as a whole (annotations of the XML root node, <nexml>) with the command

meta <- get_metadata(birds) 

This returns a data.frame of available metadata. We can see the kinds of metadata recorded from the names:

meta
                        property   datatype
1                       dc:title xsd:string
2                     dc:creator xsd:string
3                 dc:description xsd:string
4                     cc:license       <NA>
5  dcterms:bibliographicCitation xsd:string
6                     dc:creator xsd:string
7             dcterms:references       <NA>
8         prism:modificationDate xsd:string
9                   prism:volume xsd:string
10                  dc:publisher xsd:string
11         prism:publicationName xsd:string
12              prism:endingPage xsd:string
13            prism:startingPage xsd:string
14         prism:publicationDate xsd:string
15                      dc:title xsd:string
16                dc:contributor xsd:string
17                dc:contributor xsd:string
18 dcterms:bibliographicCitation xsd:string
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             content
1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Phylogeny of the Orders of Birds From Sibley and Ahlquist
2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Sibley, C. G. and Ahlquist, J. E.
3  This data set describes the phylogenetic relationships of the\n     orders of birds as reported by Sibley and Ahlquist (1990). Sibley\n     and Ahlquist inferred this phylogeny from an extensive number of\n     DNA/DNA hybridization experiments. The ``tapestry'' reported by\n     these two authors (more than 1000 species out of the ca. 9000\n     extant bird species) generated a lot of debates.\n\n     The present tree is based on the relationships among orders. The\n     branch lengths were calculated from the values of Delta T50H as\n     found in Sibley and Ahlquist (1990, fig. 353).
4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
5                                                                                                                                                                                                                                                                                                                                                                                                                                                      Sibley, C. G. and Ahlquist, J. E. (1990) Phylogeny and\n     classification of birds: a study in molecular evolution. New\n     Haven: Yale University Press.
6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           cboettig
7                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               <NA>
8                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         2013-10-04
9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 35
10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Bioinformatics
11                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Bioinformatics
12                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               528
13                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               526
14                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              2018
15                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ape 5.0: an environment for modern phylogenetics and evolutionary analyses in {R}
16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        E. Paradis
17                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        K. Schliep
18                                                                                                                                                                                                                                                                                                                                                                                                                                                                Paradis E, Schliep K (2018). "ape 5.0: an environment for modern\nphylogenetics and evolutionary analyses in R." _Bioinformatics_,\n*35*, 526-528.
       xsi.type                                              href Meta
1   LiteralMeta                                              <NA>  m16
2   LiteralMeta                                              <NA>  m17
3   LiteralMeta                                              <NA>  m18
4  ResourceMeta http://creativecommons.org/publicdomain/zero/1.0/  m19
5   LiteralMeta                                              <NA>  m20
6   LiteralMeta                                              <NA>  m21
7  ResourceMeta                                              <NA>  m32
8   LiteralMeta                                              <NA>  m33
9   LiteralMeta                                              <NA> <NA>
10  LiteralMeta                                              <NA> <NA>
11  LiteralMeta                                              <NA> <NA>
12  LiteralMeta                                              <NA> <NA>
13  LiteralMeta                                              <NA> <NA>
14  LiteralMeta                                              <NA> <NA>
15  LiteralMeta                                              <NA> <NA>
16  LiteralMeta                                              <NA> <NA>
17  LiteralMeta                                              <NA> <NA>
18  LiteralMeta                                              <NA> <NA>
   meta
1  <NA>
2  <NA>
3  <NA>
4  <NA>
5  <NA>
6  <NA>
7  <NA>
8  <NA>
9   m32
10  m32
11  m32
12  m32
13  m32
14  m32
15  m32
16  m32
17  m32
18  m32

We can also access a table of taxonomic metadata:

get_taxa(birds)
    otu            label xsi.type otus
1  ou70 Struthioniformes       NA  os4
2  ou71     Tinamiformes       NA  os4
3  ou72      Craciformes       NA  os4
4  ou73      Galliformes       NA  os4
5  ou74     Anseriformes       NA  os4
6  ou75    Turniciformes       NA  os4
7  ou76       Piciformes       NA  os4
8  ou77    Galbuliformes       NA  os4
9  ou78   Bucerotiformes       NA  os4
10 ou79      Upupiformes       NA  os4
11 ou80    Trogoniformes       NA  os4
12 ou81    Coraciiformes       NA  os4
13 ou82      Coliiformes       NA  os4
14 ou83     Cuculiformes       NA  os4
15 ou84   Psittaciformes       NA  os4
16 ou85      Apodiformes       NA  os4
17 ou86   Trochiliformes       NA  os4
18 ou87  Musophagiformes       NA  os4
19 ou88     Strigiformes       NA  os4
20 ou89    Columbiformes       NA  os4
21 ou90       Gruiformes       NA  os4
22 ou91    Ciconiiformes       NA  os4
23 ou92    Passeriformes       NA  os4

Which returns text from the otu element labels, typically used to define taxonomic names, rather than text from explicit meta elements.

We can also access metadata at a specific level (or use level=all to extract all meta elements in a list). Here we show only the first few results:

otu_meta <- get_metadata(birds, level="otus/otu")
otu_meta
# A tibble: 0 x 3
# … with 3 variables: otu <chr>, otus <chr>, Meta <chr>

Merging metadata tables

We often want to combine metadata from multiple tables. For instance, in this exercise we want to include the taxonomic identifier and id value for each species returned in the character table. This helps us more precisely identify the species whose traits are described by the table.

library("RNeXML")
library("dplyr")
library("geiger")

To begin, let’s generate a NeXML file using the tree and trait data from the geiger package’s “primates” data:

data("primates")
add_trees(primates$phy) %>% 
  add_characters(primates$dat, ., append=TRUE) %>% 
  taxize_nexml("itis") -> nex 

(Note that we’ve used dplyr’s cute pipe syntax, but unfortunately our add_ methods take the nexml object as the second argument instead of the first, so this isn’t as elegant since we need the stupid . to show where the piped output should go…)

We now read in the three tables of interest. Note that we tell get_characters to give us species labels as there own column, rather than as rownames. The latter is the default only because this plays more nicely with the default format for character matrices that is expected by geiger and other phylogenetics packages, but is in general a silly choice for data manipulation.

otu_meta <- get_metadata(nex, "otus/otu")
taxa <- get_taxa(nex)
char <- get_characters(nex, rownames_as_col = TRUE)

We can take a peek at what the tables look like, just to orient ourselves:

otu_meta
      property
1   tc:toTaxon
2   tc:toTaxon
3   tc:toTaxon
4   tc:toTaxon
5   tc:toTaxon
6   tc:toTaxon
7   tc:toTaxon
8   tc:toTaxon
9   tc:toTaxon
10  tc:toTaxon
11  tc:toTaxon
12  tc:toTaxon
13  tc:toTaxon
14  tc:toTaxon
15  tc:toTaxon
16  tc:toTaxon
17  tc:toTaxon
18  tc:toTaxon
19  tc:toTaxon
20  tc:toTaxon
21  tc:toTaxon
22  tc:toTaxon
23  tc:toTaxon
24  tc:toTaxon
25  tc:toTaxon
26  tc:toTaxon
27  tc:toTaxon
28  tc:toTaxon
29  tc:toTaxon
30  tc:toTaxon
31  tc:toTaxon
32  tc:toTaxon
33  tc:toTaxon
34  tc:toTaxon
35  tc:toTaxon
36  tc:toTaxon
37  tc:toTaxon
38  tc:toTaxon
39  tc:toTaxon
40  tc:toTaxon
41  tc:toTaxon
42  tc:toTaxon
43  tc:toTaxon
44  tc:toTaxon
45  tc:toTaxon
46  tc:toTaxon
47  tc:toTaxon
48  tc:toTaxon
49  tc:toTaxon
50  tc:toTaxon
51  tc:toTaxon
52  tc:toTaxon
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56  tc:toTaxon
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84  tc:toTaxon
85  tc:toTaxon
86  tc:toTaxon
87  tc:toTaxon
88  tc:toTaxon
89  tc:toTaxon
90  tc:toTaxon
91  tc:toTaxon
92  tc:toTaxon
93  tc:toTaxon
94  tc:toTaxon
95  tc:toTaxon
96  tc:toTaxon
97  tc:toTaxon
98  tc:toTaxon
99  tc:toTaxon
100 tc:toTaxon
101 tc:toTaxon
102 tc:toTaxon
103 tc:toTaxon
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155 tc:toTaxon
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        xsi.type   otu otus Meta
1   ResourceMeta  ou93  os5  m35
2   ResourceMeta  ou94  os5  m36
3   ResourceMeta  ou95  os5  m37
4   ResourceMeta  ou96  os5  m38
5   ResourceMeta  ou99  os5  m39
6   ResourceMeta ou100  os5  m40
7   ResourceMeta ou101  os5  m41
8   ResourceMeta ou102  os5  m42
9   ResourceMeta ou104  os5  m43
10  ResourceMeta ou107  os5  m44
11  ResourceMeta ou108  os5  m45
12  ResourceMeta ou109  os5  m46
13  ResourceMeta ou110  os5  m47
14  ResourceMeta ou111  os5  m48
15  ResourceMeta ou112  os5  m49
16  ResourceMeta ou113  os5  m50
17  ResourceMeta ou114  os5  m51
18  ResourceMeta ou115  os5  m52
19  ResourceMeta ou116  os5  m53
20  ResourceMeta ou117  os5  m54
21  ResourceMeta ou118  os5  m55
22  ResourceMeta ou119  os5  m56
23  ResourceMeta ou120  os5  m57
24  ResourceMeta ou121  os5  m58
25  ResourceMeta ou122  os5  m59
26  ResourceMeta ou123  os5  m60
27  ResourceMeta ou124  os5  m61
28  ResourceMeta ou136  os5  m62
29  ResourceMeta ou138  os5  m63
30  ResourceMeta ou140  os5  m64
31  ResourceMeta ou141  os5  m65
32  ResourceMeta ou142  os5  m66
33  ResourceMeta ou144  os5  m67
34  ResourceMeta ou145  os5  m68
35  ResourceMeta ou146  os5  m69
36  ResourceMeta ou148  os5  m70
37  ResourceMeta ou150  os5  m71
38  ResourceMeta ou151  os5  m72
39  ResourceMeta ou152  os5  m73
40  ResourceMeta ou153  os5  m74
41  ResourceMeta ou154  os5  m75
42  ResourceMeta ou155  os5  m76
43  ResourceMeta ou156  os5  m77
44  ResourceMeta ou157  os5  m78
45  ResourceMeta ou158  os5  m79
46  ResourceMeta ou159  os5  m80
47  ResourceMeta ou160  os5  m81
48  ResourceMeta ou161  os5  m82
49  ResourceMeta ou162  os5  m83
50  ResourceMeta ou164  os5  m84
51  ResourceMeta ou165  os5  m85
52  ResourceMeta ou166  os5  m86
53  ResourceMeta ou167  os5  m87
54  ResourceMeta ou168  os5  m88
55  ResourceMeta ou169  os5  m89
56  ResourceMeta ou171  os5  m90
57  ResourceMeta ou173  os5  m91
58  ResourceMeta ou174  os5  m92
59  ResourceMeta ou175  os5  m93
60  ResourceMeta ou176  os5  m94
61  ResourceMeta ou177  os5  m95
62  ResourceMeta ou178  os5  m96
63  ResourceMeta ou179  os5  m97
64  ResourceMeta ou180  os5  m98
65  ResourceMeta ou181  os5  m99
66  ResourceMeta ou182  os5 m100
67  ResourceMeta ou183  os5 m101
68  ResourceMeta ou184  os5 m102
69  ResourceMeta ou185  os5 m103
70  ResourceMeta ou186  os5 m104
71  ResourceMeta ou187  os5 m105
72  ResourceMeta ou188  os5 m106
73  ResourceMeta ou189  os5 m107
74  ResourceMeta ou190  os5 m108
75  ResourceMeta ou191  os5 m109
76  ResourceMeta ou193  os5 m110
77  ResourceMeta ou194  os5 m111
78  ResourceMeta ou195  os5 m112
79  ResourceMeta ou196  os5 m113
80  ResourceMeta ou197  os5 m114
81  ResourceMeta ou199  os5 m115
82  ResourceMeta ou200  os5 m116
83  ResourceMeta ou201  os5 m117
84  ResourceMeta ou203  os5 m118
85  ResourceMeta ou204  os5 m119
86  ResourceMeta ou208  os5 m120
87  ResourceMeta ou209  os5 m121
88  ResourceMeta ou211  os5 m122
89  ResourceMeta ou212  os5 m123
90  ResourceMeta ou213  os5 m124
91  ResourceMeta ou215  os5 m125
92  ResourceMeta ou216  os5 m126
93  ResourceMeta ou218  os5 m127
94  ResourceMeta ou219  os5 m128
95  ResourceMeta ou221  os5 m129
96  ResourceMeta ou222  os5 m130
97  ResourceMeta ou223  os5 m131
98  ResourceMeta ou224  os5 m132
99  ResourceMeta ou225  os5 m133
100 ResourceMeta ou226  os5 m134
101 ResourceMeta ou227  os5 m135
102 ResourceMeta ou228  os5 m136
103 ResourceMeta ou229  os5 m137
104 ResourceMeta ou230  os5 m138
105 ResourceMeta ou231  os5 m139
106 ResourceMeta ou232  os5 m140
107 ResourceMeta ou233  os5 m141
108 ResourceMeta ou234  os5 m142
109 ResourceMeta ou235  os5 m143
110 ResourceMeta ou236  os5 m144
111 ResourceMeta ou237  os5 m145
112 ResourceMeta ou238  os5 m146
113 ResourceMeta ou239  os5 m147
114 ResourceMeta ou240  os5 m148
115 ResourceMeta ou241  os5 m149
116 ResourceMeta ou242  os5 m150
117 ResourceMeta ou243  os5 m151
118 ResourceMeta ou244  os5 m152
119 ResourceMeta ou245  os5 m153
120 ResourceMeta ou246  os5 m154
121 ResourceMeta ou247  os5 m155
122 ResourceMeta ou248  os5 m156
123 ResourceMeta ou249  os5 m157
124 ResourceMeta ou251  os5 m158
125 ResourceMeta ou252  os5 m159
126 ResourceMeta ou253  os5 m160
127 ResourceMeta ou255  os5 m161
128 ResourceMeta ou256  os5 m162
129 ResourceMeta ou257  os5 m163
130 ResourceMeta ou258  os5 m164
131 ResourceMeta ou259  os5 m165
132 ResourceMeta ou260  os5 m166
133 ResourceMeta ou261  os5 m167
134 ResourceMeta ou262  os5 m168
135 ResourceMeta ou263  os5 m169
136 ResourceMeta ou264  os5 m170
137 ResourceMeta ou265  os5 m171
138 ResourceMeta ou266  os5 m172
139 ResourceMeta ou267  os5 m173
140 ResourceMeta ou268  os5 m174
141 ResourceMeta ou269  os5 m175
142 ResourceMeta ou270  os5 m176
143 ResourceMeta ou271  os5 m177
144 ResourceMeta ou272  os5 m178
145 ResourceMeta ou273  os5 m179
146 ResourceMeta ou274  os5 m180
147 ResourceMeta ou275  os5 m181
148 ResourceMeta ou276  os5 m182
149 ResourceMeta ou277  os5 m183
150 ResourceMeta ou278  os5 m184
151 ResourceMeta ou283  os5 m185
152 ResourceMeta ou284  os5 m186
153 ResourceMeta ou285  os5 m187
154 ResourceMeta ou286  os5 m188
155 ResourceMeta ou290  os5 m189
156 ResourceMeta ou292  os5 m190
157 ResourceMeta ou294  os5 m191
158 ResourceMeta ou295  os5 m192
159 ResourceMeta ou296  os5 m193
160 ResourceMeta ou297  os5 m194
161 ResourceMeta ou298  os5 m195
162 ResourceMeta ou299  os5 m196
163 ResourceMeta ou300  os5 m197
164 ResourceMeta ou302  os5 m198
165 ResourceMeta ou304  os5 m199
166 ResourceMeta ou305  os5 m200
167 ResourceMeta ou306  os5 m201
168 ResourceMeta ou307  os5 m202
169 ResourceMeta ou308  os5 m203
170 ResourceMeta ou309  os5 m204
171 ResourceMeta ou312  os5 m205
172 ResourceMeta ou315  os5 m206
173 ResourceMeta ou316  os5 m207
174 ResourceMeta ou317  os5 m208
175 ResourceMeta ou318  os5 m209
176 ResourceMeta ou319  os5 m210
177 ResourceMeta ou321  os5 m211
178 ResourceMeta ou322  os5 m212
179 ResourceMeta ou323  os5 m213
180 ResourceMeta ou325  os5 m214
taxa
      otu                        label xsi.type otus
1    ou93  Allenopithecus_nigroviridis       NA  os5
2    ou94          Allocebus_trichotis       NA  os5
3    ou95            Alouatta_belzebul       NA  os5
4    ou96              Alouatta_caraya       NA  os5
5    ou97           Alouatta_coibensis       NA  os5
6    ou98               Alouatta_fusca       NA  os5
7    ou99            Alouatta_palliata       NA  os5
8   ou100               Alouatta_pigra       NA  os5
9   ou101                Alouatta_sara       NA  os5
10  ou102           Alouatta_seniculus       NA  os5
11  ou103                 Aotus_azarai       NA  os5
12  ou104              Aotus_brumbacki       NA  os5
13  ou105           Aotus_hershkovitzi       NA  os5
14  ou106              Aotus_infulatus       NA  os5
15  ou107              Aotus_lemurinus       NA  os5
16  ou108                Aotus_miconax       NA  os5
17  ou109              Aotus_nancymaae       NA  os5
18  ou110              Aotus_nigriceps       NA  os5
19  ou111            Aotus_trivirgatus       NA  os5
20  ou112             Aotus_vociferans       NA  os5
21  ou113            Arctocebus_aureus       NA  os5
22  ou114      Arctocebus_calabarensis       NA  os5
23  ou115             Ateles_belzebuth       NA  os5
24  ou116                Ateles_chamek       NA  os5
25  ou117             Ateles_fusciceps       NA  os5
26  ou118             Ateles_geoffroyi       NA  os5
27  ou119            Ateles_marginatus       NA  os5
28  ou120              Ateles_paniscus       NA  os5
29  ou121                Avahi_laniger       NA  os5
30  ou122      Brachyteles_arachnoides       NA  os5
31  ou123               Cacajao_calvus       NA  os5
32  ou124       Cacajao_melanocephalus       NA  os5
33  ou125          Callicebus_brunneus       NA  os5
34  ou126         Callicebus_caligatus       NA  os5
35  ou127       Callicebus_cinerascens       NA  os5
36  ou128           Callicebus_cupreus       NA  os5
37  ou129      Callicebus_donacophilus       NA  os5
38  ou130            Callicebus_dubius       NA  os5
39  ou131        Callicebus_hoffmannsi       NA  os5
40  ou132          Callicebus_modestus       NA  os5
41  ou133            Callicebus_moloch       NA  os5
42  ou134          Callicebus_oenanthe       NA  os5
43  ou135           Callicebus_olallae       NA  os5
44  ou136        Callicebus_personatus       NA  os5
45  ou137         Callicebus_torquatus       NA  os5
46  ou138            Callimico_goeldii       NA  os5
47  ou139         Callithrix_argentata       NA  os5
48  ou140            Callithrix_aurita       NA  os5
49  ou141         Callithrix_flaviceps       NA  os5
50  ou142         Callithrix_geoffroyi       NA  os5
51  ou143      Callithrix_humeralifera       NA  os5
52  ou144           Callithrix_jacchus       NA  os5
53  ou145            Callithrix_kuhlii       NA  os5
54  ou146       Callithrix_penicillata       NA  os5
55  ou147           Callithrix_pygmaea       NA  os5
56  ou148              Cebus_albifrons       NA  os5
57  ou149                 Cebus_apella       NA  os5
58  ou150              Cebus_capucinus       NA  os5
59  ou151              Cebus_olivaceus       NA  os5
60  ou152            Cercocebus_agilis       NA  os5
61  ou153         Cercocebus_galeritus       NA  os5
62  ou154         Cercocebus_torquatus       NA  os5
63  ou155       Cercopithecus_ascanius       NA  os5
64  ou156      Cercopithecus_campbelli       NA  os5
65  ou157         Cercopithecus_cephus       NA  os5
66  ou158          Cercopithecus_diana       NA  os5
67  ou159          Cercopithecus_dryas       NA  os5
68  ou160  Cercopithecus_erythrogaster       NA  os5
69  ou161     Cercopithecus_erythrotis       NA  os5
70  ou162        Cercopithecus_hamlyni       NA  os5
71  ou163        Cercopithecus_lhoesti       NA  os5
72  ou164          Cercopithecus_mitis       NA  os5
73  ou165           Cercopithecus_mona       NA  os5
74  ou166      Cercopithecus_neglectus       NA  os5
75  ou167      Cercopithecus_nictitans       NA  os5
76  ou168     Cercopithecus_petaurista       NA  os5
77  ou169       Cercopithecus_pogonias       NA  os5
78  ou170        Cercopithecus_preussi       NA  os5
79  ou171       Cercopithecus_sclateri       NA  os5
80  ou172        Cercopithecus_solatus       NA  os5
81  ou173          Cercopithecus_wolfi       NA  os5
82  ou174           Cheirogaleus_major       NA  os5
83  ou175          Cheirogaleus_medius       NA  os5
84  ou176         Chiropotes_albinasus       NA  os5
85  ou177           Chiropotes_satanas       NA  os5
86  ou178         Chlorocebus_aethiops       NA  os5
87  ou179           Colobus_angolensis       NA  os5
88  ou180              Colobus_guereza       NA  os5
89  ou181            Colobus_polykomos       NA  os5
90  ou182              Colobus_satanas       NA  os5
91  ou183 Daubentonia_madagascariensis       NA  os5
92  ou184           Erythrocebus_patas       NA  os5
93  ou185            Eulemur_coronatus       NA  os5
94  ou186               Eulemur_fulvus       NA  os5
95  ou187               Eulemur_macaco       NA  os5
96  ou188               Eulemur_mongoz       NA  os5
97  ou189          Eulemur_rubriventer       NA  os5
98  ou190         Euoticus_elegantulus       NA  os5
99  ou191            Euoticus_pallidus       NA  os5
100 ou192                Galago_alleni       NA  os5
101 ou193              Galago_gallarum       NA  os5
102 ou194             Galago_matschiei       NA  os5
103 ou195                Galago_moholi       NA  os5
104 ou196          Galago_senegalensis       NA  os5
105 ou197          Galagoides_demidoff       NA  os5
106 ou198      Galagoides_zanzibaricus       NA  os5
107 ou199              Gorilla_gorilla       NA  os5
108 ou200             Hapalemur_aureus       NA  os5
109 ou201            Hapalemur_griseus       NA  os5
110 ou202              Hapalemur_simus       NA  os5
111 ou203                 Homo_sapiens       NA  os5
112 ou204             Hylobates_agilis       NA  os5
113 ou205           Hylobates_concolor       NA  os5
114 ou206         Hylobates_gabriellae       NA  os5
115 ou207            Hylobates_hoolock       NA  os5
116 ou208            Hylobates_klossii       NA  os5
117 ou209                Hylobates_lar       NA  os5
118 ou210         Hylobates_leucogenys       NA  os5
119 ou211             Hylobates_moloch       NA  os5
120 ou212           Hylobates_muelleri       NA  os5
121 ou213           Hylobates_pileatus       NA  os5
122 ou214        Hylobates_syndactylus       NA  os5
123 ou215                  Indri_indri       NA  os5
124 ou216         Lagothrix_flavicauda       NA  os5
125 ou217         Lagothrix_lagotricha       NA  os5
126 ou218                  Lemur_catta       NA  os5
127 ou219      Leontopithecus_caissara       NA  os5
128 ou220    Leontopithecus_chrysomela       NA  os5
129 ou221   Leontopithecus_chrysopygus       NA  os5
130 ou222       Leontopithecus_rosalia       NA  os5
131 ou223           Lepilemur_dorsalis       NA  os5
132 ou224           Lepilemur_edwardsi       NA  os5
133 ou225           Lepilemur_leucopus       NA  os5
134 ou226           Lepilemur_microdon       NA  os5
135 ou227         Lepilemur_mustelinus       NA  os5
136 ou228       Lepilemur_ruficaudatus       NA  os5
137 ou229    Lepilemur_septentrionalis       NA  os5
138 ou230          Lophocebus_albigena       NA  os5
139 ou231            Loris_tardigradus       NA  os5
140 ou232             Macaca_arctoides       NA  os5
141 ou233            Macaca_assamensis       NA  os5
142 ou234              Macaca_cyclopis       NA  os5
143 ou235          Macaca_fascicularis       NA  os5
144 ou236               Macaca_fuscata       NA  os5
145 ou237                 Macaca_maura       NA  os5
146 ou238               Macaca_mulatta       NA  os5
147 ou239            Macaca_nemestrina       NA  os5
148 ou240                 Macaca_nigra       NA  os5
149 ou241              Macaca_ochreata       NA  os5
150 ou242               Macaca_radiata       NA  os5
151 ou243               Macaca_silenus       NA  os5
152 ou244                Macaca_sinica       NA  os5
153 ou245              Macaca_sylvanus       NA  os5
154 ou246             Macaca_thibetana       NA  os5
155 ou247              Macaca_tonkeana       NA  os5
156 ou248       Mandrillus_leucophaeus       NA  os5
157 ou249            Mandrillus_sphinx       NA  os5
158 ou250         Microcebus_coquereli       NA  os5
159 ou251           Microcebus_murinus       NA  os5
160 ou252             Microcebus_rufus       NA  os5
161 ou253         Miopithecus_talapoin       NA  os5
162 ou254             Nasalis_concolor       NA  os5
163 ou255             Nasalis_larvatus       NA  os5
164 ou256           Nycticebus_coucang       NA  os5
165 ou257          Nycticebus_pygmaeus       NA  os5
166 ou258      Otolemur_crassicaudatus       NA  os5
167 ou259           Otolemur_garnettii       NA  os5
168 ou260                 Pan_paniscus       NA  os5
169 ou261              Pan_troglodytes       NA  os5
170 ou262              Papio_hamadryas       NA  os5
171 ou263           Perodicticus_potto       NA  os5
172 ou264              Phaner_furcifer       NA  os5
173 ou265       Pithecia_aequatorialis       NA  os5
174 ou266            Pithecia_albicans       NA  os5
175 ou267            Pithecia_irrorata       NA  os5
176 ou268            Pithecia_monachus       NA  os5
177 ou269            Pithecia_pithecia       NA  os5
178 ou270               Pongo_pygmaeus       NA  os5
179 ou271             Presbytis_comata       NA  os5
180 ou272          Presbytis_femoralis       NA  os5
181 ou273           Presbytis_frontata       NA  os5
182 ou274              Presbytis_hosei       NA  os5
183 ou275         Presbytis_melalophos       NA  os5
184 ou276         Presbytis_potenziani       NA  os5
185 ou277          Presbytis_rubicunda       NA  os5
186 ou278            Presbytis_thomasi       NA  os5
187 ou279            Procolobus_badius       NA  os5
188 ou280         Procolobus_pennantii       NA  os5
189 ou281           Procolobus_preussi       NA  os5
190 ou282      Procolobus_rufomitratus       NA  os5
191 ou283             Procolobus_verus       NA  os5
192 ou284          Propithecus_diadema       NA  os5
193 ou285      Propithecus_tattersalli       NA  os5
194 ou286        Propithecus_verreauxi       NA  os5
195 ou287          Pygathrix_avunculus       NA  os5
196 ou288              Pygathrix_bieti       NA  os5
197 ou289           Pygathrix_brelichi       NA  os5
198 ou290            Pygathrix_nemaeus       NA  os5
199 ou291          Pygathrix_roxellana       NA  os5
200 ou292             Saguinus_bicolor       NA  os5
201 ou293         Saguinus_fuscicollis       NA  os5
202 ou294           Saguinus_geoffroyi       NA  os5
203 ou295           Saguinus_imperator       NA  os5
204 ou296             Saguinus_inustus       NA  os5
205 ou297            Saguinus_labiatus       NA  os5
206 ou298            Saguinus_leucopus       NA  os5
207 ou299               Saguinus_midas       NA  os5
208 ou300              Saguinus_mystax       NA  os5
209 ou301         Saguinus_nigricollis       NA  os5
210 ou302             Saguinus_oedipus       NA  os5
211 ou303         Saguinus_tripartitus       NA  os5
212 ou304          Saimiri_boliviensis       NA  os5
213 ou305            Saimiri_oerstedii       NA  os5
214 ou306             Saimiri_sciureus       NA  os5
215 ou307                Saimiri_ustus       NA  os5
216 ou308           Saimiri_vanzolinii       NA  os5
217 ou309       Semnopithecus_entellus       NA  os5
218 ou310             Tarsius_bancanus       NA  os5
219 ou311               Tarsius_dianae       NA  os5
220 ou312              Tarsius_pumilus       NA  os5
221 ou313             Tarsius_spectrum       NA  os5
222 ou314             Tarsius_syrichta       NA  os5
223 ou315         Theropithecus_gelada       NA  os5
224 ou316       Trachypithecus_auratus       NA  os5
225 ou317     Trachypithecus_cristatus       NA  os5
226 ou318     Trachypithecus_francoisi       NA  os5
227 ou319          Trachypithecus_geei       NA  os5
228 ou320        Trachypithecus_johnii       NA  os5
229 ou321      Trachypithecus_obscurus       NA  os5
230 ou322       Trachypithecus_phayrei       NA  os5
231 ou323      Trachypithecus_pileatus       NA  os5
232 ou324       Trachypithecus_vetulus       NA  os5
233 ou325            Varecia_variegata       NA  os5
head(char)
                         taxa        x
1 Allenopithecus_nigroviridis 8.465900
2         Allocebus_trichotis 4.368181
3           Alouatta_belzebul 8.729074
4             Alouatta_caraya 8.628735
5          Alouatta_coibensis 8.764053
6              Alouatta_fusca 8.554489

Now that we have nice data.frame objects for all our data, it’s easy to join them into the desired table with a few obvious dplyr commands:

taxa %>% 
  left_join(char, by = c("label" = "taxa")) %>% 
  left_join(otu_meta, by = "otu") %>%
  select(otu, label, x, href)
      otu                        label         x
1    ou93  Allenopithecus_nigroviridis  8.465900
2    ou94          Allocebus_trichotis  4.368181
3    ou95            Alouatta_belzebul  8.729074
4    ou96              Alouatta_caraya  8.628735
5    ou97           Alouatta_coibensis  8.764053
6    ou98               Alouatta_fusca  8.554489
7    ou99            Alouatta_palliata  8.791790
8   ou100               Alouatta_pigra  8.881836
9   ou101                Alouatta_sara  8.796339
10  ou102           Alouatta_seniculus  8.767173
11  ou103                 Aotus_azarai  7.127694
12  ou104              Aotus_brumbacki  6.401917
13  ou105           Aotus_hershkovitzi  6.684612
14  ou106              Aotus_infulatus  7.122867
15  ou107              Aotus_lemurinus  6.781058
16  ou108                Aotus_miconax  6.684612
17  ou109              Aotus_nancymaae  6.678342
18  ou110              Aotus_nigriceps  6.966024
19  ou111            Aotus_trivirgatus  6.815640
20  ou112             Aotus_vociferans  6.771936
21  ou113            Arctocebus_aureus  5.459586
22  ou114      Arctocebus_calabarensis  5.552960
23  ou115             Ateles_belzebuth  8.812843
24  ou116                Ateles_chamek  8.872067
25  ou117             Ateles_fusciceps  9.112728
26  ou118             Ateles_geoffroyi  8.937218
27  ou119            Ateles_marginatus  8.738735
28  ou120              Ateles_paniscus  9.072227
29  ou121                Avahi_laniger  6.927558
30  ou122      Brachyteles_arachnoides  9.268609
31  ou123               Cacajao_calvus  8.137396
32  ou124       Cacajao_melanocephalus  8.051978
33  ou125          Callicebus_brunneus  6.747587
34  ou126         Callicebus_caligatus  6.899723
35  ou127       Callicebus_cinerascens  6.899723
36  ou128           Callicebus_cupreus  7.021084
37  ou129      Callicebus_donacophilus  6.801283
38  ou130            Callicebus_dubius  6.899723
39  ou131        Callicebus_hoffmannsi  6.975414
40  ou132          Callicebus_modestus  6.899723
41  ou133            Callicebus_moloch  6.872128
42  ou134          Callicebus_oenanthe  6.899723
43  ou135           Callicebus_olallae  6.899723
44  ou136        Callicebus_personatus  7.237059
45  ou137         Callicebus_torquatus  7.106606
46  ou138            Callimico_goeldii  6.324359
47  ou139         Callithrix_argentata  5.910797
48  ou140            Callithrix_aurita  5.961005
49  ou141         Callithrix_flaviceps  5.926926
50  ou142         Callithrix_geoffroyi  5.834811
51  ou143      Callithrix_humeralifera  5.926926
52  ou144           Callithrix_jacchus  5.673323
53  ou145            Callithrix_kuhlii  5.926926
54  ou146       Callithrix_penicillata  5.828946
55  ou147           Callithrix_pygmaea  4.828314
56  ou148              Cebus_albifrons  7.832014
57  ou149                 Cebus_apella  7.922986
58  ou150              Cebus_capucinus  8.009695
59  ou151              Cebus_olivaceus  7.937375
60  ou152            Cercocebus_agilis  8.870663
61  ou153         Cercocebus_galeritus  8.865029
62  ou154         Cercocebus_torquatus  8.894259
63  ou155       Cercopithecus_ascanius  8.171882
64  ou156      Cercopithecus_campbelli  8.199739
65  ou157         Cercopithecus_cephus  8.143227
66  ou158          Cercopithecus_diana  8.382518
67  ou159          Cercopithecus_dryas  7.930206
68  ou160  Cercopithecus_erythrogaster  8.143227
69  ou161     Cercopithecus_erythrotis  8.086410
70  ou162        Cercopithecus_hamlyni  8.438150
71  ou163        Cercopithecus_lhoesti  8.579229
72  ou164          Cercopithecus_mitis  8.525161
73  ou165           Cercopithecus_mona  8.289037
74  ou166      Cercopithecus_neglectus  8.579229
75  ou167      Cercopithecus_nictitans  8.567886
76  ou168     Cercopithecus_petaurista  8.083329
77  ou169       Cercopithecus_pogonias  8.183118
78  ou170        Cercopithecus_preussi  8.544808
79  ou171       Cercopithecus_sclateri  8.029433
80  ou172        Cercopithecus_solatus  8.567886
81  ou173          Cercopithecus_wolfi  8.089482
82  ou174           Cheirogaleus_major  6.104793
83  ou175          Cheirogaleus_medius  5.283204
84  ou176         Chiropotes_albinasus  7.937375
85  ou177           Chiropotes_satanas  7.996317
86  ou178         Chlorocebus_aethiops  8.301522
87  ou179           Colobus_angolensis  9.103868
88  ou180              Colobus_guereza  9.210340
89  ou181            Colobus_polykomos  9.060680
90  ou182              Colobus_satanas  9.121509
91  ou183 Daubentonia_madagascariensis  7.919356
92  ou184           Erythrocebus_patas  8.988446
93  ou185            Eulemur_coronatus  7.438384
94  ou186               Eulemur_fulvus  7.779049
95  ou187               Eulemur_macaco  7.816014
96  ou188               Eulemur_mongoz  7.478735
97  ou189          Eulemur_rubriventer  7.620705
98  ou190         Euoticus_elegantulus  5.690359
99  ou191            Euoticus_pallidus  5.627621
100 ou192                Galago_alleni  5.521461
101 ou193              Galago_gallarum  5.365976
102 ou194             Galago_matschiei  5.267858
103 ou195                Galago_moholi  5.375278
104 ou196          Galago_senegalensis  5.594711
105 ou197          Galagoides_demidoff  4.206184
106 ou198      Galagoides_zanzibaricus  4.997212
107 ou199              Gorilla_gorilla 11.643954
108 ou200             Hapalemur_aureus  7.358831
109 ou201            Hapalemur_griseus  6.862758
110 ou202              Hapalemur_simus  7.620705
111 ou203                 Homo_sapiens 10.980195
112 ou204             Hylobates_agilis  8.675905
113 ou205           Hylobates_concolor  8.768730
114 ou206         Hylobates_gabriellae  9.047821
115 ou207            Hylobates_hoolock  8.809863
116 ou208            Hylobates_klossii  8.674197
117 ou209                Hylobates_lar  8.635865
118 ou210         Hylobates_leucogenys  8.898366
119 ou211             Hylobates_moloch  8.677610
120 ou212           Hylobates_muelleri  8.687779
121 ou213           Hylobates_pileatus  8.630522
122 ou214        Hylobates_syndactylus  9.296518
123 ou215                  Indri_indri  9.065315
124 ou216         Lagothrix_flavicauda  9.020390
125 ou217         Lagothrix_lagotricha  8.743532
126 ou218                  Lemur_catta  7.878534
127 ou219      Leontopithecus_caissara  6.405228
128 ou220    Leontopithecus_chrysomela  6.352629
129 ou221   Leontopithecus_chrysopygus  6.486161
130 ou222       Leontopithecus_rosalia  6.385194
131 ou223           Lepilemur_dorsalis  6.232448
132 ou224           Lepilemur_edwardsi  6.711740
133 ou225           Lepilemur_leucopus  6.396930
134 ou226           Lepilemur_microdon  6.863803
135 ou227         Lepilemur_mustelinus  6.508769
136 ou228       Lepilemur_ruficaudatus  6.637258
137 ou229    Lepilemur_septentrionalis  6.638568
138 ou230          Lophocebus_albigena  8.903815
139 ou231            Loris_tardigradus  5.517453
140 ou232             Macaca_arctoides  9.148465
141 ou233            Macaca_assamensis  9.054855
142 ou234              Macaca_cyclopis  8.658693
143 ou235          Macaca_fascicularis  8.431635
144 ou236               Macaca_fuscata  9.220291
145 ou237                 Macaca_maura  8.894259
146 ou238               Macaca_mulatta  8.771835
147 ou239            Macaca_nemestrina  8.970813
148 ou240                 Macaca_nigra  8.906529
149 ou241              Macaca_ochreata  7.919356
150 ou242               Macaca_radiata  8.517193
151 ou243               Macaca_silenus  8.699515
152 ou244                Macaca_sinica  8.446771
153 ou245              Macaca_sylvanus  9.350102
154 ou246             Macaca_thibetana  9.268609
155 ou247              Macaca_tonkeana  9.220291
156 ou248       Mandrillus_leucophaeus  9.560997
157 ou249            Mandrillus_sphinx  9.729134
158 ou250         Microcebus_coquereli  5.793014
159 ou251           Microcebus_murinus  4.198705
160 ou252             Microcebus_rufus  3.881564
161 ou253         Miopithecus_talapoin  7.130899
162 ou254             Nasalis_concolor  8.979354
163 ou255             Nasalis_larvatus  9.417355
164 ou256           Nycticebus_coucang  6.878326
165 ou257          Nycticebus_pygmaeus  5.840642
166 ou258      Otolemur_crassicaudatus  7.130899
167 ou259           Otolemur_garnettii  6.701960
168 ou260                 Pan_paniscus 10.468801
169 ou261              Pan_troglodytes 10.716638
170 ou262              Papio_hamadryas  9.735069
171 ou263           Perodicticus_potto  6.984716
172 ou264              Phaner_furcifer  6.016157
173 ou265       Pithecia_aequatorialis  7.774856
174 ou266            Pithecia_albicans  7.937375
175 ou267            Pithecia_irrorata  7.749322
176 ou268            Pithecia_monachus  7.654443
177 ou269            Pithecia_pithecia  7.420579
178 ou270               Pongo_pygmaeus 10.860920
179 ou271             Presbytis_comata  9.039552
180 ou272          Presbytis_femoralis  8.797851
181 ou273           Presbytis_frontata  8.853665
182 ou274              Presbytis_hosei  8.725832
183 ou275         Presbytis_melalophos  8.748305
184 ou276         Presbytis_potenziani  8.774931
185 ou277          Presbytis_rubicunda  8.773385
186 ou278            Presbytis_thomasi  8.765615
187 ou279            Procolobus_badius  8.808369
188 ou280         Procolobus_pennantii  9.122601
189 ou281           Procolobus_preussi  9.094930
190 ou282      Procolobus_rufomitratus  8.995909
191 ou283             Procolobus_verus  8.289037
192 ou284          Propithecus_diadema  8.794825
193 ou285      Propithecus_tattersalli  8.171882
194 ou286        Propithecus_verreauxi  8.202482
195 ou287          Pygathrix_avunculus  9.164296
196 ou288              Pygathrix_bieti  9.118225
197 ou289           Pygathrix_brelichi  9.305651
198 ou290            Pygathrix_nemaeus  9.417355
199 ou291          Pygathrix_roxellana  9.510445
200 ou292             Saguinus_bicolor  6.142037
201 ou293         Saguinus_fuscicollis  5.976351
202 ou294           Saguinus_geoffroyi  6.200509
203 ou295           Saguinus_imperator  6.016157
204 ou296             Saguinus_inustus  6.688355
205 ou297            Saguinus_labiatus  6.234411
206 ou298            Saguinus_leucopus  6.124683
207 ou299               Saguinus_midas  6.293419
208 ou300              Saguinus_mystax  6.326149
209 ou301         Saguinus_nigricollis  6.109248
210 ou302             Saguinus_oedipus  6.139885
211 ou303         Saguinus_tripartitus  5.953243
212 ou304          Saimiri_boliviensis  6.690842
213 ou305            Saimiri_oerstedii  6.570883
214 ou306             Saimiri_sciureus  6.620073
215 ou307                Saimiri_ustus  6.791221
216 ou308           Saimiri_vanzolinii  6.664409
217 ou309       Semnopithecus_entellus  9.441452
218 ou310             Tarsius_bancanus  4.736198
219 ou311               Tarsius_dianae  4.709530
220 ou312              Tarsius_pumilus  4.808111
221 ou313             Tarsius_spectrum  5.111988
222 ou314             Tarsius_syrichta  4.753590
223 ou315         Theropithecus_gelada  9.680344
224 ou316       Trachypithecus_auratus  9.181941
225 ou317     Trachypithecus_cristatus  8.872067
226 ou318     Trachypithecus_francoisi  9.008224
227 ou319          Trachypithecus_geei  9.031214
228 ou320        Trachypithecus_johnii  9.268609
229 ou321      Trachypithecus_obscurus  8.870663
230 ou322       Trachypithecus_phayrei  8.948976
231 ou323      Trachypithecus_pileatus  9.323669
232 ou324       Trachypithecus_vetulus  8.969542
233 ou325            Varecia_variegata  8.261010
                                                                                    href
1   http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572992
2   http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572857
3   http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572935
4   http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572936
5                                                                                   <NA>
6                                                                                   <NA>
7   http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572939
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9   http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572941
10  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572942
11                                                                                  <NA>
12  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572944
13                                                                                  <NA>
14                                                                                  <NA>
15  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572949
16  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572947
17  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572945
18  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572946
19  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572951
20  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572952
21  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572887
22  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572888
23  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572954
24  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572955
25  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572957
26  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572958
27  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572956
28  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572953
29  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572881
30  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572959
31  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572983
32  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572984
33                                                                                  <NA>
34                                                                                  <NA>
35                                                                                  <NA>
36                                                                                  <NA>
37                                                                                  <NA>
38                                                                                  <NA>
39                                                                                  <NA>
40                                                                                  <NA>
41                                                                                  <NA>
42                                                                                  <NA>
43                                                                                  <NA>
44  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572962
45                                                                                  <NA>
46  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572909
47                                                                                  <NA>
48  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572911
49  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572912
50  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572913
51                                                                                  <NA>
52  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572915
53  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572916
54  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572918
55                                                                                  <NA>
56  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572975
57                                                                                  <NA>
58  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572977
59  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572978
60  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572993
61  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572994
62  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572995
63  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572996
64  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572997
65  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572998
66  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572999
67  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573000
68  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573001
69  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573002
70  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573003
71                                                                                  <NA>
72  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573005
73  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573006
74  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573007
75  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573008
76  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573009
77  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573010
78                                                                                  <NA>
79  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573014
80                                                                                  <NA>
81  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573011
82  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572858
83  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572859
84  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572985
85  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572986
86  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=552515
87  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573035
88  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573036
89  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573037
90  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573038
91  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572886
92  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573015
93  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572865
94  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572864
95  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572866
96  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572867
97  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572868
98  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572893
99  http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572894
100                                                                                 <NA>
101 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572896
102 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572897
103 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572898
104 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572899
105 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572900
106                                                                                 <NA>
107 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573080
108 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572869
109 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572870
110                                                                                 <NA>
111 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180092
112 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573069
113                                                                                 <NA>
114                                                                                 <NA>
115                                                                                 <NA>
116 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573073
117 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573074
118                                                                                 <NA>
119 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573076
120 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573077
121 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573078
122                                                                                 <NA>
123 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572882
124 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572961
125                                                                                 <NA>
126 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572872
127 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572921
128                                                                                 <NA>
129 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572920
130 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572922
131 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572874
132 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572875
133 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572876
134 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572877
135 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572878
136 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572879
137 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572880
138 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573016
139 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572889
140 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573017
141 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573018
142 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573019
143 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180098
144 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=555659
145 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573020
146 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180099
147 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573021
148 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573022
149 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573023
150 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573024
151 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573025
152 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573026
153 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573027
154 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573028
155 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573029
156 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573030
157 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573031
158                                                                                 <NA>
159 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572861
160 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572862
161 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573032
162                                                                                 <NA>
163 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573040
164 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572890
165 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572891
166 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572902
167 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572903
168 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573081
169 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573082
170 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573033
171 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572892
172 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572863
173 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572987
174 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572988
175 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572989
176 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572990
177 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572991
178 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573083
179 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573041
180 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573042
181 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573043
182 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573044
183 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573045
184 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573046
185 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573047
186 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573048
187                                                                                 <NA>
188                                                                                 <NA>
189                                                                                 <NA>
190                                                                                 <NA>
191 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573053
192 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572883
193 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572884
194 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572885
195                                                                                 <NA>
196                                                                                 <NA>
197                                                                                 <NA>
198 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573057
199                                                                                 <NA>
200 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572923
201                                                                                 <NA>
202 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572925
203 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572926
204 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572927
205 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572928
206 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572929
207 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572930
208 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572931
209                                                                                 <NA>
210 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572933
211                                                                                 <NA>
212 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572979
213 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572980
214 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180095
215 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572981
216 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572982
217 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573059
218                                                                                 <NA>
219                                                                                 <NA>
220 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572906
221                                                                                 <NA>
222                                                                                 <NA>
223 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573034
224 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573060
225 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573061
226 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573062
227 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573063
228                                                                                 <NA>
229 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573065
230 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573066
231 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573067
232                                                                                 <NA>
233 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572873

Because these are all from the same otus block anyway, we haven’t selected that column, but were it of interest it is also available in the taxa table.