--- title: "Handling Metadata in RNeXML" author: - Carl Boettiger - Scott Chamberlain - Rutger Vos - Hilmar Lapp output: html_vignette --- ## 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: ```r library('RNeXML') data(bird.orders) ``` Create an `nexml` object for the phylogeny `bird.orders` and add appropriate metadata: ```r 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: ```r 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. ```r 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: ```r 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: ```r 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. ```r 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: ```r 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. ```r 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: ```r 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, ``) with the command ```r meta <- get_metadata(birds) ``` This returns a data.frame of available metadata. We can see the kinds of metadata recorded from the names: ```r meta ``` ``` property datatype 1 dc:title xsd:string 2 dc:creator xsd:string 3 dc:description xsd:string 4 cc:license 5 dcterms:bibliographicCitation xsd:string 6 dc:creator xsd:string 7 dcterms:references 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 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 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 phylogenetics and evolutionary analyses in R."\n_Bioinformatics_, *35*, 526-528. xsi.type href Meta meta 1 LiteralMeta m544 2 LiteralMeta m545 3 LiteralMeta m546 4 ResourceMeta http://creativecommons.org/publicdomain/zero/1.0/ m547 5 LiteralMeta m548 6 LiteralMeta m549 7 ResourceMeta m560 8 LiteralMeta m561 9 LiteralMeta m560 10 LiteralMeta m560 11 LiteralMeta m560 12 LiteralMeta m560 13 LiteralMeta m560 14 LiteralMeta m560 15 LiteralMeta m560 16 LiteralMeta m560 17 LiteralMeta m560 18 LiteralMeta m560 ``` We can also access a table of taxonomic metadata: ```r get_taxa(birds) ``` ``` otu label xsi.type otus 1 ou362 Struthioniformes NA os8 2 ou363 Tinamiformes NA os8 3 ou364 Craciformes NA os8 4 ou365 Galliformes NA os8 5 ou366 Anseriformes NA os8 6 ou367 Turniciformes NA os8 7 ou368 Piciformes NA os8 8 ou369 Galbuliformes NA os8 9 ou370 Bucerotiformes NA os8 10 ou371 Upupiformes NA os8 11 ou372 Trogoniformes NA os8 12 ou373 Coraciiformes NA os8 13 ou374 Coliiformes NA os8 14 ou375 Cuculiformes NA os8 15 ou376 Psittaciformes NA os8 16 ou377 Apodiformes NA os8 17 ou378 Trochiliformes NA os8 18 ou379 Musophagiformes NA os8 19 ou380 Strigiformes NA os8 20 ou381 Columbiformes NA os8 21 ou382 Gruiformes NA os8 22 ou383 Ciconiiformes NA os8 23 ou384 Passeriformes NA os8 ``` 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: ```r otu_meta <- get_metadata(birds, level="otus/otu") otu_meta ``` ``` # A tibble: 0 x 3 # … with 3 variables: otu , otus , Meta ``` ## 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. ```r 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: ```r 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. ```r 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: ```r otu_meta ``` ``` property href xsi.type otu otus 1 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572992 ResourceMeta ou385 os9 2 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572857 ResourceMeta ou386 os9 3 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572935 ResourceMeta ou387 os9 4 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572936 ResourceMeta ou388 os9 5 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945168 ResourceMeta ou389 os9 6 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945164 ResourceMeta ou390 os9 7 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572939 ResourceMeta ou391 os9 8 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572940 ResourceMeta ou392 os9 9 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572941 ResourceMeta ou393 os9 10 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572942 ResourceMeta ou394 os9 11 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944172 ResourceMeta ou395 os9 12 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572944 ResourceMeta ou396 os9 13 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572949 ResourceMeta ou397 os9 14 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945149 ResourceMeta ou398 os9 15 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572949 ResourceMeta ou399 os9 16 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572947 ResourceMeta ou400 os9 17 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572945 ResourceMeta ou401 os9 18 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572946 ResourceMeta ou402 os9 19 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572951 ResourceMeta ou403 os9 20 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572952 ResourceMeta ou404 os9 21 tc:toTaxon 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http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572881 ResourceMeta ou413 os9 30 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572959 ResourceMeta ou414 os9 31 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572983 ResourceMeta ou415 os9 32 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572984 ResourceMeta ou416 os9 33 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025131 ResourceMeta ou417 os9 34 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025134 ResourceMeta ou418 os9 35 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025122 ResourceMeta ou419 os9 36 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025127 ResourceMeta ou420 os9 37 tc:toTaxon 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http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572896 ResourceMeta ou485 os9 102 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572897 ResourceMeta ou486 os9 103 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572898 ResourceMeta ou487 os9 104 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572899 ResourceMeta ou488 os9 105 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572900 ResourceMeta ou489 os9 106 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=1025177 ResourceMeta ou490 os9 107 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573080 ResourceMeta ou491 os9 108 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572869 ResourceMeta ou492 os9 109 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572870 ResourceMeta ou493 os9 110 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944072 ResourceMeta ou494 os9 111 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180092 ResourceMeta ou495 os9 112 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573069 ResourceMeta ou496 os9 113 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944286 ResourceMeta ou497 os9 114 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944292 ResourceMeta ou498 os9 115 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945338 ResourceMeta ou499 os9 116 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573073 ResourceMeta ou500 os9 117 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573074 ResourceMeta ou501 os9 118 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944290 ResourceMeta ou502 os9 119 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573076 ResourceMeta ou503 os9 120 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573077 ResourceMeta ou504 os9 121 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573078 ResourceMeta ou505 os9 122 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944293 ResourceMeta ou506 os9 123 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572882 ResourceMeta ou507 os9 124 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572961 ResourceMeta ou508 os9 125 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944187 ResourceMeta ou509 os9 126 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572872 ResourceMeta ou510 os9 127 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572921 ResourceMeta ou511 os9 128 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572920 ResourceMeta ou513 os9 129 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572922 ResourceMeta ou514 os9 130 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572874 ResourceMeta ou515 os9 131 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572875 ResourceMeta ou516 os9 132 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572876 ResourceMeta ou517 os9 133 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572877 ResourceMeta ou518 os9 134 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572878 ResourceMeta ou519 os9 135 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572879 ResourceMeta ou520 os9 136 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572880 ResourceMeta ou521 os9 137 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573016 ResourceMeta ou522 os9 138 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572889 ResourceMeta ou523 os9 139 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573017 ResourceMeta ou524 os9 140 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573018 ResourceMeta ou525 os9 141 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573019 ResourceMeta ou526 os9 142 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180098 ResourceMeta ou527 os9 143 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=555659 ResourceMeta ou528 os9 144 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573020 ResourceMeta ou529 os9 145 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180099 ResourceMeta ou530 os9 146 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573021 ResourceMeta ou531 os9 147 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573022 ResourceMeta ou532 os9 148 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573023 ResourceMeta ou533 os9 149 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573024 ResourceMeta ou534 os9 150 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573025 ResourceMeta ou535 os9 151 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573026 ResourceMeta ou536 os9 152 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573027 ResourceMeta ou537 os9 153 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573028 ResourceMeta ou538 os9 154 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573029 ResourceMeta ou539 os9 155 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573030 ResourceMeta ou540 os9 156 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573031 ResourceMeta ou541 os9 157 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944041 ResourceMeta ou542 os9 158 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572861 ResourceMeta ou543 os9 159 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572862 ResourceMeta ou544 os9 160 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573032 ResourceMeta ou545 os9 161 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944263 ResourceMeta ou546 os9 162 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=573040 ResourceMeta ou547 os9 163 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572890 ResourceMeta ou548 os9 164 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572891 ResourceMeta ou549 os9 165 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572902 ResourceMeta ou550 os9 166 tc:toTaxon http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572903 ResourceMeta ou551 os9 Meta 1 m563 2 m564 3 m565 4 m566 5 m567 6 m568 7 m569 8 m570 9 m571 10 m572 11 m573 12 m574 13 m575 14 m576 15 m577 16 m578 17 m579 18 m580 19 m581 20 m582 21 m583 22 m584 23 m585 24 m586 25 m587 26 m588 27 m589 28 m590 29 m591 30 m592 31 m593 32 m594 33 m595 34 m596 35 m597 36 m598 37 m599 38 m600 39 m601 40 m602 41 m603 42 m604 43 m605 44 m606 45 m607 46 m608 47 m609 48 m610 49 m611 50 m612 51 m613 52 m614 53 m615 54 m616 55 m617 56 m618 57 m619 58 m620 59 m621 60 m622 61 m623 62 m624 63 m625 64 m626 65 m627 66 m628 67 m629 68 m630 69 m631 70 m632 71 m633 72 m634 73 m635 74 m636 75 m637 76 m638 77 m639 78 m640 79 m641 80 m642 81 m643 82 m644 83 m645 84 m646 85 m647 86 m648 87 m649 88 m650 89 m651 90 m652 91 m653 92 m654 93 m655 94 m656 95 m657 96 m658 97 m659 98 m660 99 m661 100 m662 101 m663 102 m664 103 m665 104 m666 105 m667 106 m668 107 m669 108 m670 109 m671 110 m672 111 m673 112 m674 113 m675 114 m676 115 m677 116 m678 117 m679 118 m680 119 m681 120 m682 121 m683 122 m684 123 m685 124 m686 125 m687 126 m688 127 m689 128 m690 129 m691 130 m692 131 m693 132 m694 133 m695 134 m696 135 m697 136 m698 137 m699 138 m700 139 m701 140 m702 141 m703 142 m704 143 m705 144 m706 145 m707 146 m708 147 m709 148 m710 149 m711 150 m712 151 m713 152 m714 153 m715 154 m716 155 m717 156 m718 157 m719 158 m720 159 m721 160 m722 161 m723 162 m724 163 m725 164 m726 165 m727 166 m728 [ reached 'max' / getOption("max.print") -- omitted 66 rows ] ``` ```r taxa ``` ``` otu label xsi.type otus 1 ou385 Allenopithecus_nigroviridis NA os9 2 ou386 Allocebus_trichotis NA os9 3 ou387 Alouatta_belzebul NA os9 4 ou388 Alouatta_caraya NA os9 5 ou389 Alouatta_coibensis NA os9 6 ou390 Alouatta_fusca NA os9 7 ou391 Alouatta_palliata NA os9 8 ou392 Alouatta_pigra NA os9 9 ou393 Alouatta_sara NA os9 10 ou394 Alouatta_seniculus NA os9 11 ou395 Aotus_azarai NA os9 12 ou396 Aotus_brumbacki NA os9 13 ou397 Aotus_hershkovitzi NA os9 14 ou398 Aotus_infulatus NA os9 15 ou399 Aotus_lemurinus NA os9 16 ou400 Aotus_miconax NA os9 17 ou401 Aotus_nancymaae NA os9 18 ou402 Aotus_nigriceps NA os9 19 ou403 Aotus_trivirgatus NA os9 20 ou404 Aotus_vociferans NA os9 21 ou405 Arctocebus_aureus NA os9 22 ou406 Arctocebus_calabarensis NA os9 23 ou407 Ateles_belzebuth NA os9 24 ou408 Ateles_chamek NA os9 25 ou409 Ateles_fusciceps NA os9 26 ou410 Ateles_geoffroyi NA os9 27 ou411 Ateles_marginatus NA os9 28 ou412 Ateles_paniscus NA os9 29 ou413 Avahi_laniger NA os9 30 ou414 Brachyteles_arachnoides NA os9 31 ou415 Cacajao_calvus NA os9 32 ou416 Cacajao_melanocephalus NA os9 33 ou417 Callicebus_brunneus NA os9 34 ou418 Callicebus_caligatus NA os9 35 ou419 Callicebus_cinerascens NA os9 36 ou420 Callicebus_cupreus NA os9 37 ou421 Callicebus_donacophilus NA os9 38 ou422 Callicebus_dubius NA os9 39 ou423 Callicebus_hoffmannsi NA os9 40 ou424 Callicebus_modestus NA os9 41 ou425 Callicebus_moloch NA os9 42 ou426 Callicebus_oenanthe NA os9 43 ou427 Callicebus_olallae NA os9 44 ou428 Callicebus_personatus NA os9 45 ou429 Callicebus_torquatus NA os9 46 ou430 Callimico_goeldii NA os9 47 ou431 Callithrix_argentata NA os9 48 ou432 Callithrix_aurita NA os9 49 ou433 Callithrix_flaviceps NA os9 50 ou434 Callithrix_geoffroyi NA os9 51 ou435 Callithrix_humeralifera NA os9 52 ou436 Callithrix_jacchus NA os9 53 ou437 Callithrix_kuhlii NA os9 54 ou438 Callithrix_penicillata NA os9 55 ou439 Callithrix_pygmaea NA os9 56 ou440 Cebus_albifrons NA os9 57 ou441 Cebus_apella NA os9 58 ou442 Cebus_capucinus NA os9 59 ou443 Cebus_olivaceus NA os9 60 ou444 Cercocebus_agilis NA os9 61 ou445 Cercocebus_galeritus NA os9 62 ou446 Cercocebus_torquatus NA os9 63 ou447 Cercopithecus_ascanius NA os9 64 ou448 Cercopithecus_campbelli NA os9 65 ou449 Cercopithecus_cephus NA os9 66 ou450 Cercopithecus_diana NA os9 67 ou451 Cercopithecus_dryas NA os9 68 ou452 Cercopithecus_erythrogaster NA os9 69 ou453 Cercopithecus_erythrotis NA os9 70 ou454 Cercopithecus_hamlyni NA os9 71 ou455 Cercopithecus_lhoesti NA os9 72 ou456 Cercopithecus_mitis NA os9 73 ou457 Cercopithecus_mona NA os9 74 ou458 Cercopithecus_neglectus NA os9 75 ou459 Cercopithecus_nictitans NA os9 76 ou460 Cercopithecus_petaurista NA os9 77 ou461 Cercopithecus_pogonias NA os9 78 ou462 Cercopithecus_preussi NA os9 79 ou463 Cercopithecus_sclateri NA os9 80 ou464 Cercopithecus_solatus NA os9 81 ou465 Cercopithecus_wolfi NA os9 82 ou466 Cheirogaleus_major NA os9 83 ou467 Cheirogaleus_medius NA os9 84 ou468 Chiropotes_albinasus NA os9 85 ou469 Chiropotes_satanas NA os9 86 ou470 Chlorocebus_aethiops NA os9 87 ou471 Colobus_angolensis NA os9 88 ou472 Colobus_guereza NA os9 89 ou473 Colobus_polykomos NA os9 90 ou474 Colobus_satanas NA os9 91 ou475 Daubentonia_madagascariensis NA os9 92 ou476 Erythrocebus_patas NA os9 93 ou477 Eulemur_coronatus NA os9 94 ou478 Eulemur_fulvus NA os9 95 ou479 Eulemur_macaco NA os9 96 ou480 Eulemur_mongoz NA os9 97 ou481 Eulemur_rubriventer NA os9 98 ou482 Euoticus_elegantulus NA os9 99 ou483 Euoticus_pallidus NA os9 100 ou484 Galago_alleni NA os9 101 ou485 Galago_gallarum NA os9 102 ou486 Galago_matschiei NA os9 103 ou487 Galago_moholi NA os9 104 ou488 Galago_senegalensis NA os9 105 ou489 Galagoides_demidoff NA os9 106 ou490 Galagoides_zanzibaricus NA os9 107 ou491 Gorilla_gorilla NA os9 108 ou492 Hapalemur_aureus NA os9 109 ou493 Hapalemur_griseus NA os9 110 ou494 Hapalemur_simus NA os9 111 ou495 Homo_sapiens NA os9 112 ou496 Hylobates_agilis NA os9 113 ou497 Hylobates_concolor NA os9 114 ou498 Hylobates_gabriellae NA os9 115 ou499 Hylobates_hoolock NA os9 116 ou500 Hylobates_klossii NA os9 117 ou501 Hylobates_lar NA os9 118 ou502 Hylobates_leucogenys NA os9 119 ou503 Hylobates_moloch NA os9 120 ou504 Hylobates_muelleri NA os9 121 ou505 Hylobates_pileatus NA os9 122 ou506 Hylobates_syndactylus NA os9 123 ou507 Indri_indri NA os9 124 ou508 Lagothrix_flavicauda NA os9 125 ou509 Lagothrix_lagotricha NA os9 126 ou510 Lemur_catta NA os9 127 ou511 Leontopithecus_caissara NA os9 128 ou512 Leontopithecus_chrysomela NA os9 129 ou513 Leontopithecus_chrysopygus NA os9 130 ou514 Leontopithecus_rosalia NA os9 131 ou515 Lepilemur_dorsalis NA os9 132 ou516 Lepilemur_edwardsi NA os9 133 ou517 Lepilemur_leucopus NA os9 134 ou518 Lepilemur_microdon NA os9 135 ou519 Lepilemur_mustelinus NA os9 136 ou520 Lepilemur_ruficaudatus NA os9 137 ou521 Lepilemur_septentrionalis NA os9 138 ou522 Lophocebus_albigena NA os9 139 ou523 Loris_tardigradus NA os9 140 ou524 Macaca_arctoides NA os9 141 ou525 Macaca_assamensis NA os9 142 ou526 Macaca_cyclopis NA os9 143 ou527 Macaca_fascicularis NA os9 144 ou528 Macaca_fuscata NA os9 145 ou529 Macaca_maura NA os9 146 ou530 Macaca_mulatta NA os9 147 ou531 Macaca_nemestrina NA os9 148 ou532 Macaca_nigra NA os9 149 ou533 Macaca_ochreata NA os9 150 ou534 Macaca_radiata NA os9 151 ou535 Macaca_silenus NA os9 152 ou536 Macaca_sinica NA os9 153 ou537 Macaca_sylvanus NA os9 154 ou538 Macaca_thibetana NA os9 155 ou539 Macaca_tonkeana NA os9 156 ou540 Mandrillus_leucophaeus NA os9 157 ou541 Mandrillus_sphinx NA os9 158 ou542 Microcebus_coquereli NA os9 159 ou543 Microcebus_murinus NA os9 160 ou544 Microcebus_rufus NA os9 161 ou545 Miopithecus_talapoin NA os9 162 ou546 Nasalis_concolor NA os9 163 ou547 Nasalis_larvatus NA os9 164 ou548 Nycticebus_coucang NA os9 165 ou549 Nycticebus_pygmaeus NA os9 166 ou550 Otolemur_crassicaudatus NA os9 167 ou551 Otolemur_garnettii NA os9 168 ou552 Pan_paniscus NA os9 169 ou553 Pan_troglodytes NA os9 170 ou554 Papio_hamadryas NA os9 171 ou555 Perodicticus_potto NA os9 172 ou556 Phaner_furcifer NA os9 173 ou557 Pithecia_aequatorialis NA os9 174 ou558 Pithecia_albicans NA os9 175 ou559 Pithecia_irrorata NA os9 176 ou560 Pithecia_monachus NA os9 177 ou561 Pithecia_pithecia NA os9 178 ou562 Pongo_pygmaeus NA os9 179 ou563 Presbytis_comata NA os9 180 ou564 Presbytis_femoralis NA os9 181 ou565 Presbytis_frontata NA os9 182 ou566 Presbytis_hosei NA os9 183 ou567 Presbytis_melalophos NA os9 184 ou568 Presbytis_potenziani NA os9 185 ou569 Presbytis_rubicunda NA os9 186 ou570 Presbytis_thomasi NA os9 187 ou571 Procolobus_badius NA os9 188 ou572 Procolobus_pennantii NA os9 189 ou573 Procolobus_preussi NA os9 190 ou574 Procolobus_rufomitratus NA os9 191 ou575 Procolobus_verus NA os9 192 ou576 Propithecus_diadema NA os9 193 ou577 Propithecus_tattersalli NA os9 194 ou578 Propithecus_verreauxi NA os9 195 ou579 Pygathrix_avunculus NA os9 196 ou580 Pygathrix_bieti NA os9 197 ou581 Pygathrix_brelichi NA os9 198 ou582 Pygathrix_nemaeus NA os9 199 ou583 Pygathrix_roxellana NA os9 200 ou584 Saguinus_bicolor NA os9 201 ou585 Saguinus_fuscicollis NA os9 202 ou586 Saguinus_geoffroyi NA os9 203 ou587 Saguinus_imperator NA os9 204 ou588 Saguinus_inustus NA os9 205 ou589 Saguinus_labiatus NA os9 206 ou590 Saguinus_leucopus NA os9 207 ou591 Saguinus_midas NA os9 208 ou592 Saguinus_mystax NA os9 209 ou593 Saguinus_nigricollis NA os9 210 ou594 Saguinus_oedipus NA os9 211 ou595 Saguinus_tripartitus NA os9 212 ou596 Saimiri_boliviensis NA os9 213 ou597 Saimiri_oerstedii NA os9 214 ou598 Saimiri_sciureus NA os9 215 ou599 Saimiri_ustus NA os9 216 ou600 Saimiri_vanzolinii NA os9 217 ou601 Semnopithecus_entellus NA os9 218 ou602 Tarsius_bancanus NA os9 219 ou603 Tarsius_dianae NA os9 220 ou604 Tarsius_pumilus NA os9 221 ou605 Tarsius_spectrum NA os9 222 ou606 Tarsius_syrichta NA os9 223 ou607 Theropithecus_gelada NA os9 224 ou608 Trachypithecus_auratus NA os9 225 ou609 Trachypithecus_cristatus NA os9 226 ou610 Trachypithecus_francoisi NA os9 227 ou611 Trachypithecus_geei NA os9 228 ou612 Trachypithecus_johnii NA os9 229 ou613 Trachypithecus_obscurus NA os9 230 ou614 Trachypithecus_phayrei NA os9 231 ou615 Trachypithecus_pileatus NA os9 232 ou616 Trachypithecus_vetulus NA os9 233 ou617 Varecia_variegata NA os9 ``` ```r 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: ```r taxa %>% left_join(char, by = c("label" = "taxa")) %>% left_join(otu_meta, by = "otu") %>% select(otu, label, x, href) ``` ``` otu label x 1 ou385 Allenopithecus_nigroviridis 8.465900 2 ou386 Allocebus_trichotis 4.368181 3 ou387 Alouatta_belzebul 8.729074 4 ou388 Alouatta_caraya 8.628735 5 ou389 Alouatta_coibensis 8.764053 6 ou390 Alouatta_fusca 8.554489 7 ou391 Alouatta_palliata 8.791790 8 ou392 Alouatta_pigra 8.881836 9 ou393 Alouatta_sara 8.796339 10 ou394 Alouatta_seniculus 8.767173 11 ou395 Aotus_azarai 7.127694 12 ou396 Aotus_brumbacki 6.401917 13 ou397 Aotus_hershkovitzi 6.684612 14 ou398 Aotus_infulatus 7.122867 15 ou399 Aotus_lemurinus 6.781058 16 ou400 Aotus_miconax 6.684612 17 ou401 Aotus_nancymaae 6.678342 18 ou402 Aotus_nigriceps 6.966024 19 ou403 Aotus_trivirgatus 6.815640 20 ou404 Aotus_vociferans 6.771936 21 ou405 Arctocebus_aureus 5.459586 22 ou406 Arctocebus_calabarensis 5.552960 23 ou407 Ateles_belzebuth 8.812843 24 ou408 Ateles_chamek 8.872067 25 ou409 Ateles_fusciceps 9.112728 26 ou410 Ateles_geoffroyi 8.937218 27 ou411 Ateles_marginatus 8.738735 28 ou412 Ateles_paniscus 9.072227 29 ou413 Avahi_laniger 6.927558 30 ou414 Brachyteles_arachnoides 9.268609 31 ou415 Cacajao_calvus 8.137396 32 ou416 Cacajao_melanocephalus 8.051978 33 ou417 Callicebus_brunneus 6.747587 34 ou418 Callicebus_caligatus 6.899723 35 ou419 Callicebus_cinerascens 6.899723 36 ou420 Callicebus_cupreus 7.021084 37 ou421 Callicebus_donacophilus 6.801283 38 ou422 Callicebus_dubius 6.899723 39 ou423 Callicebus_hoffmannsi 6.975414 40 ou424 Callicebus_modestus 6.899723 41 ou425 Callicebus_moloch 6.872128 42 ou426 Callicebus_oenanthe 6.899723 43 ou427 Callicebus_olallae 6.899723 44 ou428 Callicebus_personatus 7.237059 45 ou429 Callicebus_torquatus 7.106606 46 ou430 Callimico_goeldii 6.324359 47 ou431 Callithrix_argentata 5.910797 48 ou432 Callithrix_aurita 5.961005 49 ou433 Callithrix_flaviceps 5.926926 50 ou434 Callithrix_geoffroyi 5.834811 51 ou435 Callithrix_humeralifera 5.926926 52 ou436 Callithrix_jacchus 5.673323 53 ou437 Callithrix_kuhlii 5.926926 54 ou438 Callithrix_penicillata 5.828946 55 ou439 Callithrix_pygmaea 4.828314 56 ou440 Cebus_albifrons 7.832014 57 ou441 Cebus_apella 7.922986 58 ou442 Cebus_capucinus 8.009695 59 ou443 Cebus_olivaceus 7.937375 60 ou444 Cercocebus_agilis 8.870663 61 ou445 Cercocebus_galeritus 8.865029 62 ou446 Cercocebus_torquatus 8.894259 63 ou447 Cercopithecus_ascanius 8.171882 64 ou448 Cercopithecus_campbelli 8.199739 65 ou449 Cercopithecus_cephus 8.143227 66 ou450 Cercopithecus_diana 8.382518 67 ou451 Cercopithecus_dryas 7.930206 68 ou452 Cercopithecus_erythrogaster 8.143227 69 ou453 Cercopithecus_erythrotis 8.086410 70 ou454 Cercopithecus_hamlyni 8.438150 71 ou455 Cercopithecus_lhoesti 8.579229 72 ou456 Cercopithecus_mitis 8.525161 73 ou457 Cercopithecus_mona 8.289037 74 ou458 Cercopithecus_neglectus 8.579229 75 ou459 Cercopithecus_nictitans 8.567886 76 ou460 Cercopithecus_petaurista 8.083329 77 ou461 Cercopithecus_pogonias 8.183118 78 ou462 Cercopithecus_preussi 8.544808 79 ou463 Cercopithecus_sclateri 8.029433 80 ou464 Cercopithecus_solatus 8.567886 81 ou465 Cercopithecus_wolfi 8.089482 82 ou466 Cheirogaleus_major 6.104793 83 ou467 Cheirogaleus_medius 5.283204 84 ou468 Chiropotes_albinasus 7.937375 85 ou469 Chiropotes_satanas 7.996317 86 ou470 Chlorocebus_aethiops 8.301522 87 ou471 Colobus_angolensis 9.103868 88 ou472 Colobus_guereza 9.210340 89 ou473 Colobus_polykomos 9.060680 90 ou474 Colobus_satanas 9.121509 91 ou475 Daubentonia_madagascariensis 7.919356 92 ou476 Erythrocebus_patas 8.988446 93 ou477 Eulemur_coronatus 7.438384 94 ou478 Eulemur_fulvus 7.779049 95 ou479 Eulemur_macaco 7.816014 96 ou480 Eulemur_mongoz 7.478735 97 ou481 Eulemur_rubriventer 7.620705 98 ou482 Euoticus_elegantulus 5.690359 99 ou483 Euoticus_pallidus 5.627621 100 ou484 Galago_alleni 5.521461 101 ou485 Galago_gallarum 5.365976 102 ou486 Galago_matschiei 5.267858 103 ou487 Galago_moholi 5.375278 104 ou488 Galago_senegalensis 5.594711 105 ou489 Galagoides_demidoff 4.206184 106 ou490 Galagoides_zanzibaricus 4.997212 107 ou491 Gorilla_gorilla 11.643954 108 ou492 Hapalemur_aureus 7.358831 109 ou493 Hapalemur_griseus 6.862758 110 ou494 Hapalemur_simus 7.620705 111 ou495 Homo_sapiens 10.980195 112 ou496 Hylobates_agilis 8.675905 113 ou497 Hylobates_concolor 8.768730 114 ou498 Hylobates_gabriellae 9.047821 115 ou499 Hylobates_hoolock 8.809863 116 ou500 Hylobates_klossii 8.674197 117 ou501 Hylobates_lar 8.635865 118 ou502 Hylobates_leucogenys 8.898366 119 ou503 Hylobates_moloch 8.677610 120 ou504 Hylobates_muelleri 8.687779 121 ou505 Hylobates_pileatus 8.630522 122 ou506 Hylobates_syndactylus 9.296518 123 ou507 Indri_indri 9.065315 124 ou508 Lagothrix_flavicauda 9.020390 125 ou509 Lagothrix_lagotricha 8.743532 126 ou510 Lemur_catta 7.878534 127 ou511 Leontopithecus_caissara 6.405228 128 ou512 Leontopithecus_chrysomela 6.352629 129 ou513 Leontopithecus_chrysopygus 6.486161 130 ou514 Leontopithecus_rosalia 6.385194 131 ou515 Lepilemur_dorsalis 6.232448 132 ou516 Lepilemur_edwardsi 6.711740 133 ou517 Lepilemur_leucopus 6.396930 134 ou518 Lepilemur_microdon 6.863803 135 ou519 Lepilemur_mustelinus 6.508769 136 ou520 Lepilemur_ruficaudatus 6.637258 137 ou521 Lepilemur_septentrionalis 6.638568 138 ou522 Lophocebus_albigena 8.903815 139 ou523 Loris_tardigradus 5.517453 140 ou524 Macaca_arctoides 9.148465 141 ou525 Macaca_assamensis 9.054855 142 ou526 Macaca_cyclopis 8.658693 143 ou527 Macaca_fascicularis 8.431635 144 ou528 Macaca_fuscata 9.220291 145 ou529 Macaca_maura 8.894259 146 ou530 Macaca_mulatta 8.771835 147 ou531 Macaca_nemestrina 8.970813 148 ou532 Macaca_nigra 8.906529 149 ou533 Macaca_ochreata 7.919356 150 ou534 Macaca_radiata 8.517193 151 ou535 Macaca_silenus 8.699515 152 ou536 Macaca_sinica 8.446771 153 ou537 Macaca_sylvanus 9.350102 154 ou538 Macaca_thibetana 9.268609 155 ou539 Macaca_tonkeana 9.220291 156 ou540 Mandrillus_leucophaeus 9.560997 157 ou541 Mandrillus_sphinx 9.729134 158 ou542 Microcebus_coquereli 5.793014 159 ou543 Microcebus_murinus 4.198705 160 ou544 Microcebus_rufus 3.881564 161 ou545 Miopithecus_talapoin 7.130899 162 ou546 Nasalis_concolor 8.979354 163 ou547 Nasalis_larvatus 9.417355 164 ou548 Nycticebus_coucang 6.878326 165 ou549 Nycticebus_pygmaeus 5.840642 166 ou550 Otolemur_crassicaudatus 7.130899 167 ou551 Otolemur_garnettii 6.701960 168 ou552 Pan_paniscus 10.468801 169 ou553 Pan_troglodytes 10.716638 170 ou554 Papio_hamadryas 9.735069 171 ou555 Perodicticus_potto 6.984716 172 ou556 Phaner_furcifer 6.016157 173 ou557 Pithecia_aequatorialis 7.774856 174 ou558 Pithecia_albicans 7.937375 175 ou559 Pithecia_irrorata 7.749322 176 ou560 Pithecia_monachus 7.654443 177 ou561 Pithecia_pithecia 7.420579 178 ou562 Pongo_pygmaeus 10.860920 179 ou563 Presbytis_comata 9.039552 180 ou564 Presbytis_femoralis 8.797851 181 ou565 Presbytis_frontata 8.853665 182 ou566 Presbytis_hosei 8.725832 183 ou567 Presbytis_melalophos 8.748305 184 ou568 Presbytis_potenziani 8.774931 185 ou569 Presbytis_rubicunda 8.773385 186 ou570 Presbytis_thomasi 8.765615 187 ou571 Procolobus_badius 8.808369 188 ou572 Procolobus_pennantii 9.122601 189 ou573 Procolobus_preussi 9.094930 190 ou574 Procolobus_rufomitratus 8.995909 191 ou575 Procolobus_verus 8.289037 192 ou576 Propithecus_diadema 8.794825 193 ou577 Propithecus_tattersalli 8.171882 194 ou578 Propithecus_verreauxi 8.202482 195 ou579 Pygathrix_avunculus 9.164296 196 ou580 Pygathrix_bieti 9.118225 197 ou581 Pygathrix_brelichi 9.305651 198 ou582 Pygathrix_nemaeus 9.417355 199 ou583 Pygathrix_roxellana 9.510445 200 ou584 Saguinus_bicolor 6.142037 201 ou585 Saguinus_fuscicollis 5.976351 202 ou586 Saguinus_geoffroyi 6.200509 203 ou587 Saguinus_imperator 6.016157 204 ou588 Saguinus_inustus 6.688355 205 ou589 Saguinus_labiatus 6.234411 206 ou590 Saguinus_leucopus 6.124683 207 ou591 Saguinus_midas 6.293419 208 ou592 Saguinus_mystax 6.326149 209 ou593 Saguinus_nigricollis 6.109248 210 ou594 Saguinus_oedipus 6.139885 211 ou595 Saguinus_tripartitus 5.953243 212 ou596 Saimiri_boliviensis 6.690842 213 ou597 Saimiri_oerstedii 6.570883 214 ou598 Saimiri_sciureus 6.620073 215 ou599 Saimiri_ustus 6.791221 216 ou600 Saimiri_vanzolinii 6.664409 217 ou601 Semnopithecus_entellus 9.441452 218 ou602 Tarsius_bancanus 4.736198 219 ou603 Tarsius_dianae 4.709530 220 ou604 Tarsius_pumilus 4.808111 221 ou605 Tarsius_spectrum 5.111988 222 ou606 Tarsius_syrichta 4.753590 223 ou607 Theropithecus_gelada 9.680344 224 ou608 Trachypithecus_auratus 9.181941 225 ou609 Trachypithecus_cristatus 8.872067 226 ou610 Trachypithecus_francoisi 9.008224 227 ou611 Trachypithecus_geei 9.031214 228 ou612 Trachypithecus_johnii 9.268609 229 ou613 Trachypithecus_obscurus 8.870663 230 ou614 Trachypithecus_phayrei 8.948976 231 ou615 Trachypithecus_pileatus 9.323669 232 ou616 Trachypithecus_vetulus 8.969542 233 ou617 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 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945168 6 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=945164 7 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=572939 8 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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 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=944269 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.