peerj_json_files/PeerJ_Json_141.json

{
    "v1_Abstract": "BioNames is a web database of taxonomic names for animals, linked to the primary literature and, wherever possible, to phylogenetic trees. It aims to provide a taxonomic \"dashboard\" where at a glance we can see a summary of the taxonomic and phylogenetic information we have for a given taxon and hence provide a quick answer to the basic question \"what is this taxon?\" BioNames combines classifications from the Global Biodiversity Information Facility (GBIF) and GenBank, images from the Encyclopedia of Life (EOL), animal names from the Index of Organism Names (ION), and bibliographic data from multiple sources including the Biodiversity Heritage Library (BHL) and CrossRef. The user interface includes display of full text articles, interactive timelines of taxonomic publications, and zoomable phylogenies. It is available at http://bionames.org.",
    "v2_Abstract": "BioNames is a web database of taxonomic names for animals, linked to the primary literature and, wherever possible, to phylogenetic trees. It aims to provide a taxonomic \"dashboard\" where at a glance we can see a summary of the taxonomic and phylogenetic information we have for a given taxon and hence provide a quick answer to the basic question \"what is this taxon?\" BioNames combines classifications from the Global Biodiversity Information Facility (GBIF) and GenBank, imagery from the Encyclopedia of Life (EOL), animal names from the Index of Organism Names (ION), and bibliographic data from multiple sources including the Biodiversity Heritage Library (BHL) and CrossRef. The user interface includes display of full text articles, interactive timelines of taxonomic publications, and zoomable phylogenies. It is available at http://bionames.org.",
    "v1_text": "materials & methods : BioNames integrates data on taxonomic names and classifications, literature, and phylogenies from a variety of sources. Given the inevitable differences in how different databases treat the same data (as well as internal inconsistencies within individual databases), considerable effort must be spent cleaning and reconciling data. Much of this process involves mapping \"strings\" to \"things\" (Bollacker et al. 2008), or more precisely, mapping strings to identifiers for things. results : BioNames comprises a CouchDB database and a web interface. Key features of the interface are outlined below. 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t acknowledgements : I thank Ryan Schenk for his work on the BioNames, and Cyndy Parr (EOL) for managing the EOL Computational Challenge and providing helpful feedback on the development of BioNames. Mark Holder and an anonymous reviewer provided detailed and helpful comments on the 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t manuscript. Some of the ideas in this manuscriptpresented here were first explored in a talk at the \"Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond\" symposium held at The Natural History Museum, London, October 28th 2011. I thank Ellinor Michel for the invitation to speak at that meeting. discussion : The EOL Computational Data Challenge imposed a deadline on the first release of BioNames, however development of both the database and web interface is ongoing. Below I discuss some potential applications and future directions. impact of taxonomic literature : The taxonomic community has long felt disadvantaged by the role of citation-based \"impact factor\" in assessing the importance of taxonomic research (Garfield 2001; Krell 2000; Werner 2006) especially as much of the taxonomic literature appears in relatively low-impact journals. A common proposal is to include citations to the taxonomic authority for every name mentioned in a scientific paper (W\u00e4gele et al. 2011). Regardless of the merits of this idea, in practice these citations are often hard to locate, which is another motivation for BioNames. There is additional value in surfacing identifiers for the taxonomic literature. In addition to helping construct citation networks, global identifiers can facilitate computing other measures of the value of a taxonomic paper. There is a growing interest in additional measures of postpublication impact of a publication in terms of activity such as social bookmarking, and commentary on web sites (\"alt-metrics\") (Yan and Gerstein 2011). Gathering these metrics is greatly facilitated by using standard bibliographic identifiers (otherwise, how do we know whether two commentators are discussing the same article or not?). If taxonomic literature is be part of this burgeoning conversation then it needs to be able to be identified unambiguously. taxon names : At present the taxonomic scope of BioNames is restricted to names covered by the International Code of Zoological Nomenclature (animals and those eukaryotes not covered by the International Code of Nomenclature for algae, fungi, and plants). Taxonomic names were obtained from the Index of Organism Names (ION; http://www.organismnames.com). Each name in ION has a Life Science Identifier (LSID) (Martin et al. 2005) which uniquely identifies that name. LSIDs can be dereferenced to return metadata in Resource Description Framework format (RDF) (Page 2008b). I used the TDWG LSID resolver (http://lsid.tdwg.org) to obtain the metadata for each LSID. ION LSIDs provide basic information on a taxonomic name using the TDWG Taxon Name LSID Ontology (http://rs.tdwg.org/ontology/voc/TaxonName), in many cases including bibliographic details for the publication where the name first appeared (Fig. 2). The publication in which the name first appeared is listed in the contents of the \"PublishedIn\" property. In the example in Figure 2 this is the string \"Description of a new species of Pinnotheres, and redescription of P. novaezelandiae (Brachyura: Pinnotheridae). New Zealand Journal of Zoology, 10(2) 1983: 151-162. 158 (Zoological Record Volume 120)\". I used regular 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t expressions to parse citation strings into their component parts (e.g., article title, journal, volume, pagination), and then attempted to locate the corresponding reference in an external database (see below). database : Once aggregated, cleaned, and reconciled, the data was converted to JSON (JavaScript Object Notation) and stored in a CouchDB database. CouchDB is a \"NoSQL\" document database that stores objects in JSON format. Unlike typical SQL databases, CouchDB does not have a database schema and does not support ad hoc queries. Instead CouchDB accepts semi-structured documents, and the user developer defines fixed queries or \"views\" (Anderson et al. 2010). phylogeny viewer : Screenshot of phylogeny from PhyLoTA as displayed in BioNames. The user can zoom in and out and pan, as well as change the layout of the tree. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 11 Relative importance of different publishers of taxonomic literature Bubble chart showing relative numbers of taxonomic articles made available online by different publishers. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t availability : BioNames is accessible at http://bionames.org. The source code used to build the web site is available on GitHub http://github.com/rdmpage/bionames. Scripts used to fetch, clean, and reconcile the data are archived in http://github.com/rdmpage/bionames-data eol challenge : In response to the Encyclopedia of Life (EOL) Computational Data Challenge (http://eol.org/info/323) I constructed BioNames (http://bionames.org) (Page 2012). Its goal is to create a database of taxonomic names for animals linked to the primary literature and, wherever possible, to phylogenetic trees. Using existing globally unique identifiers for taxonomic names, concepts, publications, and sequences rather than cryptic text strings (for example, abbreviated bibliographic citations) simplifies the task of linking \u2014 we can rely on exact matching of identifiers rather than approximate matching between names for what may or may not be the same entity. This is particularly relevant once we start to aggregate information from different databases, where the same information (e.g., a publication) may be represented by different strings. Furthermore, if we use existing identifiers we increase the potential to connect to other databases (Page 2008a). This paper outlines how BioNames was built, describes the user interface, and discusses future plans. 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t bibliographic identifiers : When populating BioNames every effort has been made to map each bibliographic string to a corresponding identifier, such as a Digital Object identifier (DOI). For the example in Figure 2, the citation string \"Description of a new species of Pinnotheres, and redescription of P. novaezelandiae (Brachyura: Pinnotheridae). New Zealand Journal of Zoology, 10(2) 1983: 151- 162. 158 (Zoological Record Volume 120)\" corresponds to the article with the DOI 10.1080/03014223.1983.10423904. Once we have a DOI, we can then use services such as those provided by CrossRef (http://www.crossref.org) to retrieve author and publisher information for an article (see Fig. 11 below for one use of publisher information). While DOIs are the best-known bibliographic identifier, there are several others that are relevant to the taxonomic literature (Page 2009). DOIs are themselves based on Handles (http://hdl.handle.net), an identifier widely used by digital repositories such as DSpace (Smith et al. 2003). A number of journals, such as the Bulletins and Novitates of the American Museum of Natural History are available in DSpace repositories and consequently have Handles. Other major archives such as JSTOR (http://www.jstor.org/) and the Japanese National Institute of Informatics (CiNii; http://ci.nii.ac.jp/) have their own unique identifiers (typically integer numbers that are part of a URL). 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Having a variety of identifiers can complicate the task of finding existing identifiers for a particular publication. Whereas for some identifiers, such as DOIs, and CiNii NAIDs (National Institute of Informatics Article IDs), and BioStor reference ids there are search tools (e.g., http://search.crossref.org) or OpenURL resolvers for this task (Van de Sompel & Beit-Arie 2001) (e.g., http://biostor.org/openurl), for other identifiers there may be no obvious way to find the identifier other than by using a search engine. Another strategy is to build a local database of bibliographic data and match citations strings to that database. I used Mendeley (http://www.mendeley.com) to store bibliographic data harvested from journal or taxon-specific web pages in publicly accessible \u201cgroups\u201d, and then queried the local copy of the Mendeley Desktop database to search for references that matched the citation strings. For the example in Figure 2, the citation string \"Description of a new species of Pinnotheres, and redescription of P. novaezelandiae (Brachyura: Pinnotheridae). New Zealand Journal of Zoology, 10(2) 1983: 151-162. 158 (Zoological Record Volume 120)\" corresponds to the article with the DOI 10.1080/03014223.1983.10423904. Once we have a DOI, we can then use services such as those provided by CrossRef (http://www.crossref.org) to retrieve author and publisher information for an article (see Fig. 11 below for one use of publisher information). Identifiers also exist for aggregations of publications, such as journals. The historical practice of abbreviating journal titles in citations has led to a plethora of ways to refer to the same journal. For example, the BioStor database (http://biostor.org; Page 2011b) has accumulated more than ten variations on the name of the journal Bulletin of Zoological Nomenclature (such as \"Bull Zool Nomen\", \"Bull Zool Nom.\", \"Bull. Zool. Nomencl.\", etc.). This practice, presumably motivated by the desire to conserve space on the printed page, complicates efforts to match citations to identifiers. One approach to tackling this problem is to map abbreviations to journal-level 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t globally unique identifiers, such as International Standard Serial Numbers (ISSNs) (for the Bulletin of Zoological Nomenclature the ISSN is 0007-5167). In addition to reducing ambiguity, there are web services such as that provided by WorldCat (http://www.worldcat.org) that take ISSNs and return the history of name changes for a journal, which in turn can help clarify the (often complicated) history of long-lived journals.. Where possible each journal in BioNames was associated with its corresponding ISSN. If an ISSN is not available for a journal, then the corresponding OCLC Control Number was used as the identifier for the journal. documents : Taxonomic publications are available under a variety of licenses, ranging from explicitly open access licenses (MacCallum 2007) to articles that are \"free\", to articles that are behind a paywall. Archives such as JSTOR and CiNii have a mixture of free and subscription-based content. Many smaller journals, often published by scientific societies, are providing their content online for free, if not explicitly under an open license. The Biodiversity Heritage Library (the single largest source of taxonomic articles in BioNames, Fig. 11) makes its content available under a Creative Commons license. Where PDFs were available online either \"for free\" or under open access, these were downloaded and locally cached. Pages were extracted and converted into bitmap images for subsequent display in a web browser. Closed-access publications that are available online are linked to by their identifier (e.g., DOI). Access to some of these publications may be available for short-term \"rent\" by services such as DeepDyve (http://www.deepdyve.com): where possible BioNames includes a link those services. 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t clustering taxonomic names : Taxonomic names comprise a \"canonical\" name and the name's authorship, for example Homo sapiens Linnaeus comprises the canonical name \"Homo sapiens\" and the authorship string \"Linnaeus\". Names in taxonomic databases such as ION display numerous variations in spelling of authors and/or variation in the year of publication, and instances of the same canonical name published by different authors (e.g., homonyms), so the names were clustered before populating BioNames. For each set of taxon names with the same canonical name the authorship was compared. If one name lacked an author and the other had an author, the names were automatically merged into a cluster. Given more than two names a graph was constructed where the nodes are the authorship strings, and a pair of nodes is connected if their corresponding strings were sufficiently similar. String similarity was computed by converting the strings to a \"finger print\" comprising lower case letters with all accented characters replaced by non-accented equivalents, and all punctuation removed, then finding the longest common subsequence of the two strings. By definition the characters in a common subsequence do not need to be consecutive, so the method allows for insertion and deletion of characters. If the length of the subsequence relative to the each of the two input strings was longer than a specified threshold (by default, 0.8, where identical strings have a similarity of 1.0) then the two author strings were connected by an edge in the graph. The components of the graph correspond to clusters of names with similar authorship strings, and were treated as being the same name. Figure 3 shows a graph for the different names that all have \"Rhacophorus\" as the canonical name. Mapping names to taxa 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t BioNames includes two taxonomic classifications, sourced from GBIF (http://uat.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c) and NCBI (ftp://ftp.ncbi.nih.gov/pub/taxonomy), respectively. These provide the user with a way to navigate through taxonomic names, as well as view data associated with each classification (e.g., phylogenies). These classifications also provide an explicit definition of the scope of a taxon (i.e., the \u201ctaxon concept\u201d). A higher taxon comprises the set of taxa below that taxon in the classification. A terminal taxon (the lowest taxon in a classification) in GBIF can be defined as the set of occurrences linked to that taxon, a terminal taxon in NCBI can be defined as the set of sequences linked to that taxon. Ideally there would be a one-to-one mapping between a taxonomic name and a taxon, but complications often arise. In addition to the well-known problems of synonymy (more than one name for the same taxon) and homonymy (the same name used for different taxa), name and taxon databases may store slightly different representations of the same name. For example, ION has four records for the name \"Nystactes\" (each name is followed by its LSID): Nystactes urn:lsid:organismnames.com:name:2787598 Nystactes Bohlke urn:lsid:organismnames.com:name:2735131 Nystactes Gloger 1827 urn:lsid:organismnames.com:name:4888093 Nystactes Kaup 1829 urn:lsid:organismnames.com:name:4888094 GBIF has three taxa with this name (the number is the GBIF species id): Nystactes B\u00f6hlke, 1957 2403398 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Nystactes Gloger, 1827 2475109 Nystactes Kaup, 1829 3239722 Note the differences in the name string (\"o\" versus \"\u00f6\" in \"B\u00f6hlke\", presence or absence of years and commas). To automate the mapping of names to concepts in cases like this I constructed a bipartite graph where the nodes are taxon names, divided into two sets based upon which database they came from (e.g., one set of names from ION, the other from GBIF). I then connect the nodes of the graph by edges whose weights are the similarity of the two strings computed using the longest common subsequence that the two strings share. For example, Figure 4 shows the graph for \"Nystactes\", where the nodes corresponding to ION names are enclosed in ovals, and the names from GBIF are enclosed in rectangles. Computing the maximum weighted bipartite matching of this graph creates a map between the two sets of names. Ideally GBIF should have only one entry for Nystactes because each animal name (with a few exceptions) must be unique. If a newer name has already been published before, then it should be replaced by a new name. In this case, Nystactes (B\u00f6hlke 1957) has since been replaced by Nystactichthys (B\u00f6hlke 1958), and Nystactes (Kaup 1829) by Paramyotis (Bianchi 1916). Unfortunately these changes have not yet percolated their way from the primary literature into the GBIF taxonomy. Graph depicting similarity between different authorship strings associated with the name \"Rhacophorus\". The components of this graph correspond to the name clusters recognised by BioNames. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 4 Matching taxonomic names to taxa Bipartite graph of string similarities between taxonomic names containing the string \"Nystactes\" in the ION and GBIF databases. Solid edges in the graph represent the maximum weighted bipartite matching, and define the mapping between ION name (ovals) and GBIF names (rectangles). PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 5 images : To help the user recognise the taxa being displayed images for as many taxa as possible were obtained using EOL's API, which provides access to both the images, and a mapping between GBIF and NCBI taxon concept identifiers and the corresponding record in EOL. 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t phylogenies : Phylogenies were obtained from the PhyLoTA database (http://phylota.net) (Sanderson et al. 2008). This database contains eukaryote phylogenies constructed from automatically assembled clusters of nucleotide sequences (loosely corresponding to \"genes\"). A MySQL data dump was downloaded (version 184, corresponding to the GenBank release of the same version number) and used to populate a local MySQL database. Metadata for the sequences in each phylogeny was obtained from the European Bioinformatics Institute (EBI; http://www.ebi.ac.uk), and used to populate the MySQL database with basic information such as taxon and locality information, as well as bibliographic details for the sources of the sequences. Phylogenies from PhyLOTA are rendered in an interactive viewer using the Scalable Vector Graphics (SVG) format. The user can zoom in and out, and change the drawing style. Terminal taxa with the same label have the same colour (Fig. 10). This makes it easier to recognise clusters of sequences from the same taxon (e.g., conspecific samples), as well as highlight possible errors (e.g., mislabelled or misidentified sequences). At present the colours are arbitrarily chosen, other schemes could be added in future (Lespinats and Fertil 2011). search : BioNames features a simple search interface that takes a scientific name and returns matching taxonomic names and concepts, together with any publications and phylogenies that contain the name. Figure 5 shows an example search result. Screenshot of the search results for a query BioNames. The results include names that match the query, taxon concepts from GBIF and NCBI with thumbnail images from EOL, phylogenies containing members of the genus, and relevant taxonomic publications. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 6 document display : BioNames uses the DocumentCloud (https://github.com/documentcloud/document-viewer) viewer to display both PDFs, and page images from digital archives such as BioStor and Gallica (http://gallica.bnf.fr/) (Fig. 6). journals : Much of the work in populating BioNames comprises mapping citation to string to bibliographic identifiers and, where possible, linking those citations to full text. For each journal that has a ISSN, BioNames has a corresponding web page that lists all the articles from that journal that are in the database, and provides a graphical summary of how many of those articles have been located online (Fig. 7). timeline : BioNames can display timelines of the numbers of taxonomic names published in higher taxonomic groups, inspired by Taxatoy (Sarkar et al. 2008) (Fig. 8). For a given node in the 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t taxonomic hierarchy the children of that node are displayed as a treemap where the size of each cell is proportional to the log of the number of taxa in the subtree rooted on that child taxon. The number of names in that taxon published in each year is displayed as an interactive chart. Clicking on an individual year will list the corresponding publications for that year. taxa : Each GBIF or NCBI taxon in BioNames has a corresponding web page that lists the associated taxonomic names, publications linked to those names, and other relevant data (e.g., Fig. 9). dashboard : The BioNames web site features a \"dashboard\" which displays various summaries of the data it contains. For example, Fig. 11 shows a bubble chart of the number of articles different publishers have made available online. \"Publisher\" in this context is broadly defined to include digital 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t archives such as BioStor and JSTOR, repositories using DSpace, and commercial publishers such as Elsevier, Informa UK, Magnolia Press, Springer, and Wiley. 273 274 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t links : BioNames makes extensive use of identifiers to clean and link data, but the real value of identifiers becomes apparent when they are shared, that is, when different databases use the same identifiers for the same entities, instead of minting their own. Reusing identifiers can enable unexpected connections between databases. For example, the PubMed biomedical literature database has a record (PMID:948206) for the paper \"Monograph on \u2018Lithoglyphopsis\u2019 aperta, the snail host of Mekong River Schistosomiasis\" (Davis et al. 1976). The PubMed record contains the abstract for the paper, but not a link to where the user can obtain a digital version of the paper. However, this reference is in a volume that has been scanned by the Biodiversity Heritage Library, and the article has been extracted by BioStor (http://biostor.org/reference/102054). If PubMed was linked to BHL, users of PubMed could go straight to the content of the article. But this is just the start. The Davis et al. paper also mentions museum specimens in the collection of the Academy of Natural Sciences of Drexel University, Philadelphia. Metadata for these specimens has been aggregated by GBIF, and the BioStor page for this article displays those links (http://biostor.org/reference/102054). In an ideal world we should be able seamlessly to traverse the path PubMed \u2192 BioStor \u2192 GBIF. Likewise, we should be able to traverse the path in the other direction. At present, a user of GBIF simply sees metadata for these specimens and a 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t locality map. They are unaware that these specimens have been cited in a paper (Davis et al. 1976) which demonstrates that the snails host the Mekong River schistosome. This connection would be trivial to make if the reciprocal link was made: GBIF \u2192 BioStor. Furthermore, a link BioStor \u2192 PubMed would give us access to Medical Subject Headings (MeSH) for the schistosome paper. Hence we could imagine ultimately searching a database of museum specimens (GBIF) using queries from a controlled vocabulary of biomedical terms (MeSH). Making these connections requires not only that we have digital identifiers, but also that where ever possible we reuse existing identifiers. In practice forging these links can be hard work (Page 2011a), and many links may be missing from existing databases (Miller et al. 2009). However, if we restrict ourselves to project-specific identifiers then we stymie attempts to create a network of connected biodiversity data. text mining : Much of the value of a scientific publication lies dormant unless it is accessible to text mining, which requires access to full text. Where possible BioNames stores information on the publisher of each article (Fig. 11), which could then be used to prioritise discussions with publishers on gaining access to full text (Van Noorden 2012). Fortunately, the single largest \"publisher\" of content in BioNames is BioStor (Page 2011b), which contains scans and OCR text from the Biodiversity Heritage Library. BHL makes its content available under a Creative Commons license, and so can be readily mined. Indeed, the text has already been indexed by tools that can recognise taxonomic names (Akella et al. 2012). 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t dark taxa : One of the original motivations for constructing BioNames is the rise of \"dark taxa\" in genomics databases (Page 2011c). These are taxa that have been sequenced and added to GenBank, but which lack formal Linnaean names. Typically they will have a name that comprises a genus name and some combination of letters and numbers to make the name unique within GenBank (e.g. a 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t specimen code or the first letter of the lastnames of the researchers that deposited the sequence). It is clear that some dark taxa do, in fact, have names. For example, consider the frog \"Gephyromantis aff. blanci MV-2005\" (NCBI taxonomy id 321743), which has a single DNA sequence AY848308 associated with it. This sequence was published as part of a DNA barcoding study (Vences et al. 2005). If we enter the accession number AY848308 into Google we find two documents, one the supplementary table for (Vences et al. 2005), the other a subsequent paper (Vences and Riva 2007) that describes the frog with this sequence as a new species, Gephyromantis runewsweeki. This example is relatively straightforward, but it still required significant time to track down the species description. A key question facing attempts to find names for dark taxa is whether the methods available can be scaled to handle the magnitude of the problem. Alternatively, one could argue that newer technologies such as DNA barcoding make classical taxonomy less relevant, and perhaps the effort in digitising older literature and exposing the taxonomic names it contains is misplaced. A counter argument would be that the taxonomic literature potentially contains a wealth of information on ecology, morphology and behaviour, often for taxa in areas that have been subsequently altered by human activity. Given the rarity of many taxa (Lim et al. 2011), and the uneven taxonomic and geographic distribution of taxonomic expertise (May 1998; Gaston and May 1992), for many species the only significant data on their biology may reside in the legacy literature (possibly under a different name (Solow et al. 1995)). As this legacy becomes more accessible through projects such as BHL (and services that build upon that project; Page 2011a) there will be considerable opportunities to mine that literature for basic biological data (Thessen et al. 2012). 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t publishing platform : Recently some taxonomic journals have begun to mark up taxonomic names and descriptions (Penev et al. 2010), which is a precursor to linking names and data together. But these developments leave open the problem of what these links will point to. If we have a database of all taxonomic names and the associated literature (such as BioNames aims to be for zoological names), then such a database would provide an obvious destination for those links. Indeed, ultimately, we could envisage publishing new taxonomic publications within such a database, so that each new publication becomes simply another document within the database (Gerstein and Junker 2002). In the same way, we could use automated methods to extend the process of tagging names, specimens and literature cited to the legacy literature (Page 2010), so that the entire body of taxonomic knowledge becomes a single interwoven web of names, citations, publications, and data. taberlet, p., coissac, e., pompanon, f., brochmann, c., & willerslev, e. : (2012). Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21(8), 2045\u20132050. doi:10.1111/j.1365-294X.2012.05470.x 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Thessen, A. E., Cui, H., & Mozzherin, D. (2012). Applications of Natural Language Processing in Biodiversity Science. Advances in Bioinformatics, 2012, 1\u201317. doi:10.1155/2012/391574 Van de Sompel, H., & Beit-Arie, O. (2001). Open Linking in the Scholarly Information Environment Using the OpenURL Framework. D-Lib Magazine, 7(3). doi:10.1045/march2001-vandesompel Van Noorden, R. (2012). Trouble at the text mine. Nature, 483(7388), 134\u2013135. doi:10.1038/483134a Vences M, Riva IDL (2007) A new species of Gephyromantis from Ranomafana National Park, south-eastern Madagascar (Amphibia, Anura, Mantellidae). Spixiana 30(1): 135-143. Vences, M., Thomas, M., van der Meijden, A., Chiari, Y., & Vieites, D. R. (2005).Frontiers in Zoology, 2(1), 5. doi:10.1186/1742-9994-2-5 W\u00e4gele, H., Klussmann-Kolb, A., Kuhlmann, M., Haszprunar, G., Lindberg, D., Koch, A., & W\u00e4gele, J. W. (2011). The taxonomist - an endangered race. A practical proposal for its survival. Frontiers in Zoology, 8(1), 25. doi:10.1186/1742-9994-8-25 Werner, Y. L. (2006). The case of impact factor versus taxonomy: a proposal. Journal of Natural History, 40(21-22), 1285\u20131286. doi:10.1080/00222930600903660 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Yan, K.-K., & Gerstein, M. (2011). The Spread of Scientific Information: Insights from the Web Usage Statistics in PLoS Article-Level Metrics. (A. Vespignani, Ed.)PLoS ONE, 6(5), e19917. doi:10.1371/journal.pone.0019917 Zhang, Z.-Q. (2006). The making of a mega-journal in taxonomy. Zootaxa, 1385, 67-68. 537 538 539 540 PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 1 taxonomy data model : Simplified diagram of the relationships between the core entities that make up taxonomy, such as authors, publications, taxon names, and taxa. Relationships between entities are represented by lines, those in black are the focus of BioNames. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 2 rdf for taxon name : The RDF retrieved by dereferencing the LSID urn:lsid:organismnames.com:name:371873, which identifies the taxonomic name Pinnotheres atrinicola. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 3 displaying an article : Screenshot of BioNames displaying a document from BioStor (Conle and Hennemann 2002). The document viewer can display page images, thumbnails, and (where available) text. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 7 Screenshot of the page in BioNames for the journal Proceedings of the Entomological Society of Washington (ISSN 0013-8797). The centre column lists the articles in a volume selected by the user using the index on the left. The right hand column displays basic data about the journal, and a graphical display of how many articles have been mapped to a globally unique identifier. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 8 Timeline of taxonomic names for birds Screenshot of the distribution overtime of publications of new names for birds (Aves). The treemap on the left displays taxa below Aves in the taxonomic hierarchy, the chart on the right displays the number of publications in each year that publish a new bird name. The user has clicked on \"2012\", resulting in a list of the papers published in that year appearing below the timeline. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 9 bibliography for a taxon : Screenshot of the bibliography tab on a taxon page in BioNames. This example shows the publications relevant to the bat genus Rousettus, including those for synonyms. The user can select publications from a given time slice and/or combination of synonyms. PeerJ reviewing PDF | (v2013:08:749:1:0:NEW 2 Oct 2013) R ev ie w in g M an us cr ip t Figure 10",
    "v2_text": "results : BioNames comprises a CouchDB database and a web interface. Key features of the interface are outlined below. acknowledgements : I thank Ryan Schenk for his work on the BioNames, and Cyndy Parr (EOL) for managing the EOL Computational Challenge and providing helpful feedback on the development of BioNames. Some of the ideas in this manuscript were first explored in a talk at the \"Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond\" symposium held at The Natural History Museum, London, October 28th 2011. I thank Ellinor Michel for the invitation to speak at that meeting. 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t discussion : The EOL Computational Data Challenge imposed a deadline on the first release of BioNames, however development of both the database and web interface is ongoing. Below I discuss some potential applications and future directions. impact of taxonomic literature : The taxonomic community has long felt disadvantaged by the role of citation-based \"impact factor\" in assessing the importance of taxonomic research (Garfield 2001; Krell 2000; Werner 2006) especially as much of the taxonomic literature appears in relatively low-impact journals. A common proposal is to include citations to the taxonomic authority for every name mentioned in a scientific paper (W\u00e4gele et al. 2011). Regardless of the merits of this idea, in practice these citations are often hard to locate, which is another motivation for BioNames. There is additional value in surfacing identifiers for the taxonomic literature. In addition to helping construct citation networks, global identifiers can facilitate computing other measures of the value of a taxonomic paper. There is a growing interest in additional measures of postpublication impact of a publication in terms of activity such as social bookmarking, and commentary on web sites (\"alt-metrics\") (Yan and Gerstein 2011). Gathering these metrics is greatly facilitated by using standard bibliographic identifiers (otherwise, how do we know whether two commentators are discussing the same article or not?). If taxonomic literature is be part of this burgeoning conversation then it needs to be able to be identified unambiguously. taxon names : At present the taxonomic scope of BioNames is restricted to names covered by the International Code of Zoological Nomenclature (animals and those eukaryotes not covered by the International Code of Nomenclature for algae, fungi, and plants). Taxonomic names were obtained from the Index of Organism Names (ION; http://www.organismnames.com). Each name in ION has a Life Science Identifier (LSID) (Martin et al. 2005) which uniquely identifies that name. LSIDs can be dereferenced to return metadata in Resource Description Framework format (RDF) (Page 2008b). ION LSIDs provide basic information on a taxonomic name using the TDWG Taxon Name LSID Ontology (http://rs.tdwg.org/ontology/voc/TaxonName), in many cases including bibliographic details for the publication where the name first appeared (Fig. 2). The publication in which the name first appeared is listed in the contents of the \"PublishedIn\" property. In the example in Figure 2 this is the string \"Description of a new species of Pinnotheres, and redescription of P. novaezelandiae (Brachyura: Pinnotheridae). New Zealand Journal of Zoology, 10(2) 1983: 151-162. 158 (Zoological Record Volume 120)\". I used regular expressions to parse citation strings into their component parts (e.g., article title, journal, volume, pagination), and then attempted to locate the corresponding reference in an external database (see below). 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t database : Once aggregated, cleaned, and reconciled, the data was converted to JSON (JavaScript Object Notation) and stored in a CouchDB database. CouchDB is a \"NoSQL\" document database that stores objects in JSON format. Unlike typical SQL databases, CouchDB does not have a database schema and does not support ad hoc queries. Instead CouchDB accepts semi-structured documents, and the user defines fixed queries or \"views\" (Anderson et al. 2010). phylogeny viewer : Screenshot of phylogeny from PhyLoTA as displayed in BioNames. The user can zoom in and out and pan, as well as change the layout of the tree. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 11 Relative importance of different publishers of taxonomic literature Bubble chart showing relative numbers of taxonomic articles made available online by different publishers. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t availability : BioNames is accessible at http://bionames.org. The source code used to build the web site is available on GitHub http://github.com/rdmpage/bionames. Scripts used to fetch, clean, and reconcile the data are archived in http://github.com/rdmpage/bionames-data eol challenge : In response to the Encyclopedia of Life (EOL) Computational Data Challenge (http://eol.org/info/323) I constructed BioNames (http://bionames.org) (Page 2012). Its goal is to create a database of taxonomic names linked to the primary literature and, wherever possible, to phylogenetic trees. Using existing globally unique identifiers for taxonomic names, concepts, publications, and sequences rather than cryptic text strings (for example, abbreviated bibliographic citations) simplifies the task of linking \u2014 we can rely on exact matching of identifiers rather than approximate matching between names for what may or may not be the same entity. This is particularly relevant once we start to aggregate information from different databases, where the same information (e.g., a publication) may be represented by different strings. Furthermore, if we use existing identifiers we increase the potential to connect to other databases (Page 2008a). This paper outlines how BioNames was built, describes the user interface, and discusses future plans. Materials & Methods 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t BioNames integrates data on taxonomic names and classifications, literature, and phylogenies from a variety of sources. Given the inevitable differences in how different databases treat the same data (as well as internal inconsistencies within individual databases), considerable effort must be spent cleaning and reconciling data. Much of this process involves mapping \"strings\" to \"things\" (Bollacker et al. 2008), or more precisely, mapping strings to identifiers for things. bibliographic identifiers : When populating BioNames every effort has been made to map each bibliographic string to a corresponding identifier, such as a Digital Object identifier (DOI). While DOIs are the bestknown bibliographic identifier, there are several others that are relevant to the taxonomic literature (Page 2009). DOIs are themselves based on Handles (http://hdl.handle.net), an identifier widely used by digital repositories such as DSpace (Smith et al. 2003). A number of journals, such as the Bulletins and Novitates of the American Museum of Natural History are available in DSpace repositories and consequently have Handles. Other major archives such as JSTOR (http://www.jstor.org/) and the Japanese National Institute of Informatics (CiNii; http://ci.nii.ac.jp/) have their own unique identifiers (typically integer numbers that are part of a URL). Having a variety of identifiers can complicate the task of finding existing identifiers for a particular publication. Whereas for some identifiers, such as DOIs and CiNii NAIDs (National Institute of Informatics Article IDs) there are OpenURL resolvers for this task (Van de Sompel & Beit-Arie 2001), for other identifiers there may be no obvious way to find the identifier other than by using a search engine. For the example in Figure 2, the citation string \"Description of a new species of Pinnotheres, and redescription of P. novaezelandiae (Brachyura: Pinnotheridae). New Zealand Journal of Zoology, 10(2) 1983: 151-162. 158 (Zoological Record Volume 120)\" corresponds to the article with the DOI 10.1080/03014223.1983.10423904. Once we have a DOI, we can then use services such as those provided by CrossRef (http://www.crossref.org) to retrieve author and publisher information for an article (see Fig. 11 below for one use of publisher information). 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Identifiers also exist for aggregations of publications, such as journals. The historical practice of abbreviating journal titles in citations has led to a plethora of ways to refer to the same journal. For example, the BioStor database (http://biostor.org; Page 2011b) has accumulated more than ten variations on the name of the journal Bulletin of Zoological Nomenclature (such as \"Bull Zool Nomen\", \"Bull Zool Nom.\", \"Bull. Zool. Nomencl.\", etc.). This practice, presumably motivated by the desire to conserve space on the printed page, complicates efforts to match citations to identifiers. One approach to tackling this problem is to map abbreviations to journal-level globally unique identifiers, such as International Standard Serial Numbers (ISSNs) (for the Bulletin of Zoological Nomenclature the ISSN is 0007-5167). In addition to reducing ambiguity, there are web services such as that provided by WorldCat (http://www.worldcat.org) that take ISSNs and return the history of name changes for a journal, which in turn can help clarify the (often complicated) history of long-lived journals. documents : Taxonomic publications are available under a variety of licenses, ranging from explicitly open access licenses (MacCallum 2007) to articles that are \"free\", to articles that are behind a paywall. Archives such as JSTOR and CiNii have a mixture of free and subscription-based content. Many smaller journals, often published by scientific societies, are providing their content online for free, if not explicitly under an open license. The Biodiversity Heritage Library (the single largest source of taxonomic articles in BioNames, Fig. 11) makes its content available under a Creative Commons license. Where PDFs were available online either \"for free\" or under open access, these were downloaded and locally cached. Pages were extracted and converted into bitmap images for subsequent display in a web browser. 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Closed-access publications that are available online are linked to by their identifier (e.g., DOI). Access to some of these publications may be available for short-term \"rent\" by services such as DeepDyve (http://www.deepdyve.com): where possible BioNames includes a link those services. clustering taxonomic names : Taxonomic names comprise a \"canonical\" name and the name's authorship, for example Homo sapiens Linnaeus comprises the canonical name \"Homo sapiens\" and the authorship string \"Linnaeus\". Names in taxonomic databases such as ION display numerous variations in spelling of authors, and instances of the same canonical name published by different authors (e.g., homonyms), so the names were clustered before populating BioNames. For each set of taxon names with the same canonical name the authorship was compared. If one name lacked an author and the other had an author, the names were automatically merged into a cluster. Given more than two names a graph was constructed where the nodes are the authorship strings, and a pair of nodes is connected if their corresponding strings were sufficiently similar. String similarity was computed by converting the strings to a \"finger print\" comprising lower case letters with all accented characters replaced by non-accented equivalents, and all punctuation removed, then finding the longest common subsequence of the two strings. If the length of the subsequence relative to the input strings was longer than a specified threshold (by default, 0.8, where identical strings have a similarity of 1.0) then the two author strings were connected by an edge in the graph. The components of the graph correspond to clusters of names with similar authorship strings, and were treated as being the same name. Figure 3 shows a graph for the different names that all have \"Rhacophorus\" as the canonical name. 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Graph depicting similarity between different authorship strings associated with the name \"Rhacophorus\". The components of this graph correspond to the name clusters recognised by BioNames. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 4 Matching taxonomic names to taxa Bipartite graph of string similarities between taxonomic names containing the string \"Nystactes\" in the ION and GBIF databases. Solid edges in the graph represent the maximum weighted bipartite matching, and define the mapping between ION and GBIF names. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 5 mapping names to taxa : BioNames includes two taxonomic classifications, sourced from GBIF (http://uat.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c) and NCBI (ftp://ftp.ncbi.nih.gov/pub/taxonomy), respectively. These provide the user with a way to navigate through taxonomic names, as well as view data associated with each classification (e.g., phylogenies). Ideally there would be a one-to-one mapping between a taxonomic name and a taxon, but complications often arise. In addition to the well-known problems of synonymy (more than one name for the same taxon) and homonymy (the same name used for different taxa), name and taxon databases may store slightly different representations of the same name. For example, ION has four records for the name \"Nystactes\" (each name is followed by its LSID): Nystactes urn:lsid:organismnames.com:name:2787598 Nystactes Bohlke urn:lsid:organismnames.com:name:2735131 Nystactes Gloger 1827 urn:lsid:organismnames.com:name:4888093 Nystactes Kaup 1829 urn:lsid:organismnames.com:name:4888094 GBIF has three taxa with this name (the number is the GBIF species id): Nystactes B\u00f6hlke, 1957 2403398 Nystactes Gloger, 1827 2475109 Nystactes Kaup, 1829 3239722 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Note the differences in the name string (\"o\" versus \"\u00f6\" in \"B\u00f6hlke\", presence or absence of years and commas). To automate the mapping of names to concepts in cases like this I constructed a bipartite graph where the nodes are taxon names, divided into two sets based upon which database they came from (e.g., one set of names from ION, the other from GBIF). I then connect the nodes of the graph by edges whose weights are the similarity of the two strings computed using the longest common subsequence that the two strings share. For example, Figure 4 shows the graph for \"Nystactes\". Computing the maximum weighted bipartite matching of this graph creates a map between the two sets of names. Ideally GBIF should have only one entry for Nystactes because each animal name (with a few exceptions) must be unique. If a newer name has already been published before, then it should be replaced by a new name. In this case, Nystactes (B\u00f6hlke 1957) has since been replaced by Nystactichthys (B\u00f6hlke 1958), and Nystactes (Kaup 1829) by Paramyotis (Bianchi 1916). Unfortunately these changes have not yet percolated their way from the primary literature into the GBIF taxonomy. images : To help the user recognise the taxa being displayed images for as many taxa as possible were obtained using EOL's API, which provides access to both the images, and a mapping between GBIF and NCBI taxon concept identifiers and the corresponding record in EOL. phylogenies : Phylogenies were obtained from the PhyLoTA database (http://phylota.net) (Sanderson et al. 2008). This database contains eukaryote phylogenies constructed from automatically assembled clusters of nucleotide sequences (loosely corresponding to \"genes\"). A MySQL data dump was 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t downloaded (version 184, corresponding to the GenBank release of the same version number) and used to populate a local MySQL database. Metadata for the sequences in each phylogeny was obtained from the European Bioinformatics Institute (EBI; http://www.ebi.ac.uk), and used to populate the MySQL database with basic information such as taxon and locality information, as well as bibliographic details for the sources of the sequences. Phylogenies from PhyLOTA are rendered in an interactive viewer using the Scalable Vector Graphics (SVG) format. The user can zoom in and out, and change the drawing style. Terminal taxa with the same label have the same colour (Fig. 10). This makes it easier to recognise clusters of sequences from the same taxon (e.g., conspecific samples), as well as highlight possible errors (e.g., mislabelled or misidentified sequences). At present the colours are arbitrarily chosen, other schemes could be added in future (Lespinats and Fertil 2011). search : BioNames features a simple search interface that takes a scientific name and returns matching taxonomic names and concepts, together with any publications and phylogenies that contain the name. Figure 5 shows an example search result. 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Screenshot of the search results for a query BioNames. The results include names that match the query, taxon concepts from GBIF and NCBI with thumbnail images from EOL, phylogenies containing members of the genus, and relevant taxonomic publications. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 6 document display : BioNames uses the DocumentCloud (https://github.com/documentcloud/document-viewer) viewer to display both PDFs, and page images from digital archives such as BioStor and Gallica (http://gallica.bnf.fr/) (Fig. 6). journals : Much of the work in populating BioNames comprises mapping citation to string to bibliographic identifiers and, where possible, linking those citations to full text. For each journal that has a ISSN, BioNames has a corresponding web page that lists all the articles from that journal that are in the database, and provides a graphical summary of how many of those articles have been located online (Fig. 7). timeline : BioNames can display timelines of the numbers of taxonomic names published in higher taxonomic groups, inspired by Taxatoy (Sarkar et al. 2008) (Fig. 8). For a given node in the taxonomic hierarchy the children of that node are displayed as a treemap where the size of each cell is proportional to the log of the number of taxa in the subtree rooted on that child taxon. The number of names in that taxon published in each year is displayed as an interactive chart. Clicking on an individual year will list the corresponding publications for that year. 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t taxa : Each GBIF or NCBI taxon in BioNames has a corresponding web page that lists the associated taxonomic names, publications linked to those names, and other relevant data (e.g., Fig. 9). dashboard : The BioNames web site features a \"dashboard\" which displays various summaries of the data it contains. For example, Fig. 11 shows a bubble chart of the number of articles different publishers have made available online. \"Publisher\" in this context is broadly defined to include digital archives such as BioStor and JSTOR, repositories using DSpace, and commercial publishers such as Elsevier, Informa UK, Magnolia Press, Springer, and Wiley. 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t links : BioNames makes extensive use of identifiers to clean and link data, but the real value of identifiers becomes apparent when they are shared, that is, when different databases use the same identifiers for the same entities, instead of minting their own. Reusing identifiers can enable unexpected connections between databases. For example, the PubMed biomedical literature database has a record (PMID:948206) for the paper \"Monograph on \u2018Lithoglyphopsis\u2019 aperta, the snail host of Mekong River Schistosomiasis\" (Davis et al. 1976). The PubMed record contains the abstract for the paper, but not a link to where the user can obtain a digital version of the paper. However, this reference is in a volume that has been scanned by the Biodiversity Heritage Library, and the article has been extracted by BioStor (http://biostor.org/reference/102054). If PubMed was linked to BHL, users of PubMed could go straight to the content of the article. But this is just the start. The Davis et al. paper also mentions museum specimens in the collection of the Academy of Natural Sciences of Drexel University, Philadelphia. Metadata for these specimens has been aggregated by GBIF, and the BioStor page for this article displays those links (http://biostor.org/reference/102054). In an ideal world we should be able seamlessly to traverse the path PubMed \u2192 BioStor \u2192 GBIF. Likewise, we should be able to traverse the path in the other direction. At present, a user of GBIF simply sees metadata for these specimens and a 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t locality map. They are unaware that these specimens have been cited in a paper (Davis et al. 1976) which demonstrates that the snails host the Mekong River schistosome. This connection would be trivial to make if the reciprocal link was made: GBIF \u2192 BioStor. Furthermore, a link BioStor \u2192 PubMed would give us access to Medical Subject Headings (MeSH) for the schistosome paper. Hence we could imagine ultimately searching a database of museum specimens (GBIF) using queries from a controlled vocabulary of biomedical terms (MeSH). Making these connections requires not only that we have digital identifiers, but also that where ever possible we reuse existing identifiers. In practice forging these links can be hard work (Page 2011a), and many links may be missing from existing databases (Miller et al. 2009). However, if we restrict ourselves to project-specific identifiers then we stymie attempts to create a network of connected biodiversity data. text mining : Much of the value of a scientific publication lies dormant unless it is accessible to text mining, which requires access to full text. Where possible BioNames stores information on the publisher of each article (Fig. 11), which could then be used to prioritise discussions with publishers on gaining access to full text (Van Noorden 2012). Fortunately, the single largest \"publisher\" of content in BioNames is BioStor (Page 2011b), which contains scans and OCR text from the Biodiversity Heritage Library. BHL makes its content available under a Creative Commons license, and so can be readily mined. Indeed, the text has already been indexed by tools that can recognise taxonomic names (Akella et al. 2012). 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t dark taxa : One of the original motivations for constructing BioNames is the rise of \"dark taxa\" in genomics databases (Page 2011c). It is clear that some dark taxa do, in fact, have names. For example, consider the frog \"Gephyromantis aff. blanci MV-2005\" (NCBI taxonomy id 321743), which has a single DNA sequence AY848308 associated with it. This sequence was published as part of a 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t DNA barcoding study (Vences et al. 2005). If we enter the accession number AY848308 into Google we find two documents, one the supplementary table for (Vences et al. 2005), the other a subsequent paper (Vences and Riva 2007) that describes the frog with this sequence as a new species, Gephyromantis runewsweeki. This example is relatively straightforward, but it still required significant time to track down the species description. A key question facing attempts to find names for dark taxa is whether the methods available can be scaled to handle the magnitude of the problem. Alternatively, one could argue that newer technologies such as DNA barcoding make classical taxonomy less relevant, and perhaps the effort in digitising older literature and exposing the taxonomic names it contains is misplaced. A counter argument would be that the taxonomic literature potentially contains a wealth of information on ecology, morphology and behaviour, often for taxa in areas that have been subsequently altered by human activity. Given the rarity of many taxa (Lim et al. 2011), and the uneven taxonomic and geographic distribution of taxonomic expertise (May 1998; Gaston and May 1992), for many species the only significant data on their biology may reside in the legacy literature (possibly under a different name (Solow et al. 1995)). As this legacy becomes more accessible through projects such as BHL (and services that build upon that project; Page 2011a) there will be considerable opportunities to mine that literature for basic biological data (Thessen et al. 2012). publishing platform : Recently some taxonomic journals have begun to mark up taxonomic names and descriptions (Penev et al. 2010), which is a precursor to linking names and data together. But these developments leave open the problem of what these links will point to. If we have a database of 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t all taxonomic names and the associated literature (such as BioNames aims to be for zoological names), then such a database would provide an obvious destination for those links. Indeed, ultimately, we could envisage publishing new taxonomic publications within such a database, so that each new publication becomes simply another document within the database (Gerstein and Junker 2002). In the same way, we could use automated methods to extend the process of tagging names, specimens and literature cited to the legacy literature (Page 2010), so that the entire body of taxonomic knowledge becomes a single interwoven web of names, citations, publications, and data. taberlet, p., coissac, e., pompanon, f., brochmann, c., & willerslev, e. : (2012). Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21(8), 2045\u20132050. doi:10.1111/j.1365-294X.2012.05470.x Thessen, A. E., Cui, H., & Mozzherin, D. (2012). Applications of Natural Language Processing in Biodiversity Science. Advances in Bioinformatics, 2012, 1\u201317. doi:10.1155/2012/391574 Van de Sompel, H., & Beit-Arie, O. (2001). Open Linking in the Scholarly Information Environment Using the OpenURL Framework. D-Lib Magazine, 7(3). doi:10.1045/march2001-vandesompel Van Noorden, R. (2012). Trouble at the text mine. Nature, 483(7388), 134\u2013135. doi:10.1038/483134a Vences M, Riva IDL (2007) A new species of Gephyromantis from Ranomafana National Park, south-eastern Madagascar (Amphibia, Anura, Mantellidae). Spixiana 30(1): 135-143. Vences, M., Thomas, M., van der Meijden, A., Chiari, Y., & Vieites, D. R. (2005).Frontiers in Zoology, 2(1), 5. doi:10.1186/1742-9994-2-5 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t W\u00e4gele, H., Klussmann-Kolb, A., Kuhlmann, M., Haszprunar, G., Lindberg, D., Koch, A., & W\u00e4gele, J. W. (2011). The taxonomist - an endangered race. A practical proposal for its survival. Frontiers in Zoology, 8(1), 25. doi:10.1186/1742-9994-8-25 Werner, Y. L. (2006). The case of impact factor versus taxonomy: a proposal. Journal of Natural History, 40(21-22), 1285\u20131286. doi:10.1080/00222930600903660 Yan, K.-K., & Gerstein, M. (2011). The Spread of Scientific Information: Insights from the Web Usage Statistics in PLoS Article-Level Metrics. (A. Vespignani, Ed.)PLoS ONE, 6(5), e19917. doi:10.1371/journal.pone.0019917 498 499 500 501 502 503 504 505 PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 1 taxonomy data model : Simplified diagram of the relationships between the core entities that make up taxonomy, such as authors, publications, taxon names, and taxa. Relationships between entities are represented by lines, those in black are the focus of BioNames. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 2 rdf for taxon name : The RDF retrieved by dereferencing the LSID urn:lsid:organismnames.com:name:371873, which identifies the taxonomic name Pinnotheres atrinicola. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 3 displaying an article : Screenshot of BioNames displaying a document from BioStor (Conle and Hennemann 2002). The document viewer can display page images, thumbnails, and (where available) text. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 7 Screenshot of the page in BioNames for the journal Proceedings of the Entomological Society of Washington (ISSN 0013-8797). The centre column lists the articles in a volume selected by the user using the index on the left. The right hand column displays basic data about the journal, and a graphical display of how many articles have been mapped to a globally unique identifier. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 8 Timeline of taxonomic names for birds Screenshot of the distribution overtime of publications of new names for birds (Aves). The treemap on the left displays taxa below Aves in the taxonomic hierarchy, the chart on the right displays the number of publications in each year that publish a new bird name. The user has clicked on \"2012\", resulting in a list of the papers published in that year appearing below the timeline. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 9 bibliography for a taxon : Screenshot of the bibliography tab on a taxon page in BioNames. This example shows the publications relevant to the bat genus Rousettus, including those for synonyms. The user can select publications from a given time slice and/or combination of synonyms. PeerJ reviewing PDF | (v2013:08:749:0:0:REVIEW 28 Aug 2013) R ev ie w in g M an us cr ip t Figure 10",
    "url": "https://peerj.com/articles/191/reviews/",
    "review_1": "William Jungers \u00b7 Oct 8, 2013 \u00b7 Academic Editor\nACCEPT\nThank you for your cooperation in the review process. I think the reviewer suggestions and your corresponding emendations have served to improve your study substantially. The diversity of North American archaic primates is fascinating.",
    "review_2": "William Jungers \u00b7 Sep 12, 2013 \u00b7 Academic Editor\nMINOR REVISIONS\nIf theses are the best photographs the author can produce, then I think they are adequate if not \"perfect\" -- as the re-review notes.\n\nUnless you disagree, in your final version please make reference to \"the diagnostic trait for this genus.\"\nPlease try to clarify or modify text with respect to\n\"flanged\" and \"reduced\" (small, smaller, smallest?)\n\nPlease correct the statement about your characters since some lower dental features are part of the phylogenetic analysis. I urge you to reflect upon (and perhaps comment on) your decision to limit your characters to those observed only on Palaeocene species.",
    "review_3": "Mary Silcox \u00b7 Sep 11, 2013\nBasic reporting\nThe author has submitted somewhat improved versions of the images of the teeth. I think it is up to the editor to determine whether these are adequate. It is now possible to see most of the relevant morphology, so my personal assessment is that they are borderline publishable. However, I would not chose to publish an image that has residue partially coating the occlusal surface of the tooth.\nExperimental design\nI'm experiencing some confusion about the phylogenetic analysis. In his rebuttal letter, the author states that \" The character matrix is composed of only upper dental traits\", but this is clearly not true (e.g. characters 19-22 all pertain to the lower i1). In any case, it would be a terrible idea to so restrict an analysis. Authors sometimes do this on the mistaken belief that only characters that can be coded for a fossil will affect that fossil's position in a tree. But the common practice of molecular backboning shows why this idea is fallacious. Even though no fossil can be coded for molecular characters, by influencing the relationships of all the OTHER taxa in an analysis, those data will end up influencing the position of the fossil in question. This is also true for morphological data, both with respect to character partitions AND taxon sampling, which is why I think it makes no sense to restrict the analysis to species alive in the Paleocene. However, the goals of this paper are limited in scope, and the results of the analysis are not unreasonable, so this could meet the standard of publishable on those bases.\n\nThe character list is generally improved over the preceding revision, although a few characters are still not clear:\n\nch. 1: adding \"flanged\" does not help, since this is also not standard anatomical terminology.\nch. 10: the author has once again used \"reduced\", which implies an evolutionary direction, and as such is inappropriate\nValidity of the findings\nI am convinced that the species is new and pertains to Zanycteris. I'm puzzled as to why the author continues not to make reference to the diagnostic trait for this genus (i.e., anteriorly protruding parastylar lobe on M1). Surely it wouldn't be difficult to add that in? Or does he disagree?\nCite this review as\nSilcox M (2013) Peer Review #1 of \"A new species of the archaic primate Zanycteris from the late Paleocene of western Colorado and the phylogenetic position of the family Picrodontidae (v0.2)\". PeerJ https://doi.org/10.7287/peerj.191v0.2/reviews/1",
    "review_4": "William Jungers \u00b7 Jul 8, 2013 \u00b7 Academic Editor\nMAJOR REVISIONS\nTwo reviewers see real merit in your paper on these rare fossil primates, but both request much better photographs (especially since you are creating a new type specimen). Both reviewers also raise substantive issues with your phylogenetic analysis that need to be addressed (and which may require new analyses). Additional recommendations are mostly constructive, and attention to these suggestions will serve to improve the diagnosis and the discussion of its significance for primate paleobiology. Careful editing is needed to eliminate various typos and spelling errors.",
    "pdf_1": "https://peerj.com/articles/191v0.3/submission",
    "pdf_2": "https://peerj.com/articles/191v0.2/submission",
    "review_5": "Gregg F Gunnell \u00b7 Jun 30, 2013\nBasic reporting\nThis paper describes a new species of Zanycteris from the Paleocene of Colorado....it is well written and well organized and I had only a few minor comments which I detail below. In general I find no problem with publishing this paper once the minor fixes are made.\nExperimental design\nNot applicable\nValidity of the findings\nThere seems no doubt that Z. honeyi is a new species of Zanycteris - I found the ecological analysis a little wanting - I agree that the teeth of Z. honeyi are of a frugivorous animal, similar to Ariteus (often mis-spelled in the mansucript as Artiteus) - but I'm not sure why thet \"restricts the stratographic range\" of picrodontids to the middle and late Paleocene only - surely there were plenty of fruits available in the Eocene as well....all of those real primates must have been eating something in the Eocene\nAdditional comments\nI find this paper to be more or less good as it is...there are few places where it needs a little editing or rewording....\n\nThe only major complaint I have is that Figure 1 showing the holotype specimen really is unacceptable for publication - it is blurry and out of focus - the buccal view is nearly impossible to interpret at all - in this day and age of microCT scanners and microscopic imaging with stacking software surely much better images than these can be provided. Also, it looks like there is still adhering matrix on the occlusal surfaces of the molars - this should be cleaned off beofre re-imaging.\n\nAlso I have a list of otrher comments:\n\nAbstract - Ariteus is mis-spelled in fourth line from bottom\n\nMethods and Material section - \"diverse fauna of fossil mammals\" is cited in line 39 and repeated again in line 42 citing Table 1 (I didn't see Table 1 anywhere) - no need to repeat this same information twice\n\nComparisons of Z. honeyi - lines 104-105 the authors notes differnces with Picrodus - he should cite the Scott and Fox, 2005 publication here\n\nDiscussion - line 146 - I think I'd be a little less dogmatic here and say that the \"molar teeth were probably specialized for cutting....\"\n\nLine 15 - Ariteus mis-spelled again\n\nLine 155 - paracone and metacone cusps (delete the \"s\" after paracone and metacone)\n\nLines 162-165 - I see no basis for saying this - yes paromomyids and picrodontids are different dentally but no actual analysis has been done to substantiate the claim that picrodontids were limited to the middle and late Paleocene by their dental specializations - very few plesiadapiforms made it past the end of the Paleocene in general - I think I'd just drop these lines.\n\nI'm not entirely sure why yet another phylogenetic analysis is being run here - the strict consensus tree differs quiet a lot from other, more rigorous trees - there are so many polytomy's that I'm not sure I believe any of what is being depicted....also the tooth images on the tree are so small as to be unrecognizable as teeth - probably should just eliminate them\n\nThat's all I have\nCite this review as\nGunnell GF (2013) Peer Review #1 of \"A new species of the archaic primate Zanycteris from the late Paleocene of western Colorado and the phylogenetic position of the family Picrodontidae (v0.1)\". PeerJ https://doi.org/10.7287/peerj.191v0.1/reviews/1",
    "pdf_3": "https://peerj.com/articles/191v0.1/submission",
    "review 6": "Mary Silcox \u00b7 Jun 17, 2013\nBasic reporting\nPicrodontids are incredibly rare primates, so this paper is certainly worthy of publication. However, there are a few significant issues with the paper that need to be addressed before it can be published. Most serious, the argument for the attribution to Zanycteris is not clearly made. As discussed by both Silcox and Gunnell (2008) and Scott and Fox (2005) the key diagnostic difference between this genus and Picrodus is an anteriorly protruding parastylar lobe in the former, and yet the author suggests that the new specimen belongs in Zanycteris on the basis of a \u201cshorten [sic] parastyle\u201d. Looking at the image, I think that the specimen is actually Zanycteris and does have an anteriorly protruding parastylar lobe, but this certainly isn\u2019t clear in the discussion. What\u2019s more, the image of the specimen is very poor, which makes it difficult to determine if the description as presented is correct. For example, I really can\u2019t tell if the M2 is complete or broken buccally\u2014this is critically important since the relative size of M1 vs. M2 is the key diagnostic trait for the new species. In the buccal view it is impossible to tell tooth from bone\u2014I actually think it would be okay to just cut this figure. For upper teeth, a buccal view isn\u2019t really needed. In the occlusal view it is clear that the specimen has been terribly over-whitened, so that there is a thick layer of whitening material coating the whole specimen, with beaded up material obscuring a good part of the morphology. My guess is that moisture either on the specimen, or in the bulb of the whitening tube, caused the powder to bead up. The image is also somewhat out of focus. Simply put, Figure 1 is not publishable as is. The specimen needs to be cleaned, and a much lighter layer of whitening used. Alternatively, an SEM or microCT image could be substituted. A few more minor details: Abstract, line 5: should be \u201cBY a single specimen\u201d\nAbstract line 6: should be \u201cshortenED parastyle\u201d\nAbstract line 9: should be \u201csimilarLY sized upper second molar\u201d\nAbstract line 12: should be cristid obliqua, not cristid oblique Line 20: \u201cmore recently studies\u2026\u201d requires a reference \u2013the key paper here is Szalay 1968\nLine 25: should be \u201cis strengthenED by the\u2026\u201d\nLine 28: \u201cThe enlarged incisor is considered a synapomorphy of Plesiadapiformes\u2026\u201d Clemens did suggest this, but Plesiadapiformes has never come out as a monophyletic group (in a holophyletic sense, i.e., excluding euprimates or Dermoptera) in any cladistic analysis. And it doesn\u2019t come out as demonstrably monophyletic in your own results\u2014Purgatorius is part of an unresolved polytomy with the rest of the plesiadapiforms and Plagiomenidae, Apatemyidae etc. For this reason, it is inappropriate to talk about this character as a synapomorphy, at least without a qualification.\nLine 31: refs are needed for the time span of picrodontids (i.e., after \u201cin North America\u201d)\nLine 69: It is standard to include several more layers in the systematic paleontology listing (e.g., at a minimum Order and Family)\nLine 94: It is unclear what \u201cthe broad protocone spreads into the postprotocrista\u201d means. Clarify.\nLines 163, 164: when used informally, taxonomic names should not be capitalized (e.g., should be paromomyids and picrodontids)\nFigure 2: \u201cElpidophorus\u201d and \u201cstonleyi\u201d are spelled incorrectly\nExperimental design\nWith respect to the phylogenetic analysis, it seems strange to me to limit the sample to Paleocene mammals. Because of the vagaries of fossil preservation, it is not necessarily the case that younger forms are irrelevant in assessing the ancestry of older forms. This is particularly an issue with respect to the discussion about the possible ancestors of different plesiadapiform groups (lines 133-135). Without including Premnoides douglassi, the putative ancestor of Paromomyidae (see Gunnell, 1989), it really isn\u2019t appropriate to discuss the possible descendants of the mentioned palaechthonids. I\u2019m not necessarily suggesting that the author needs to expand his sample, since the systematic questions he is asking here are fairly limited in scope. However, he should resist the temptation to over-interpret the results. There are also a number of issues of clarity with the character list that need to be addressed: Character 1: not clear what is meant by a \u201cwinged postcingulum\u201d\u2014this is not standard dental terminology. Please define and clarify. Character 4: how close to they need to be in size for it to be \u201cnearly\u201d? Define more precisely. Characters 5, 6, 12: These characters are essentially written as double negatives (i.e., the \u201cpresent\u201d state implies the absence of something), which is confusing, and non-standard. Re-write (e.g., \u201cPostprotocrista on M2 Present = 0, Absent = 1) Character 7: \u201creduced\u201d implies an evolutionary direction. Define based on observed morphology (e.g., short) Characters 8, 13, 14: It is inappropriate and imprecise to make reference to a particular genus in the definition of a character. Describe what\u2019s there. Character 10: It is a bad idea to combine two potentially independent elements of morphology in a single character (e.g., size and position in this case) since you have no way of knowing a priori if they always covary. Character 14: groove in what position? Character 112: Not clear what is meant by \u201csmall\u201d and \u201cenlarged\u201d here. Enlarged relative to what?\nValidity of the findings\nThere is an inaccuracy in how the results are reported. On lines 127-128 the author states that \u201cThe strict consensus tree shows Zanycteris honeyi as the sister-taxa [sic] to Zanycteris paleocenus\u2026\u201d No, it doesn\u2019t\u2014the two taxa form a polytomy with Picrodus. The nature of their relationships is unresolved on the tree as presented. This must be clarified. Also, \u201ctaxa\u201d is plural\u2014it would be the sister taxON.\nAdditional comments\nI as glad to see that you named this for Jim Honey. He was a very nice man--I was sorry to hear of his passing.\nCite this review as\nSilcox M (2013) Peer Review #2 of \"A new species of the archaic primate Zanycteris from the late Paleocene of western Colorado and the phylogenetic position of the family Picrodontidae (v0.1)\". PeerJ https://doi.org/10.7287/peerj.191v0.1/reviews/2",
    "all_reviews": "Review 1: William Jungers \u00b7 Oct 8, 2013 \u00b7 Academic Editor\nACCEPT\nThank you for your cooperation in the review process. I think the reviewer suggestions and your corresponding emendations have served to improve your study substantially. The diversity of North American archaic primates is fascinating.\nReview 2: William Jungers \u00b7 Sep 12, 2013 \u00b7 Academic Editor\nMINOR REVISIONS\nIf theses are the best photographs the author can produce, then I think they are adequate if not \"perfect\" -- as the re-review notes.\n\nUnless you disagree, in your final version please make reference to \"the diagnostic trait for this genus.\"\nPlease try to clarify or modify text with respect to\n\"flanged\" and \"reduced\" (small, smaller, smallest?)\n\nPlease correct the statement about your characters since some lower dental features are part of the phylogenetic analysis. I urge you to reflect upon (and perhaps comment on) your decision to limit your characters to those observed only on Palaeocene species.\nReview 3: Mary Silcox \u00b7 Sep 11, 2013\nBasic reporting\nThe author has submitted somewhat improved versions of the images of the teeth. I think it is up to the editor to determine whether these are adequate. It is now possible to see most of the relevant morphology, so my personal assessment is that they are borderline publishable. However, I would not chose to publish an image that has residue partially coating the occlusal surface of the tooth.\nExperimental design\nI'm experiencing some confusion about the phylogenetic analysis. In his rebuttal letter, the author states that \" The character matrix is composed of only upper dental traits\", but this is clearly not true (e.g. characters 19-22 all pertain to the lower i1). In any case, it would be a terrible idea to so restrict an analysis. Authors sometimes do this on the mistaken belief that only characters that can be coded for a fossil will affect that fossil's position in a tree. But the common practice of molecular backboning shows why this idea is fallacious. Even though no fossil can be coded for molecular characters, by influencing the relationships of all the OTHER taxa in an analysis, those data will end up influencing the position of the fossil in question. This is also true for morphological data, both with respect to character partitions AND taxon sampling, which is why I think it makes no sense to restrict the analysis to species alive in the Paleocene. However, the goals of this paper are limited in scope, and the results of the analysis are not unreasonable, so this could meet the standard of publishable on those bases.\n\nThe character list is generally improved over the preceding revision, although a few characters are still not clear:\n\nch. 1: adding \"flanged\" does not help, since this is also not standard anatomical terminology.\nch. 10: the author has once again used \"reduced\", which implies an evolutionary direction, and as such is inappropriate\nValidity of the findings\nI am convinced that the species is new and pertains to Zanycteris. I'm puzzled as to why the author continues not to make reference to the diagnostic trait for this genus (i.e., anteriorly protruding parastylar lobe on M1). Surely it wouldn't be difficult to add that in? Or does he disagree?\nCite this review as\nSilcox M (2013) Peer Review #1 of \"A new species of the archaic primate Zanycteris from the late Paleocene of western Colorado and the phylogenetic position of the family Picrodontidae (v0.2)\". PeerJ https://doi.org/10.7287/peerj.191v0.2/reviews/1\nReview 4: William Jungers \u00b7 Jul 8, 2013 \u00b7 Academic Editor\nMAJOR REVISIONS\nTwo reviewers see real merit in your paper on these rare fossil primates, but both request much better photographs (especially since you are creating a new type specimen). Both reviewers also raise substantive issues with your phylogenetic analysis that need to be addressed (and which may require new analyses). Additional recommendations are mostly constructive, and attention to these suggestions will serve to improve the diagnosis and the discussion of its significance for primate paleobiology. Careful editing is needed to eliminate various typos and spelling errors.\nReview 5: Gregg F Gunnell \u00b7 Jun 30, 2013\nBasic reporting\nThis paper describes a new species of Zanycteris from the Paleocene of Colorado....it is well written and well organized and I had only a few minor comments which I detail below. In general I find no problem with publishing this paper once the minor fixes are made.\nExperimental design\nNot applicable\nValidity of the findings\nThere seems no doubt that Z. honeyi is a new species of Zanycteris - I found the ecological analysis a little wanting - I agree that the teeth of Z. honeyi are of a frugivorous animal, similar to Ariteus (often mis-spelled in the mansucript as Artiteus) - but I'm not sure why thet \"restricts the stratographic range\" of picrodontids to the middle and late Paleocene only - surely there were plenty of fruits available in the Eocene as well....all of those real primates must have been eating something in the Eocene\nAdditional comments\nI find this paper to be more or less good as it is...there are few places where it needs a little editing or rewording....\n\nThe only major complaint I have is that Figure 1 showing the holotype specimen really is unacceptable for publication - it is blurry and out of focus - the buccal view is nearly impossible to interpret at all - in this day and age of microCT scanners and microscopic imaging with stacking software surely much better images than these can be provided. Also, it looks like there is still adhering matrix on the occlusal surfaces of the molars - this should be cleaned off beofre re-imaging.\n\nAlso I have a list of otrher comments:\n\nAbstract - Ariteus is mis-spelled in fourth line from bottom\n\nMethods and Material section - \"diverse fauna of fossil mammals\" is cited in line 39 and repeated again in line 42 citing Table 1 (I didn't see Table 1 anywhere) - no need to repeat this same information twice\n\nComparisons of Z. honeyi - lines 104-105 the authors notes differnces with Picrodus - he should cite the Scott and Fox, 2005 publication here\n\nDiscussion - line 146 - I think I'd be a little less dogmatic here and say that the \"molar teeth were probably specialized for cutting....\"\n\nLine 15 - Ariteus mis-spelled again\n\nLine 155 - paracone and metacone cusps (delete the \"s\" after paracone and metacone)\n\nLines 162-165 - I see no basis for saying this - yes paromomyids and picrodontids are different dentally but no actual analysis has been done to substantiate the claim that picrodontids were limited to the middle and late Paleocene by their dental specializations - very few plesiadapiforms made it past the end of the Paleocene in general - I think I'd just drop these lines.\n\nI'm not entirely sure why yet another phylogenetic analysis is being run here - the strict consensus tree differs quiet a lot from other, more rigorous trees - there are so many polytomy's that I'm not sure I believe any of what is being depicted....also the tooth images on the tree are so small as to be unrecognizable as teeth - probably should just eliminate them\n\nThat's all I have\nCite this review as\nGunnell GF (2013) Peer Review #1 of \"A new species of the archaic primate Zanycteris from the late Paleocene of western Colorado and the phylogenetic position of the family Picrodontidae (v0.1)\". PeerJ https://doi.org/10.7287/peerj.191v0.1/reviews/1\nReview 6: Mary Silcox \u00b7 Jun 17, 2013\nBasic reporting\nPicrodontids are incredibly rare primates, so this paper is certainly worthy of publication. However, there are a few significant issues with the paper that need to be addressed before it can be published. Most serious, the argument for the attribution to Zanycteris is not clearly made. As discussed by both Silcox and Gunnell (2008) and Scott and Fox (2005) the key diagnostic difference between this genus and Picrodus is an anteriorly protruding parastylar lobe in the former, and yet the author suggests that the new specimen belongs in Zanycteris on the basis of a \u201cshorten [sic] parastyle\u201d. Looking at the image, I think that the specimen is actually Zanycteris and does have an anteriorly protruding parastylar lobe, but this certainly isn\u2019t clear in the discussion. What\u2019s more, the image of the specimen is very poor, which makes it difficult to determine if the description as presented is correct. For example, I really can\u2019t tell if the M2 is complete or broken buccally\u2014this is critically important since the relative size of M1 vs. M2 is the key diagnostic trait for the new species. In the buccal view it is impossible to tell tooth from bone\u2014I actually think it would be okay to just cut this figure. For upper teeth, a buccal view isn\u2019t really needed. In the occlusal view it is clear that the specimen has been terribly over-whitened, so that there is a thick layer of whitening material coating the whole specimen, with beaded up material obscuring a good part of the morphology. My guess is that moisture either on the specimen, or in the bulb of the whitening tube, caused the powder to bead up. The image is also somewhat out of focus. Simply put, Figure 1 is not publishable as is. The specimen needs to be cleaned, and a much lighter layer of whitening used. Alternatively, an SEM or microCT image could be substituted. A few more minor details: Abstract, line 5: should be \u201cBY a single specimen\u201d\nAbstract line 6: should be \u201cshortenED parastyle\u201d\nAbstract line 9: should be \u201csimilarLY sized upper second molar\u201d\nAbstract line 12: should be cristid obliqua, not cristid oblique Line 20: \u201cmore recently studies\u2026\u201d requires a reference \u2013the key paper here is Szalay 1968\nLine 25: should be \u201cis strengthenED by the\u2026\u201d\nLine 28: \u201cThe enlarged incisor is considered a synapomorphy of Plesiadapiformes\u2026\u201d Clemens did suggest this, but Plesiadapiformes has never come out as a monophyletic group (in a holophyletic sense, i.e., excluding euprimates or Dermoptera) in any cladistic analysis. And it doesn\u2019t come out as demonstrably monophyletic in your own results\u2014Purgatorius is part of an unresolved polytomy with the rest of the plesiadapiforms and Plagiomenidae, Apatemyidae etc. For this reason, it is inappropriate to talk about this character as a synapomorphy, at least without a qualification.\nLine 31: refs are needed for the time span of picrodontids (i.e., after \u201cin North America\u201d)\nLine 69: It is standard to include several more layers in the systematic paleontology listing (e.g., at a minimum Order and Family)\nLine 94: It is unclear what \u201cthe broad protocone spreads into the postprotocrista\u201d means. Clarify.\nLines 163, 164: when used informally, taxonomic names should not be capitalized (e.g., should be paromomyids and picrodontids)\nFigure 2: \u201cElpidophorus\u201d and \u201cstonleyi\u201d are spelled incorrectly\nExperimental design\nWith respect to the phylogenetic analysis, it seems strange to me to limit the sample to Paleocene mammals. Because of the vagaries of fossil preservation, it is not necessarily the case that younger forms are irrelevant in assessing the ancestry of older forms. This is particularly an issue with respect to the discussion about the possible ancestors of different plesiadapiform groups (lines 133-135). Without including Premnoides douglassi, the putative ancestor of Paromomyidae (see Gunnell, 1989), it really isn\u2019t appropriate to discuss the possible descendants of the mentioned palaechthonids. I\u2019m not necessarily suggesting that the author needs to expand his sample, since the systematic questions he is asking here are fairly limited in scope. However, he should resist the temptation to over-interpret the results. There are also a number of issues of clarity with the character list that need to be addressed: Character 1: not clear what is meant by a \u201cwinged postcingulum\u201d\u2014this is not standard dental terminology. Please define and clarify. Character 4: how close to they need to be in size for it to be \u201cnearly\u201d? Define more precisely. Characters 5, 6, 12: These characters are essentially written as double negatives (i.e., the \u201cpresent\u201d state implies the absence of something), which is confusing, and non-standard. Re-write (e.g., \u201cPostprotocrista on M2 Present = 0, Absent = 1) Character 7: \u201creduced\u201d implies an evolutionary direction. Define based on observed morphology (e.g., short) Characters 8, 13, 14: It is inappropriate and imprecise to make reference to a particular genus in the definition of a character. Describe what\u2019s there. Character 10: It is a bad idea to combine two potentially independent elements of morphology in a single character (e.g., size and position in this case) since you have no way of knowing a priori if they always covary. Character 14: groove in what position? Character 112: Not clear what is meant by \u201csmall\u201d and \u201cenlarged\u201d here. Enlarged relative to what?\nValidity of the findings\nThere is an inaccuracy in how the results are reported. On lines 127-128 the author states that \u201cThe strict consensus tree shows Zanycteris honeyi as the sister-taxa [sic] to Zanycteris paleocenus\u2026\u201d No, it doesn\u2019t\u2014the two taxa form a polytomy with Picrodus. The nature of their relationships is unresolved on the tree as presented. This must be clarified. Also, \u201ctaxa\u201d is plural\u2014it would be the sister taxON.\nAdditional comments\nI as glad to see that you named this for Jim Honey. He was a very nice man--I was sorry to hear of his passing.\nCite this review as\nSilcox M (2013) Peer Review #2 of \"A new species of the archaic primate Zanycteris from the late Paleocene of western Colorado and the phylogenetic position of the family Picrodontidae (v0.1)\". PeerJ https://doi.org/10.7287/peerj.191v0.1/reviews/2\n",
    "LLM_extracted_review": "['**Review 1:** The diversity of North American archaic primates is fascinating.\\n\\n**Review 2:** The photographs are adequate but not perfect. Reference to \"the diagnostic trait for this genus\" should be included. Clarification is needed regarding the terms \"flanged\" and \"reduced.\" The statement about characters should be corrected, as some lower dental features are part of the phylogenetic analysis. The decision to limit characters to those observed only on Palaeocene species should be reflected upon.\\n\\n**Review 3:** The images of the teeth have improved but are borderline publishable. Residue on the occlusal surface of the tooth is unacceptable. There is confusion regarding the phylogenetic analysis, particularly about the character matrix. The character list has improved, but some terms are still unclear or inappropriate. The author should reference the diagnostic trait for Zanycteris.\\n\\n**Review 4:** Better photographs are needed, especially for a new type specimen. Substantive issues with the phylogenetic analysis need to be addressed. Attention to constructive suggestions will improve the diagnosis and discussion. Careful editing is required to eliminate typos and spelling errors.\\n\\n**Review 5:** The paper is well written and organized, with only a few minor comments. The ecological analysis is lacking, particularly regarding the stratigraphic range of picrodontids. Figure 1 is unacceptable for publication due to blurriness and residue on the molars. Several minor edits and clarifications are needed throughout the paper.\\n\\n**Review 6:** The paper is worthy of publication, but significant issues need to be addressed. The argument for attribution to Zanycteris is unclear, and the images are poor, making it difficult to assess the specimen. The phylogenetic analysis should not be limited to Paleocene mammals, and clarity is needed in the character list. There are inaccuracies in how results are reported, particularly regarding the relationships of taxa in the consensus tree.']"
}