Surfacing the deep data of taxonomy

ZooKeys

Volumn 2016, Issue 550, 2016, Pages 247-260

  Page, Roderic D M ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Biodiversity informatics; Dark taxa; Data cleaning; Data integration; DOI; Identifiers; Literature; Taxonomy

Indexed keywords

EID: 84954448012     PISSN: 13132989     EISSN: 13132970     Source Type: Journal    
DOI: 10.3897/zookeys.550.9293     Document Type: Article

References (43)

1. Bennett NC, Jarvis JUM (2004) Cryptomys damarensis. Mammalian Species 756(1): 1-5. doi: 10.1644/756
2. Bergman MK (2001) WHITE PAPER: The Deep Web: Surfacing Hidden Value. Journal of Electronic Publishing 7(1). doi: 10.3998/3336451.0007.104
3. Cleevely RJ (2009) Charles Davies SHERBORN: geologist and scientific bibliographer. Archives of Natural History 36: 357-359. doi: 10.3366/e0260954109001089
4. Davis GM, Kitikoon V, Temcharoen P (1976) Monograph on “Lithoglyphopsis” aperta, the snail host of Mekong River schistosomiasis. Malacologia 15(2): 241-87.
5. Deans AR, Yoder MJ, Balhoff JP (2012) Time to change how we describe biodiversity. Trends in ecology & evolution 27(2): 78-84. doi: 10.1016/j.tree.2011.11.007
6. Faulkes CG, Bennett NC, Cotterill FPD, Stanley W, Mgode GF, Verheyen E (2011) Phylogeography and cryptic diversity of the solitary-dwelling silvery mole-rat, genus Heliophobius (family: Bathyergidae). In: Kitchener A (Ed.) Journal of Zoology 285(4): 324-338. doi: 10.1111/j.1469-7998.2011.00863.x
7. Garfield E (2001) Taxonomy is small, but it has its citation classics. Nature 413(6852): 107. doi: 10.1038/35093267
8. Harman K, Scott B, Rycroft S, Roberts D, Smith V (2009) Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. BMC Bioinformatics 10(Suppl 14): 6. doi: 10.1186/1471-2105-10-S14-S6
9. Hibbett D, Glotzer D (2011) Where are all the undocumented fungal species? A study of Mortierella demonstrates the need for sequence-based classification. The New phytologist 191(3): 592-596. doi: 10.1111/j.1469-8137.2011.03819.x
10. Illiger JKW (1811) Caroli Illigeri D. Acad. Reg. Scient. Berolinens. et Bavaricae Sod. Museo Zoologico Berolin. praefecti professoris extraord. Prodromus systematis mammalium et avium: additis terminis zoographicis utriusque classis, eorumque versione germanica. Sumptibus C. Salfeld, Berolini, 301 pp. doi: 10.5962/bhl.title.42403
11. Koch AC (1841) Description of Missourium, or Missouri leviathan : together with its supposed habits and Indian traditions concerning the location from whence it was exhumed; also, comparisons of the whale, crocodile and missourium with the leviathan, as described in by. Prentice and Weissinger, Louisville, Kentucky. doi: 10.5962/bhl.title.35985
12. Krell FT (2000) Impact factors aren’t relevant to taxonomy. Nature 405(6786): 507-508. doi: 10.1038/35014664
13. Lambert O, Bianucci G, Post K, de Muizon C, Salas-Gismondi R, Urbina M, Reumer J (2010a) The giant bite of a new raptorial sperm whale from the Miocene epoch of Peru. Nature 466(7302): 105-108. doi: 10.1038/nature09067
14. Lambert O, Bianucci G, Post K, de Muizon C, Salas-Gismondi R, Urbina M, Reumer J (2010b) The giant bite of a new raptorial sperm whale from the Miocene epoch of Peru. Nature 466(7310): 1134-1134. doi: 10.1038/nature09381
15. Leviton AE, Gibbs RH, Heal E, Dawson CE (1985) Standards in Herpetology and Ichthyology: Part I. Standard Symbolic Codes for Institutional Resource Collections in Herpetology and Ichthyology. Copeia 1985(3): 802-832.
16. MacCallum CJ (2007) When Is Open Access Not Open Access? PLoS Biology 5(10): e285. doi: 10.1371/journal.pbio.0050285
17. Maddison DR, Guralnick R, Hill A, Reysenbach A-L, McDade LA (2011) Ramping up biodiversity discovery via online quantum contributions. Trends in Ecology & Evolution 27(2): 72-77. doi: 10.1016/j.tree.2011.10.010
18. Martin S, Hohman MM, Liefeld T (2005) The impact of Life Science Identifier on informatics data. Drug discovery today 10(22): 1566-1572. doi: 10.1016/S1359-6446(05)03651-2
19. Müller-Wille S, Charmantier I (2011) Natural history and information overload: The case of Linnaeus. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43(1): 4-5. doi: 10.1016/j.shpsc.2011.10.021
20. Nagy LG, Petkovits T, Kovács GM, Voigt K, Vágvölgyi C, Papp T (2011) Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences. The New phytologist 191(3): 789-794. doi: 10.1111/j.1469-8137.2011.03707.x
21. Neave SA (1939) Nomenclator Zoologicus: a list of the names of the genera and subgenera in zoology from the tenth edition of Linnaeus 1758 to the end of 1935. The Zoological Society of London, London.
22. Page RDM (2006) Taxonomic names, metadata, and the Semantic Web. Biodiversity Informatics 3: 1-15. doi: 10.17161/bi.v3i0.25
23. Page RDM (2008) Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Briefings in bioinformatics 9(5): 345-354. doi: 10.1093/bib/bbn022
24. Page RDM (2009) Bioguid: resolving, discovering, and minting identifiers for biodiversity informatics. BMC Bioinformatics 10(Suppl 14): 5. doi: 10.1186/1471-2105-10-S14-S5
25. Page RDM (2011a) Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library. BMC bioinformatics 12: 187. doi: 10.1186/1471-2105-12-187
26. Page RDM (2011b) Dark taxa: GenBank in a post-taxonomic world. http://iphylo.blogspot.co.uk/2011/04/dark-taxa-genbank-in-post-taxonomic.html
27. Page RDM (2011c) Orwellian metadata: making journals disappear. http://iphylo.blogspot.co.uk/2011/09/orwellian-metadata-making-journals.html
28. Page RDM (2013) BioNames: linking taxonomy, texts, and trees. PeerJ 1: e190. doi: 10.7717/peerj.190
29. Parr CS, Guralnick R, Cellinese N, Page RDM (2011) Evolutionary informatics: unifying knowledge about the diversity of life. Trends in Ecology & Evolution 27(2): 94-103. doi: 10.1016/j.tree.2011.11.001
30. Patterson DJ, Cooper J, Kirk PM, Pyle RL, Remsen DP (2010) Names are key to the big new biology. Trends in Ecology & Evolution 25(12): 686-691. doi: 10.1016/j.tree.2010.09.004
31. Peters WCH (1846) Über neue Säugethiergattungen aus den Ordnungen der Insectenfresser und Nagethiere. Bericht über die zur Bekanntmachung geeigneten Verhandlungen der Konigl.Preuss.Akademie der Wissenschaften zu Berlin 1846: 257-259.
32. Phillips AJ, Arauco-Brown R, Oceguera-Figueroa A, Gomez GP, Beltrán M, Lai Y-T, Siddall ME (2010) Tyrannobdella rex n. gen. n. sp. and the evolutionary origins of mucosal leech infestations. PLoS ONE 5(4): e10057. doi: 10.1371/journal.pone.0010057
33. Raimond Y, Scott T, Sinclair P, Miller L, Betts S, McNamara F (2010) Case Study: Use of Semantic Web Technologies on the BBC Web Sites. http://www.w3.org/2001/sw/sweo/public/UseCases/BBC/
34. Remsen DP, Norton C, Patterson DJ (2006) Taxonomic informatics tools for the electronic Nomenclator Zoologicus. The Biological bulletin 210(1): 18-24. doi: 10.2307/4134533
35. Schindel DE, Miller SE (2010) Provisional nomenclature: the on-ramp to taxonomic names. In: Polaszek A (Ed.) Systema Naturae 250 - The Linnaean Ark. CRC Press, 109-115.
36. Segers H, Smet WHDE, Fischer C, Fontaneto D, Wallace RL, Jersabek CD (2012) Towards a List of Available Names in Zoology, partim Phylum Rotifera. Zootaxa 68: 61-68.
37. Simkin MV, Roychowdhury VP (2011) Theory of citing. Springer Optimization and Its Applications. Physics and Society; Disordered Systems and Neural Networks; Applications 57(4): 463-505. doi: 10.1007/978-1-4614-0754-6_16
38. Specht CG (2010) Mutations of citations. The Scientist. http://www.the-scientist.com/?articles.view/articleNo/29252/title/Opinion--Mutations-of-citations/
39. 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.
40. Vences M, Thomas M, van der Meijden A, Chiari Y, Vieites DR (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in zoology 2(1): 5. doi: 10.1186/1742-9994-2-5
41. Werner YL (2006) The case of impact factor versus taxonomy: a proposal. Journal of Natural History 40(21-22): 1285-1286. doi: 10.1080/00222930600903660
42. Wägele H, Klussmann-Kolb A, Kuhlmann M, Haszprunar G, Lindberg D, Koch A, Wägele JW (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
43. Yan K-K, Gerstein M (2011) The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics. PLoS ONE 6(5): e19917. doi: 10.1371/journal.pone.0019917