Bibliography

Edited on: 31 May 2016 dimus avatar dimus

2017

  1. Mozzherin DY, Myltsev AA, Patterson DJ (2017) gnparser: a powerful parser for scientific names based on Parsing Expression Grammar. BMC Bioinformatics 18: 279.

2016

  1. Patterson D, Mozzherin D, Shorthouse D, Thessen A (2016) Challenges with using names to link digital biodiversity information. Biodiversity Data Journal 4: e8080.
    We cross-map names from Catalogue of Life, DRYAD and GenBank and show that while exact string-matching allowed to connect less than 15% of names, usage of Global Names tools increased the success rate up to 90%
  2. Zermoglio PF, Guralnick RP, Wieczorek JR (2016) A Standardized Reference Data Set for Vertebrate Taxon Name Resolution. PLoS One 11: 1–20.
  3. Remsen D (2016) The use and limits of scientific names in biological informatics. ZooKeys 550: 207–223.
  4. Pyle R (2016) Towards a Global Names Architecture: The future of indexing scientific names. ZooKeys 550: 261–281.

2015

  1. Guralnick RP, Cellinese N, Deck J, Pyle RL, Kunze J, Penev L, Walls R, Hagedorn G, Agosti D, Wieczorek J, Catapano T, Page RDM (2015) Community next steps for making globally unique identifiers work for biocollections data.. ZooKeys 494: 133–54.
  2. Berghe EV, Coro G, Bailly N, Fiorellato F, Aldemita C, Ellenbroek A, Pagano P (2015) Retrieving taxa names from large biodiversity data collections using a flexible matching workflow. Ecological Informatics 28: 29–41.
  3. Guralnick RP, Cellinese N, Deck J, Pyle RL, Kunze J, Penev L, Walls R, Hagedorn G, Agosti D, Wieczorek J, Catapano T, Page RDM (2015) Community next steps for making globally unique identifiers work for biocollections data. ZooKeys.

2014

  1. Rees T (2014) Taxamatch, an algorithm for near (’fuzzy’) matching of scientific names in taxonomic databases.. PloS one 9: e107510.
  2. Egloff W, Patterson DJ, Agosti D, Hagedorn G (2014) Open exchange of scientific knowledge and European copyright: The case of biodiversity information. ZooKeys.

2013

  1. Hardisty A, Roberts D, Addink W, Aelterman B, Agosti D, Amaral-Zettler L, Ariño AH, Arvanitidis C, Backeljau T, Bailly N, Belbin L, Berendsohn W, Bertrand N, Caithness N, Campbell D, Cochrane G, Conruyt N, Culham A, Damgaard C, Davies N, Fady B, Faulwetter S, Feest A, Field D, Garnier E, Geser G, Gilbert J, Grosche, Grosser D, Herbinet B, Hobern D, Jones A, Jong Y de, King D, Knapp S, Koivula H, Los W, Meyer C, Morris R a, Morrison N, Morse D, Obst M, Pafilis E, Page LM, Page R, Pape T, Parr C, Paton A, Patterson D, Paymal E, Penev L, Pollet M, Pyle R, Raab-Straube E von, Robert V, Robertson T, Rovellotti O, Saarenmaa H, Schalk P, Schaminee J, Schofield P, Sier A, Sierra S, Smith V, Spronsen E van, Thornton-Wood S, Tienderen P van, Tol J van, Ó Tuama Éamonn, Uetz P, Vaas L, Vignes Lebbe R, Vision T, Vu D, De Wever A, White R, Willis K, Young F (2013) A decadal view of biodiversity informatics: challenges and priorities.. BMC ecology 13: 16.

2012

  1. Thessen AE, Cui H, Mozzherin D (2012) Applications of natural language processing in biodiversity science.. Advances in bioinformatics 2012: 391574.
  2. Krell F-T (2012) Electronic publication of new animal names - an interview with Frank-T. Krell, commissioner of the International Commission on Zoological Nomenclature and chair of the ICZN ZooBank Committee.. BMC evolutionary biology 12: 184.
  3. Akella LM, Norton CN, Miller H (2012) NetiNeti: discovery of scientific names from text using machine learning methods.. BMC bioinformatics 13: 211.

2011

  1. Duerr RE, Downs RR, Tilmes C, Barkstrom B, Lenhardt WC, Glassy J, Bermudez LE, Slaughter P (2011) On the utility of identification schemes for digital earth science data: an assessment and recommendations. Earth Science Informatics 4: 139–160.
  2. Baker E, Michel E (2011) Data standards, sense and stability: Scratchpads, the ICZN and ZooBank. ZooKeys 150: 167.
  3. Smith V, Penev L (2011) e-Infrastructures for data publishing in biodiversity science. ZooKeys 150.

2010

  1. Penev L, Agosti D, Georgiev T, Catapano T, Miller J, Blagoderov V, Roberts D, Smith VS, Brake I, Ryrcroft S, Scott B, Johnson NF, Morris R a, Sautter G, Chavan V, Robertson T, Remsen D, Stoev P, Parr C, Knapp S, Kress WJ, Thompson CF, Erwin T (2010) Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples.. ZooKeys 16: 1–16.
  2. Patterson DJ, Cooper J, Kirk PM, Pyle RL, Remsen DP (2010) Names are key to the big new biology. Trends in Ecology and Evolution 25: 686–691.

2008

  1. Pyle RL, Michel E (2008) ZooBank: Developing a nomenclatural tool for unifying 250 years of biological information. Zootaxa 1950: 39–50.

2007

  1. Leary PR, Remsen DP, Norton CN, Patterson DJ, Sarkar IN (2007) uBioRSS: Tracking taxonomic literature using RSS. Bioinformatics 23: 1434–1436.

2006

  1. Page RDM (2006) Taxonomic names, metadata, and the semantic web. Biodiversity Informatics 3: 1–15.
  2. Patterson DJ, Remsen D, Marino W a, Norton C (2006) Taxonomic indexing–extending the role of taxonomy.. Systematic biology 55: 367–373.

2003

  1. Pyle RL (2003) Taxonomer: a Relational Data Model for managing information relevant to taxonomic research. PhyloInformatics 1: 1–54.