Recent Submissions

  • NetiNeti : discovery of scientific names from text using machine learning methods 

    Akella, Lakshmi Manohar; Norton, Cathy N.; Miller, Holly (BioMed Central, 2012-08-22)
    A scientific name for an organism can be associated with almost all biological data. Name identification is an important step in many text mining tasks aiming to extract useful information from biological, biomedical and ...
  • The taxonomic name resolution service : an online tool for automated standardization of plant names 

    Boyle, Brad; Hopkins, Nicole; Lu, Zhenyuan; Garay, Juan Antonio Raygoza; Mozzherin, Dmitry; Rees, Tony; Matasci, Naim; Narro, Martha L.; Piel, William H.; Mckay, Sheldon J.; Lowry, Sonya; Freeland, Chris; Peet, Robert K.; Enquist, Brian J. (BioMed Central, 2013-01-16)
    The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate ...
  • Envisioning the future of science libraries at academic research institutions : a discussion 

    Feltes, Carol; Gibson, Donna S.; Miller, Holly; Norton, Cathy N.; Pollock, Ludmila (2012-12-20)
    A group of librarians, other information professionals, scientists and research administrators met to discuss the challenges that research libraries are currently facing. After the meeting a survey was conducted to obtain ...
  • The taxonomic significance of species that have only been observed once : the genus Gymnodinium (Dinoflagellata) as an example 

    Thessen, Anne E.; Patterson, David J.; Murray, Shauna A. (Public Library of Science, 2012-08-30)
    Taxonomists have been tasked with cataloguing and quantifying the Earth’s biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. ...
  • Biological nomenclature terms for facilitating communication in the naming of organisms 

    David, John; Garrity, George M.; Greuter, Werner; Hawksworth, David L.; Jahn, Regine; Kirk, Paul M.; McNeill, John; Michel, Ellinor; Knapp, Sandra; Patterson, David J.; Tindall, Brian J.; Todd, Jonathan A.; Tol, Jan van; Turland, Nicholas J. (Pensoft, 2012-05-08)
    A set of terms recommended for use in facilitating communication in biological nomenclature is presented as a table showing broadly equivalent terms used in the traditional Codes of nomenclature. These terms are intended ...
  • Applications of natural language processing in biodiversity science 

    Thessen, Anne E.; Cui, Hong; Mozzherin, Dmitry (Hindawi Publishing, 2012)
    Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature ...
  • Building research networks to support campus programs [poster] 

    Furfey, John F.; Devenish, Ann; Hurter, Colleen; Stafford, Nancy (2012-04-04)
    This poster focuses on the methods, tools and outcomes involved in creating two targeted research networks to support large, long-running research programs in the Woods Hole scientific community.
  • Mapping the biosphere : exploring species to understand the origin, organization and sustainability of biodiversity 

    Wheeler, Q. D.; Knapp, Sandra; Stevenson, D. W.; Stevenson, J.; Blum, Stan D.; Boom, B.. M.; Borisy, Gary G.; Buizer, J. L.; De Carvalho, M. R.; Cibrian, A.; Donoghue, M. J.; Doyle, V.; Gerson, E. M.; Graham, C. H.; Graves, P.; Graves, Sara J.; Guralnick, Robert P.; Hamilton, A. L.; Hanken, J.; Law, W.; Lipscomb, D. L.; Lovejoy, T. E.; Miller, Holly; Miller, J. S.; Naeem, Shahid; Novacek, M. J.; Page, L. M.; Platnick, N. I.; Porter-Morgan, H.; Raven, P. H.; Solis, M. A.; Valdecasas, A. G.; Van Der Leeuw, S.; Vasco, A.; Vermeulen, N.; Vogel, J.; Walls, R. L.; Wilson, E. O.; Woolley, J. B. (Taylor & Francis, 2012-03-27)
    The time is ripe for a comprehensive mission to explore and document Earth's species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in ...
  • Pseudo-nitzschia physiological ecology, phylogeny, toxicity, monitoring and impacts on ecosystem health 

    Trainer, Vera L.; Bates, Stephen S.; Lundholm, Nina; Thessen, Anne E.; Cochlan, William P.; Adams, Nicolaus G.; Trick, Charles G. (Elsevier B.V., 2011-11-03)
    Over the last decade, our understanding of the environmental controls on Pseudo-nitzschia blooms and domoic acid (DA) production has matured. Pseudo-nitzschia have been found along most of the world's coastlines, while the ...
  • Data hosting infrastructure for primary biodiversity data 

    Goddard, Anthony; Wilson, Nathan; Cryer, Phil; Yamashita, Grant (BioMed Central, 2011-12-15)
    Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects tasked with ...
  • Data issues in the life sciences 

    Thessen, Anne E.; Patterson, David J. (Pensoft Publishers, 2011-11-28)
    We review technical and sociological issues facing the Life Sciences as they transform into more data-centric disciplines - the “Big New Biology”. Three major challenges are: 1) lack of comprehensive standards; 2) lack of ...
  • SCOR/IODE/MBLWHOI Library collaboration on data publication [poster]  

    Raymond, Lisa; Pikula, Linda; Lowry, Roy; Urban, Ed; Moncoiffe, Gwenaelle; Pissierssens, Peter; Norton, Cathy N. (2011-05-25)
    This poster describes the development of international standards to publish oceanographic datasets. Research areas include the assignment of persistent identifiers, tracking provenance, linking datasets to publications, ...
  • Identity of epibiotic bacteria on symbiontid euglenozoans in O2-depleted marine sediments : evidence for symbiont and host co-evolution 

    Edgcomb, Virginia P.; Breglia, S. A.; Yubuki, Naoji; Beaudoin, David J.; Patterson, David J.; Leander, Brian S.; Bernhard, Joan M. (2010-06)
    A distinct subgroup of euglenozoans, referred to as the “Symbiontida,” has been described from oxygen-depleted and sulfidic marine environments. By definition, all members of this group carry epibionts that are intimately ...
  • Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life 

    Parfrey, Laura Wegener; Grant, Jessica; Tekle, Yonas I.; Lasek-Nesselquist, Erica; Morrison, Hilary G.; Sogin, Mitchell L.; Patterson, David J.; Katz, Laura A. (2010-06-01)
    An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided ...
  • Names are key to the big new biology 

    Patterson, David J.; Cooper, J.; Kirk, Paul M.; Pyle, R. L.; Remsen, David P. (2010-09-20)
    Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution, ecology), will soon benefit from an emerging names-based infrastructure. It will draw on ...
  • A model for Bioinformatics training : the Marine Biological Laboratory 

    Yamashita, Grant; Miller, Holly; Goddard, Anthony; Norton, Cathy N. (2010-08-04)
    Many areas of science such as biology, medicine, and oceanography are becoming increasingly data-rich and most programs that train scientists do not address informatics techniques or technologies that are necessary for ...
  • LigerCat : using “MeSH clouds” from journal, article, or gene citations to facilitate the identification of relevant biomedical literature 

    Sarkar, Indra Neil; Schenk, Ryan; Miller, Holly; Norton, Cathy N. (American Medical Informatics Association, 2009-11-14)
    The identification of relevant literature from within large collections is often a challenging endeavor. In the context of indexed resources, such as MEDLINE, it has been shown that keywords from a controlled vocabulary ...
  • GenBank and PubMed : how connected are they? 

    Miller, Holly; Norton, Cathy N.; Sarkar, Indra Neil (BioMed Central, 2009-06-09)
    GenBank(R) is a public repository of all publicly available molecular sequence data from a range of sources. In addition to relevant metadata (e.g., sequence description, source organism and taxonomy), publication information ...
  • Intra- and interspecies differences in growth and toxicity of Pseudo-nitzschia while using different nitrogen sources 

    Thessen, Anne E.; Bowers, H. A.; Stoecker, Diane K. (2009-01)
    Clonal cultures of plankton are widely used in laboratory experiments and have contributed greatly to knowledge of microbial systems. However, many physiological characteristics vary drastically between strains of the ...
  • CAOS software for use in character-based DNA barcoding 

    Sarkar, Indra Neil; Planet, Paul J.; DeSalle, Rob (2008-04)
    The success of character based DNA barcoding depends on the efficient identification of diagnostic character states from molecular sequences that have been organized hierarchically (e.g., according to phylogenetic methods). ...

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