Now showing items 14-29 of 29

  • 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 ...
  • Grand challenges in biodiversity informatics 

    Sarkar, Indra Neil (2007-01)
    The exponentially growing array of biological data has necessitated the development of a new information management domain, biodiversity informatics. It is one of the newest members of the ‘informatics’ sub-disciplines, ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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, ...
  • Taxonomic indexing—extending the role of taxonomy 

    Patterson, David J.; Remsen, David P.; Marino, William A.; Norton, Cathy N. (Taylor & Francis, 2006-06)
    Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing ...
  • Taxonomic informatics tools for the electronic nomenclator zoologicus 

    Remsen, David P.; Norton, Cathy N.; Patterson, David J. (Marine Biological Laboratory, 2006-02)
    Given the current trends, it seems inevitable that all biological documents will eventually exist in a digital format and be distributed across the internet. New network services and tools need to be developed to increase ...
  • 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 ...
  • 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. ...
  • uBioRSS : tracking taxonomic literature using RSS 

    Leary, Patrick R.; Remsen, David P.; Norton, Cathy N.; Patterson, David J.; Sarkar, Indra Neil (Oxford University Press, 2007-03-28)
    Web content syndication through standard formats such as RSS and ATOM has become an increasingly popular mechanism for publishers, news sources, and blogs to disseminate regularly updated content. These standardized ...