Now showing items 1-20 of 29

  • 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 ...
  • 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 ...
  • 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, ...
  • 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 ...
  • Biodiversity informatics : organizing and linking information across the spectrum of life 

    Sarkar, Indra Neil (2007-04-08)
    Biological knowledge can be inferred from three major levels of information: molecules, organisms, and ecologies. Bioinformatics is an established field that has made significant advances in the development of systems and ...
  • Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata 

    Rach, J.; DeSalle, Rob; Sarkar, Indra Neil; Schierwater, B.; Hadrys, H. (Royal Society, 2007-11-08)
    DNA barcoding has become a promising means for identifying organisms of all life stages. Currently, phenetic approaches and tree-building methods have been used to define species boundaries and discover 'cryptic species'. ...
  • Automated simultaneous analysis phylogenetics (ASAP) : an enabling tool for phlyogenomics 

    Sarkar, Indra Neil; Egan, Mary G.; Coruzzi, Gloria; Lee, Ernest K.; DeSalle, Rob (BioMed Central, 2008-02-19)
    The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck ...
  • 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). ...
  • Exploring historical trends using taxonomic name metadata 

    Sarkar, Indra Neil; Schenk, Ryan; Norton, Cathy N. (BioMed Central, 2008-05-13)
    Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical ...
  • The Encyclopedia of Life, Biodiversity Heritage Library, biodiversity informatics and beyond Web 2.0 

    Norton, Cathy N. (Great Cities Initiative of the University of Illinois at Chicago Library, 2008-08-04)
    E.O. Wilson, the noted entomologist at Harvard, "wished" for an authoritative encyclopedia of life that would be freely available on the worldwide web for the entire world. On 9 May 2007, The Encyclopedia of Life (EOL) was ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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, ...
  • 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 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 ...