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  • 1
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 240 (1972), S. 491-492 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] We have investigated the detection of increased concentrations of 14C in artists' materials to identify works of art produced since the advent of atmospheric nuclear weapons testing. The use of conventional 14C dating to determine the age of paintings is prevented by the short timescale involved ...
    Type of Medium: Electronic Resource
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  • 3
    Publication Date: 2022-05-25
    Description: © 2009 Sarkar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 2 (2009): 101, doi:10.1186/1756-0500-2-101.
    Description: 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 is recorded in the GenBank data file. The identification of literature associated with a given molecular sequence may be an essential first step in developing research hypotheses. Although many of the publications associated with GenBank records may not be linked into or part of complementary literature databases (e.g., PubMed), GenBank records associated with literature indexed in Medline are identifiable as they contain PubMed identifiers (PMIDs). Here we show that an analysis of 87,116,501 GenBank sequence files reveals that 42% are associated with a publication or patent. Of these, 71% are associated with PMIDs, and can therefore be linked to a citation record in the PubMed database. The remaining (29%) of publication-associated GenBank entries either do not have PMIDs or cite a publication that is not currently indexed by PubMed. We also identify the journal titles that are linked through citations in the GenBank files to the largest number of sequences. Our analysis suggests that GenBank contains molecular sequences from a range of disciplines beyond biomedicine, the initial scope of PubMed. The findings thus suggest opportunities to develop mechanisms for integrating biological knowledge beyond the biomedical field.
    Description: INS and HM are funded in part by a research grant from the Ellison Medical Foundation and National Library of Medicine award R01LM009725 to INS.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © The Natural History Museum, 2012. This article is posted here by permission of Taylor & Francis for reuse for non-commercial purposes only. The definitive version was published in Systematics and Biodiversity 10 (2012): 1-20, doi:10.1080/14772000.2012.665095.
    Description: 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 cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is attainable based on the strength of 250 years of progress, worldwide collections, existing experts, technological innovation and collaborative teamwork. Existing digitization projects are overcoming obstacles of the past, facilitating collaboration and mobilizing literature, data, images and specimens through cyber technologies. Charting the biosphere is enormously complex, yet necessary expertise can be found through partnerships with engineers, information scientists, sociologists, ecologists, climate scientists, conservation biologists, industrial project managers and taxon specialists, from agrostologists to zoophytologists. Benefits to society of the proposed mission would be profound, immediate and enduring, from detection of early responses of flora and fauna to climate change to opening access to evolutionary designs for solutions to countless practical problems. The impacts on the biodiversity, environmental and evolutionary sciences would be transformative, from ecosystem models calibrated in detail to comprehensive understanding of the origin and evolution of life over its 3.8 billion year history. The resultant cyber-enabled taxonomy, or cybertaxonomy, would open access to biodiversity data to developing nations, assure access to reliable data about species, and change how scientists and citizens alike access, use and think about biological diversity information.
    Description: Funds for the ‘Sustain What?’ workshop were provided by Arizona State University (Office of the President, International Institute for Species Exploration and Global Institute of Sustainability) and a grant from the US National Science Foundation (DEB-1102500 to QDW). Further support was provided by the College of Liberal Arts and Sciences, Arizona State University and NSF (DEB-0316614 to SK).
    Keywords: Biodiversity ; Bioinformatics ; Biomimicry ; Biosphere ; Conservation ; Cyberinfrastructure ; Ecology ; Evolution ; International collaboration ; Organization of science ; Origins ; Species ; Sustainability ; Systematics ; Taxonomy ; Team work
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 5
    Publication Date: 2022-05-25
    Description: The Future of Research Libraries - April 1 - 3, 2012, Banbury Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
    Description: 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 additional input from the group on several key challenges that arose from the discussions. The purpose of the meeting and survey was threefold: 1. Examine in detail, from a variety of perspectives, how the world of research is changing and the impact these changes have on the direction of research libraries. 2. Create an informed vision of how research libraries can be a vital partner to researchers. 3. Suggest a strategic approach for realizing this vision. The strategic approach presented in this white paper incorporates feedback from various sized research libraries, each with its own mission. The expectation is that individual libraries will use it as a guide in formulating strategies that are appropriate to their research communities, financial circumstances, and organizational reporting structure.
    Description: Cold Spring Harbor Laboratory, the Sloan Foundation, and The Rockefeller University
    Repository Name: Woods Hole Open Access Server
    Type: Working Paper
    Format: application/pdf
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  • 6
    Publication Date: 2022-05-25
    Description: © AMIA, 2009. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose. The definitive version was published in AMIA Annual Symposium Proceedings 2009: 563-567.
    Description: 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 (e.g., MeSH) can be used in combination to retrieve relevant search results. One effective strategy for identifying potential search terms is to examine a collection of documents for frequently occurring terms. In this way, “Tag clouds” are a popular mechanism for ascertaining terms associated with a collection of documents. Here, we present the Literature and Genomic Electronic Resource Catalogue (LigerCat) system for exploring biomedical literature through the selection of terms within a “MeSH cloud” that is generated based on an initial query using journal, article, or gene data. The resultant interface is encapsulated within a Web interface: http://ligercat.ubio.org. The system is also available for installation under an MIT license.
    Description: This work is funded in part thanks to grants from the Ellison Medical Foundation and the National Institutes of Health (R01LM009725-01A1).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 7
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Briefings in Bioinformatics 6 (2010): 610-615, doi:10.1093/bib/bbq029.
    Description: 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 managing and analyzing large amounts of data. Educational resources for scientists in informatics are scarce, yet scientists need the skills and knowledge to work with informaticians and manage graduate students and post-docs in informatics projects. The Marine Biological Laboratory houses a world-renowned library and is involved in a number of informatics projects in the sciences. The MBL has been home to the National Library of Medicine's BioMedical Informatics Course for nearly two decades and is committed to educating scientists and other scholars in informatics. In an innovative, immersive learning experience, Grant Yamashita, a biologist and post-doc at Arizona State University, visited the Science Informatics Group at MBL to learn first hand how informatics is done and how informatics teams work. Hands-on work with developers, systems administrators, librarians, and other scientists provided an invaluable education in informatics and is a model for future science informatics training.
    Description: This work was supported by the National Science Foundation [0926026 to G.Y., SES-0623176]; Jewett Foundation; Ellison Medical Foundation.
    Keywords: MBL ; Digital HPS ; Embryo Project ; MBLWHOI Library ; BioMedical Informatics course ; Informatics boot camp ; Informatics education ; Science Informatics Group
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 8
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 13 (2012): 211, doi:10.1186/1471-2105-13-211.
    Description: 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 biodiversity text sources. A scientific name acts as an important metadata element to link biological information. We present NetiNeti (Name Extraction from Textual Information-Name Extraction for Taxonomic Indexing), a machine learning based approach for recognition of scientific names including the discovery of new species names from text that will also handle misspellings, OCR errors and other variations in names. The system generates candidate names using rules for scientific names and applies probabilistic machine learning methods to classify names based on structural features of candidate names and features derived from their contexts. NetiNeti can also disambiguate scientific names from other names using the contextual information. We evaluated NetiNeti on legacy biodiversity texts and biomedical literature (MEDLINE). NetiNeti performs better (precision = 98.9% and recall = 70.5%) compared to a popular dictionary based approach (precision = 97.5% and recall = 54.3%) on a 600-page biodiversity book that was manually marked by an annotator. On a small set of PubMed Central’s full text articles annotated with scientific names, the precision and recall values are 98.5% and 96.2% respectively. NetiNeti found more than 190,000 unique binomial and trinomial names in more than 1,880,000 PubMed records when used on the full MEDLINE database. NetiNeti also successfully identifies almost all of the new species names mentioned within web pages. We present NetiNeti, a machine learning based approach for identification and discovery of scientific names. The system implementing the approach can be accessed at http://namefinding.ubio.org.
    Description: This project was funded by the Ellison Medical Foundation and a grant from the National Library of Medicine (R01 LM009725).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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