Hammock Jennifer

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Hammock
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Jennifer
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  • Article
    ENVIRONMENTS and EOL : identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life
    (Oxford University Press, 2015-01-24) Pafilis, Evangelos ; Frankild, Sune P. ; Schnetzer, Julia ; Fanini, Lucia ; Faulwetter, Sarah ; Pavloudi, Christina ; Vasileiadou, Katerina ; Leary, Patrick R. ; Hammock, Jennifer ; Schulz, Katja S. ; Parr, Cynthia Sims ; Arvanitidis, Christos ; Jensen, Lars Juhl
    The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users.
  • Article
    TraitBank : practical semantics for organism attribute data
    (IOS Press, 2016-10-11) Parr, Cynthia Sims ; Schulz, Katja S. ; Hammock, Jennifer ; Wilson, Nathan ; Leary, Patrick R. ; Rice, Jeremy J. ; Corrigan, Robert J.
    Encyclopedia of Life (EOL) has developed TraitBank (http://eol.org/traitbank), a new repository for organism attribute (trait) data. TraitBank aggregates, manages and serves attribute data for organisms across the tree of life, including life history characteristics, habitats, distributions, ecological relationships and other data types. We describe how TraitBank ingests and manages these data in a way that leverages EOL’s existing infrastructure and semantic annotations to facilitate reasoning across the TraitBank corpus and interoperability with other resources. We also discuss TraitBank’s impact on users and collaborators and the challenges and benefits of our lightweight, scalable approach to the integration of biodiversity data.
  • Thesis
    Structure, function and context : the impact of morphometry and ecology on olfactory sensitivity
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2005-02) Hammock, Jennifer
    In this thesis, the relationships of olfactory sensitivity to three biological variables were tested. The sensitivity of a marine mammal, the sea otter (Enhydra lutris) was measured in order to determine whether a marine lifestyle results in impaired olfaction. The effect of dietary relevance on sensitivity to specific odorants was evaluated. Finally, a new morphometric model of olfactory uptake efficiency was developed and tested against behavioral measurements of olfactory sensitivity in twelve mammalian species from five orders. Olfactory thresholds were obtained for the first time from two sea otters for seven odorant compounds from various natural sources. Otters were trained using operant conditioning to participate in direct behavioral testing. Sea otter olfactory sensitivity was comparable to that of previously studied terrestrial mammals. The incidence of an odorant in the diet of the olfactor was found to influence specific sensitivity to that compound but to varying degrees among different mammalian orders. Nasal cavity specimens were measured using radiologic (CT scan) and histologic (light microscopy) techniques. Surface areas and volumes of the nasal cavity were used to calculate the Olfactory Uptake Efficiency (OUE). OUE is significantly related to olfactory bulb volume. A possible relationship was found between OUE and general olfactory sensitivity.