Leary Patrick R.

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Leary
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Patrick R.
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  • Article
    Meeting report : GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)
    (Genomic Standards Consortium, 2014) Wieczorek, John ; Banki, Olaf ; Blum, Stan D. ; Deck, John ; Doring, Markus ; Droge, Gabriele ; Endresen, Dag ; Goldstein, Philip ; Leary, Patrick R. ; Krishtalka, Leonard ; O'Tuama, Eamonn ; Robbins, Robert J. ; Robertson, Tim ; Yilmaz, Pelin
    The workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide variety of sample data. Topics addressed in the workshop included 1) a review of outstanding issues in the Darwin Core standard, 2) issues relating to publishing of biodiversity data through Darwin Core Archives, 3) use of Darwin Core Archives for publishing sample and monitoring data, 4) the case for modifying the Darwin Core Text Guide specification to support many-to-many relations, and 5) the generalization of the Darwin Core Archive to a “Biodiversity Data Archive”. A wide variety of use cases were assembled and discussed in order to inform further developments.
  • 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.
  • Article
    uBioRSS : tracking taxonomic literature using RSS
    (Oxford University Press, 2007-03-28) Leary, Patrick R. ; Remsen, David P. ; Norton, Cathy N. ; Patterson, David J. ; Sarkar, Indra Neil
    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 syndication formats deliver content directly to the subscriber, allowing them to locally aggregate content from a variety of sources instead of having to find the information on multiple websites. The uBioRSS application is a "taxonomically intelligent" service customized for the biological sciences. It aggregates syndicated content from academic publishers and science news feeds, then uses a taxonomic name entity recognition algorithm to identify and index taxonomic names within those data streams. The resulting name index is cross-referenced to current global taxonomic datasets to provide context for browsing the publications by taxonomic group. This process, called taxonomic indexing, draws upon services developed specifically for biological sciences, collectively referred to as "taxonomic intelligence." Such value-added enhancements can provide biologists with accelerated and improved access to current biological content.