Now showing items 1-9 of 9

    • 500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. 

      Balhoff, JP; Dahdul, Wasila M; Lapp, Hilmar; Mabee, BP; Midford, PE; Vision, TJ; Westerfield, M (J Appl Ichthyol, 2012-06-01)
      The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie ...
    • A unified anatomy ontology of the vertebrate skeletal system. 

      Balhoff, JP; Blackburn, DC; Dahdul, Wasila M; Diehl, AD; Haendel, Melissa A; Hall, BK; Lapp, Hilmar; ... (15 authors) (PLoS One, 2012)
      The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access ...
    • Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. 

      Balhoff, JP; Dahdul, Wasila M; Engeman, J; Grande, T; Hilton, EJ; Kothari, C; Lapp, Hilmar; ... (12 authors) (PLoS One, 2010-05-20)
      BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely ...
    • Finding our way through phenotypes. 

      Anzaldo, SS; Ashburner, M; Balhoff, JP; Blackburn, DC; Blake, JA; Burleigh, JG; Chanet, B; ... (74 authors) (PLoS Biol, 2015-01)
      Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable ...
    • Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. 

      Balhoff, JP; Crompton, AW; Done, J; Druzinsky, RE; German, RZ; Haendel, Melissa A; Herrel, A; ... (17 authors) (PLoS One, 2016)
      BACKGROUND: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for ...
    • Phenex: ontological annotation of phenotypic diversity. 

      Balhoff, JP; Dahdul, Wasila M; Kothari, CR; Lapp, Hilmar; Lundberg, JG; Mabee, Paula M; Midford, PE; ... (9 authors) (PLoS One, 2010-05-05)
      BACKGROUND: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions ...
    • Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. 

      Alfaro, ME; Balhoff, JP; Bik, HM; Brown, JW; Cranston, K; Deus, H; Harmon, LJ; ... (28 authors) (BMC Bioinformatics, 2013-05-13)
      BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate ...
    • Presence-absence reasoning for evolutionary phenotypes 

      Balhoff, JP; Dececchi, TA; Lapp, Hilmar; Mabee, Paula M (Phenotype Day at International Conference on Intelligent Systems for Molecular Biology (ISBM 2014), 2014-07)
    • The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. 

      Balhoff, JP; Blackburn, DC; Dahdul, Wasila M; Dececchi, TA; Ibrahim, N; Lapp, Hilmar; Lundberg, JG; ... (12 authors) (J Biomed Semantics, 2013-11-22)
      BACKGROUND: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, ...