Now showing items 1-20 of 20

    • 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 ...
    • apex: phylogenetics with multiple genes. 

      Archer, F; Goudet, J; Harris, R; Jombart, T; Kamvar, Z; Lapp, Hilmar; Paradis, E; ... (8 authors) (Mol Ecol Resour, 2017-01)
      Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number ...
    • BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. 

      Aerts, J; Akune, Y; Antezana, E; Aoki-Kinoshita, KF; Arakawa, K; Aranda, B; Baran, J; ... (85 authors) (J Biomed Semantics, 2014-02-05)
      The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted ...
    • 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 ...
    • On the Ontological Modeling of Trees 

      Carral, D; Hitzler, P; Lapp, Hilmar; Rudolph, S (2017-10-24)
      Trees -- i.e., the type of data structure known under this name -- are central to many aspects of knowledge organization. We investigate some central design choices concerning the ontological modeling of such trees. ...
    • Overview of FEED, the feeding experiments end-user database. 

      Gapeyev, V; German, RZ; Lapp, Hilmar; Liu, X; Vinyard, CJ; Wall, CE; Williams, SH (Integr Comp Biol, 2011-08)
      The Feeding Experiments End-user Database (FEED) is a research tool developed by the Mammalian Feeding Working Group at the National Evolutionary Synthesis Center that permits synthetic, evolutionary analyses of the physiology ...
    • 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)
    • RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011. 

      Amaral-Zettler, LA; Bik, H; Blum, S; Edwards, James; Field, D; Garrity, G; Gilbert, Jack A; ... (20 authors) (Stand Genomic Sci, 2012-10-10)
      Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify ...
    • RNeXML: A package for reading and writing richly annotated phylogenetic, character and trait data in R 

      Boettiger, C; Chamberlain, S; Vos, R; Lapp, Hilmar (Methods in Ecology and Evolution, 2016-03-01)
      NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the r programming ...
    • Science incubators: synthesis centers and their role in the research ecosystem. 

      Alberts, S; Cranston, K; Kingsolver, J; Lapp, Hilmar; McClain, Craig R; Rodrigo, Allen G; Smith, R; ... (10 authors) (PLoS Biol, 2013)
      How should funding agencies enable researchers to explore high-risk but potentially high-reward science? One model that appears to work is the NSF-funded synthesis center, an incubator for community-led, innovative science.
    • Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) 

      Allen, GD; Berriman, B; Choi, S-CT; Elster, AC; Hanwell, MD; Hetherington, J; Howison, J; ... (15 authors) (Journal of Open Research Software, 2014-07-09)
      Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists’ research increasingly depends on the quality and availability of software upon ...
    • The 2015 Bioinformatics Open Source Conference (BOSC 2015). 

      Chapman, B; Cock, PJ; Davey, R; Fields, C; Harris, NL; Hokamp, K; Lapp, Hilmar; ... (8 authors) (PLoS Comput Biol, 2016-02)
      The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open ...
    • The 2016 Bioinformatics Open Source Conference (BOSC). 

      Harris, NL; Cock, PJ; Chapman, B; Fields, CJ; Hokamp, K; Lapp, Hilmar; Muñoz-Torres, M; ... (8 authors) (F1000Res, 2016)
      Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of ...
    • The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018). 

      Lapp, Hilmar; Harris, Nomi L; Wiencko, Heather; Chapman, Brad; Cock, Peter JA; Hokamp, Karsten; Fields, Chris; ... (8 authors) (F1000Research, 2018-01)
      In 2018, the annual Bioinformatics Open Source Conference was held for the first time in conjunction with the Galaxy Community Conference, as an experiment to see if we could reach people in the bioinformatics community ...
    • 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, ...