Browsing by Author "Lapp, Hilmar"
Now showing items 1-20 of 35
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500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.
(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 Logical Model of Homology for Comparative Biology.
(Systematic biology, 2020-03)There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to ... -
A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx).
(PeerJ, 2022-01)To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent ... -
A unified anatomy ontology of the vertebrate skeletal system.
(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 ... -
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.
(Database : the journal of biological databases and curation, 2018-01)Natural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would ... -
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.
(Journal of biomedical semantics, 2014-01)<h4>Background</h4>Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have ... -
apex: phylogenetics with multiple genes.
(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 ... -
Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare.
(NPJ digital medicine, 2020-01)Storing very large amounts of data and delivering them to researchers in an efficient, verifiable, and compliant manner, is one of the major challenges faced by health care providers and researchers in the life sciences. ... -
Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies.
(Systematic biology, 2022-10)Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent "parts", but ... -
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
(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 ... -
Erratum: Publisher Correction: Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare.
(NPJ digital medicine, 2020-01)[This corrects the article DOI: 10.1038/s41746-020-0235-5.]. -
Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.
(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.
(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 ... -
Meeting Report: BioSharing at ISMB 2010.
(Standards in genomic sciences, 2010-12)This report summarizes the proceedings of the one day BioSharing meeting held at the Intelligent Systems for Molecular Biology (ISMB) 2010 conference in Boston, MA, USA This inaugural BioSharing event was hosted by the Genomic ... -
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.
(Database : the journal of biological databases and curation, 2015-01)The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project ... -
Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.
(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 ... -
NeXML: rich, extensible, and verifiable representation of comparative data and metadata.
(Systematic biology, 2012-07)In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires ... -
On the Ontological Modeling of Trees
(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.
(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.
(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 ...
