Journal article
Phenex: Ontological Annotation of Phenotypic Diversity
PloS one, v 5(5), pp e10500-e10500
05 May 2010
PMID: 20463926
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
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 have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.
Methodology/Principal Findings: Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.
Conclusions/Significance: Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.
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Details
- Title
- Phenex: Ontological Annotation of Phenotypic Diversity
- Creators
- James P. Balhoff - University of North Carolina at Chapel HillWasila M. Dahdul - University of South DakotaCartik R. Kothari - University of North Carolina at Chapel HillHilmar Lapp - National Evolutionary Synthesis CenterJohn G. Lundberg - Drexel UniversityPaula Mabee - University of South DakotaPeter E. Midford - National Evolutionary Synthesis CenterMonte Westerfield - University of OregonTodd J. Vision - Natl Evolutionary Synth Ctr, Durham, NC USA
- Publication Details
- PloS one, v 5(5), pp e10500-e10500
- Publisher
- Public Library Science
- Number of pages
- 10
- Grant note
- DBI 0641025 / NSF; National Science Foundation (NSF) U41HG002659 / NATIONAL HUMAN GENOME RESEARCH INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI) NSF EF-0423641 / National Evolutionary Synthesis Center 1062542 / Div Of Biological Infrastructure; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) HG002659 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biodiversity, Earth, and Environmental Science (BEES); Academy of Natural Sciences of Drexel University
- Web of Science ID
- WOS:000277379400033
- Scopus ID
- 2-s2.0-77953796587
- Other Identifier
- 991019335513704721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Evolutionary Biology