Phenex: ontological annotation of phenotypic diversity.
| dc.contributor.author | Balhoff, James P | |
| dc.contributor.author | Dahdul, Wasila M | |
| dc.contributor.author | Kothari, Cartik R | |
| dc.contributor.author | Lapp, Hilmar | |
| dc.contributor.author | Lundberg, John G | |
| dc.contributor.author | Mabee, Paula | |
| dc.contributor.author | Midford, Peter E | |
| dc.contributor.author | Westerfield, Monte | |
| dc.contributor.author | Vision, Todd J | |
| dc.coverage.spatial | United States | |
| dc.date.accessioned | 2015-05-27T18:00:24Z | |
| dc.date.issued | 2010-05-05 | |
| dc.description.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. | |
| dc.identifier | ||
| dc.identifier.eissn | 1932-6203 | |
| dc.identifier.uri | ||
| dc.language | eng | |
| dc.publisher | Public Library of Science (PLoS) | |
| dc.relation.ispartof | PLoS One | |
| dc.relation.isversionof | 10.1371/journal.pone.0010500 | |
| dc.subject | Biodiversity | |
| dc.subject | Biological Evolution | |
| dc.subject | Computational Biology | |
| dc.subject | Internet | |
| dc.subject | Phenotype | |
| dc.subject | Semantics | |
| dc.subject | Software | |
| dc.title | Phenex: ontological annotation of phenotypic diversity. | |
| dc.type | Journal article | |
| duke.contributor.orcid | Lapp, Hilmar|0000-0001-9107-0714 | |
| pubs.author-url | ||
| pubs.begin-page | e10500 | |
| pubs.issue | 5 | |
| pubs.organisational-group | Duke | |
| pubs.organisational-group | Staff | |
| pubs.publication-status | Published online | |
| pubs.volume | 5 |
Files
Original bundle
- Name:
- Phenex: ontological annotation of phenotypic diversity..pdf
- Size:
- 884.03 KB
- Format:
- Adobe Portable Document Format
- Description:
- Accepted version