Phenex: ontological annotation of phenotypic diversity.
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 p...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2010-05-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2864769?pdf=render |
| _version_ | 1818479441469243392 |
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| author | James P Balhoff Wasila M Dahdul Cartik R Kothari Hilmar Lapp John G Lundberg Paula Mabee Peter E Midford Monte Westerfield Todd J Vision |
| author_facet | James P Balhoff Wasila M Dahdul Cartik R Kothari Hilmar Lapp John G Lundberg Paula Mabee Peter E Midford Monte Westerfield Todd J Vision |
| author_sort | James P Balhoff |
| collection | DOAJ |
| description | 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.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.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. |
| first_indexed | 2024-12-10T11:10:38Z |
| format | Article |
| id | doaj.art-2aee79c190164de9a00188e1aa7e9eeb |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T11:10:38Z |
| publishDate | 2010-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-2aee79c190164de9a00188e1aa7e9eeb2022-12-22T01:51:26ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-05-0155e1050010.1371/journal.pone.0010500Phenex: ontological annotation of phenotypic diversity.James P BalhoffWasila M DahdulCartik R KothariHilmar LappJohn G LundbergPaula MabeePeter E MidfordMonte WesterfieldTodd J VisionPhenotypic 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.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.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.http://europepmc.org/articles/PMC2864769?pdf=render |
| spellingShingle | James P Balhoff Wasila M Dahdul Cartik R Kothari Hilmar Lapp John G Lundberg Paula Mabee Peter E Midford Monte Westerfield Todd J Vision Phenex: ontological annotation of phenotypic diversity. PLoS ONE |
| title | Phenex: ontological annotation of phenotypic diversity. |
| title_full | Phenex: ontological annotation of phenotypic diversity. |
| title_fullStr | Phenex: ontological annotation of phenotypic diversity. |
| title_full_unstemmed | Phenex: ontological annotation of phenotypic diversity. |
| title_short | Phenex: ontological annotation of phenotypic diversity. |
| title_sort | phenex ontological annotation of phenotypic diversity |
| url | http://europepmc.org/articles/PMC2864769?pdf=render |
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