Limits...
Phenex: ontological annotation of phenotypic diversity.

Balhoff JP, Dahdul WM, Kothari CR, Lapp H, Lundberg JG, Mabee P, Midford PE, Westerfield M, Vision TJ - PLoS ONE (2010)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, United States of America. balhoff@nescent.org

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.

Show MeSH

Related in: MedlinePlus

Phenex screenshot of window configured with panels for editing of character and character states data, phenotypes (i.e. EQ statements), and character-by-taxon matrix.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2864769&req=5

pone-0010500-g005: Phenex screenshot of window configured with panels for editing of character and character states data, phenotypes (i.e. EQ statements), and character-by-taxon matrix.

Mentions: Phenex provides a straightforward and familiar graphical user interface (GUI) to evolutionary biologists who work routinely with lists of taxa, characters, character states, and character-by-taxon matrices. In this way, it differs from the closely related Phenote software, which is commonly used for EQ annotation of mutant phenotypes in the genetics community [4]. Both Phenote and Phenex inherit a flexible, modular interface design from the OBO-Edit application framework. The primary GUI components in Phenex include newly developed panels for editing taxa, specimens, characters, character states, character-by-taxon matrices, EQ statements, and literature citations, as shown in Figure 3, Figure 4 and Figure 5 and described below. In addition, Phenex reuses several GUI components provided by OBO-Edit and Phenote that assist users to quickly find and evaluate ontology terms. These include graphical displays of term relationships (‘Complete Ontology Tree View’), a sophisticated term ‘Search Panel’, and a textual ‘Term Info’ panel that displays synonyms, definitions, and relationships (Figure 3). All panels displaying ontology term information are updated with the currently selected term in the primary editing interface.


Phenex: ontological annotation of phenotypic diversity.

Balhoff JP, Dahdul WM, Kothari CR, Lapp H, Lundberg JG, Mabee P, Midford PE, Westerfield M, Vision TJ - PLoS ONE (2010)

Phenex screenshot of window configured with panels for editing of character and character states data, phenotypes (i.e. EQ statements), and character-by-taxon matrix.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2864769&req=5

pone-0010500-g005: Phenex screenshot of window configured with panels for editing of character and character states data, phenotypes (i.e. EQ statements), and character-by-taxon matrix.
Mentions: Phenex provides a straightforward and familiar graphical user interface (GUI) to evolutionary biologists who work routinely with lists of taxa, characters, character states, and character-by-taxon matrices. In this way, it differs from the closely related Phenote software, which is commonly used for EQ annotation of mutant phenotypes in the genetics community [4]. Both Phenote and Phenex inherit a flexible, modular interface design from the OBO-Edit application framework. The primary GUI components in Phenex include newly developed panels for editing taxa, specimens, characters, character states, character-by-taxon matrices, EQ statements, and literature citations, as shown in Figure 3, Figure 4 and Figure 5 and described below. In addition, Phenex reuses several GUI components provided by OBO-Edit and Phenote that assist users to quickly find and evaluate ontology terms. These include graphical displays of term relationships (‘Complete Ontology Tree View’), a sophisticated term ‘Search Panel’, and a textual ‘Term Info’ panel that displays synonyms, definitions, and relationships (Figure 3). All panels displaying ontology term information are updated with the currently selected term in the primary editing interface.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, United States of America. balhoff@nescent.org

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.

Show MeSH
Related in: MedlinePlus