Phenex: ontological annotation of phenotypic diversity

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.

Figure 1. NeXML fragments demonstrating embedded Phenex annotations.

A. A taxon. B. A character and character state.

Figure 2. Correspondence between Entity-Quality statements and evolutionary characters.

A. Comparison of the structure of phenotypic descriptions using character-character state vs. Entity-Quality ( =  ‘Phenotype’) syntaxes. B. The defined relationship between an attribute quality type (shape) and a value quality type (triangular) within the Phenotype and Trait Ontology (PATO).

Figure 3. Phenex screenshot of window configured with panels for browsing and searching of ontology terms and relationships.

Note that users can configure the position and size of each panel on the fly. See text for interface details of each panel; the window shows data from a publication curated by the Phenoscape project.

Figure 4. Phenex screenshot of window configured with panels for editing of taxon lists, voucher specimens, and publication information.

Figure 5. 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.

Figure 6. An example of lexigraphically dissimilar phenotype descriptions from two publications , that are semantically similar in that they pertain to the same anatomical structure.

The ‘dorsal arrector’ and the ‘posterior pectoral-spine serrae’ are both parts of the pectoral fin, which is immediately apparent to both humans and computers from the structure of the anatomy ontology. Some of the data relationships shown, such as PHENOSCAPE:exhibits and those from CDAO (Comparative Data Analysis Ontology, [30]), are not explicit in Phenex. Instead, these are generated by the interpretation of NeXML documents within the Phenoscape Knowledgebase data loading software.