Phenex: Ontological Annotation of Phenotypic Diversity

Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational analyses across studies and study systems. Phenex addresses this problem by allowing scientists to employ standard ontologies and syntax to link computable phenotype annotations to evolutionary character matrices, as well as to link taxa and specimens to ontological identifiers. Ontologies have become a foundational technology for establishing shared semantics, and, more generally, for capturing and computing with biological knowledge

3D star coordinate-based visualization of relation clusters from OWL ontologies

The recent proliferation of high-level and domain-specific ontologies has necessitated the development of prudent integration strategies. Visualization techniques are an important tool to support the data and knowledge integration initiative. This chapter reviews a methodology to visualize clusters of relations from ontologies specified using the Web Ontology Language (OWL). The relations, which in OWL are referred to as object properties, from various ontologies are organized into clusters based upon their intrinsic semantics. The intrinsic semantics of every relation from an input ontology is explicitly specified by a framework of 32 common elements; each element captures a specific aspect of the relationship between a relation’s domain and range. Using this framework, each relation can be represented in a 32-dimensional “relation space.” Relation clusters in 32 dimensions are projected to 3 dimensions using an automated 3- dimensional (3D) star coordinate-based visualization technique. Results from applying an algorithm to create and subsequently visualize relation clusters formed from the IEEE Suggested Upper Merged Ontology (SUMO) are presented in this chapter and discussed in the context of their potential utility for knowledge reuse and interoperability on the Semantic Web

3D Visualization of Relation Clusters from OWL Ontologies

Abstract- This paper presents an enhanced methodology to visualize clusters of relations from OWL ontologies. The relations are clustered by comparing their intrinsic semantics. The intrinsic semantics of every relation from an input ontology is explicitly specified by a framework of 32 common elements; each element captures a specific aspect of the relationship between a relation’s domain and range. Using this framework, each relation can be represented in a 32 dimensional “relation space.” Relation clusters in 32 dimensions are projected to 3 dimensions using an automated 3D star coordinate visualization technique. Results from the application of the proposed algorithm to visualize relation clusters from the IEEE SUMO Ontology are presented in this paper; and discussed in the context of their potential utility to knowledge reuse and interoperability on the Semantic Web

Correspondence between Entity-Quality statements and evolutionary characters.

<p>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 (<i>shape</i>) and a value quality type (<i>triangular</i>) within the Phenotype and Trait Ontology (PATO).</p

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

<p>Phenex screenshot of window configured with panels for editing of taxon lists, voucher specimens, and publication information.</p

NeXML fragments demonstrating embedded Phenex annotations.

<p>A. A taxon. B. A character and character state.</p

Metadata identifiers and XML elements used by Phenex to embed annotations with NeXML documents.

<p>Identifiers in the <a href="http://vocab.phenoscape.org/" target="_blank">http://vocab.phenoscape.org/</a> namespace are intended to be replaced with community standards as they become available.</p

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.

<p>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.</p