Hierarchical Search in Semant Eco Support Varied Ontology

Hierarchical Search in Semant. Eco Support Varied Ontology Design Patterns Session: "Semantics for Biodiversity: Interoperability with genomic and ecological semantics" Patrice Seyed, Evan Patton, and Deborah Mc. Guinness (presented by Nathan Wilson)

Introduction • Multiple ontology design patterns for modeling taxonomic classification • Vertebrate Taxonomy Ontology (VTO) – Taxons are represented as classes • ‘Ictaluridae Sub. Class. Of Siluriformes’ • Phenoscape Ontology – Taxa as Individuals • ‘Ictaluridae subclade_of Siluriformes’ • Population thinking, inference of up-propagation from descendent species populations to ancestors • ‘contains_clade o has_member -> has_member’ – A DL description of a clade is propagated up the clade taxonomy

Semant. Eco Modular Framework and the Hierarchical Search Component – Adheres to model-view-controller software architecture pattern • separation between the underlying representation and that which is presented to the user – Allowing support of varied Knowledge Representation design patterns – Supports user interface rendering for navigation along different axes (e. g. , generalization, partonomic, taxonomic)

Semant. Eco Module Framework and the Hierarchical Search Component • Semant. Eco module designers can provide custom hierarchical search facets. • Enable flexible navigation of resources via their relationships to others, to providing users with multiple paths for finding data. • Leverages Java. Script Trees library (JSTrees) • Each node maps to an RDF Resource, and the selection of a node triggers construction/execution of a SPARQL pattern for rendering immediate children nodes • A SPARQL query pattern is provided by a module designer along the axes of interest for hierarchical navigation, for retrieving a tree’s root and children nodes. • A data-level SPARQL pattern for search using tree selections is ultimately composed in conjunction

Flow • Client interface selection maps to REST-ful web request • Server side SPARQL Query executed, results to client as JSON

Phenoscape Faceted App

SPARQL Query for “Roots” prefix pheno: <http: //vocab. phenoscape. org/> select DISTINCT ? child ? parent where { graph <http: //phenoscape-example>{ ? child pheno: subclade_of ? parent. FILTER NOT EXISTS { ? parent pheno: subclade_of ? z } } }

SPARQL Query for “Children” prefix pheno: <http: //vocab. phenoscape. org/> select DISTINCT ? child ? parent where { graph <http: //phenoscape-example>{ ? child pheno: subclade_of <Client selection URI>. } }

Conclusions • Enables one to develop ontologies and semantic web applications independently • Either conceptualization described above for taxon modeling can be leveraged in the Hierarchical Search Facet component with the appropriate supporting SPARQL queries in place. • This suits our immediate needs for semantic search in Semant. Eco as a portal and as an architecture, for a semantically-enabled monitoring environment it supports flexible search backed by semantics.

References • http: //phenoscape. org/wiki/Individual-based_taxonomy • James P. Balhoff, Peter E. Midford, Hilmar Lapp: Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies. International Conference on Biomedical Ontologies, Buffalo, NY 2011