Hierarchical Search in SemantEco Support Varied Ontology Design Patterns

Session: "Semantics for Biodiversity: Interoperability with genomic and ecological

semantics"

Patrice Seyed, Evan Patton, and Deborah McGuinness

(presented by Nathan Wilson)

Introduction• Multiple ontology design patterns for modeling taxonomic

classification• Vertebrate Taxonomy Ontology (VTO)– Taxons are represented as classes

• ‘Ictaluridae SubClassOf 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

SemantEco 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)

SemantEco Module Framework and the Hierarchical Search Component

• SemantEco 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 JavaScript 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 ?parentwhere { 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 ?parentwhere { 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 SemantEco 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