Semantic Species Taxonomy Shima Izadpanahi CMPE583 Term project.

Semantic Species Taxonomy

Shima IzadpanahiShima Izadpanahi

CMPE583 Term projectCMPE583 Term project

OUTLINE

TaxonomyTaxonomy Platforms Species taxonomySpecies taxonomy Ontology Development Application

SScientific cientific CClassification of lassification of organisms organisms

Taxonomy:Taxonomy: is the is the practice and science practice and science of classification.of classification.

SScientific cientific classificationclassification:: is a is a method by which method by which biologists group and biologists group and categorize species of categorize species of organisms. organisms.

The hierarchy of scientific classification.The hierarchy of scientific classification.

Classification Classification hierarchy:kingdomhierarchy:kingdom

•kingdom is the highest taxonomic rank .

There are six kingdoms (Animalia, Plantae, Fungi, Protoctista, Archaea, and Monera)

Classification hierarchy, Classification hierarchy, phylumphylum

Each kingdom is divided into smaller groups called phylum.

phyla can be thought of as grouping animals based on general body plan. Chordata (animals with notochords) and order is Carnivora (mammals that eat meat). The best known animal phyla are the Mollusca, Porifera, Cnidaria, Platyhelminthes, Nematoda, Annelida, Arthropoda, Echinodermata, and Chordata, the phylum to which humans belong.

Classification Classification hierarchy,Classhierarchy,Class

For example, Mammalia is the class used in the classification of panthers, whose phylum is Chordata (animals with notochords) and order is Carnivora (mammals that eat meat).and family is Felidae (family of cats) and Genus is panthera (the cats )And species is (panthera pardus)

PLATFORMSProtégé: Is Graphical ontology editor, An open source application, Easy to use ,Platform independent

Java: Platform independent programming environment, Object oriented has Powerful APIs .(JDK 5)

JBuilder 2006: IDE for java, Provided by Borland company

JSP: For developing dynamic websites Jena: Java API for ontology manipulation, Provided by

HP labs, Create and manipulate RDF graphs. (Jena 2.2) RDQL: Ontology query language for Jena Tomcat: web server for handling jsp request (Tomcat (Tomcat

server 5.5)server 5.5)

Ontology Classes Ontology Classes •Kingdom: the highest rank in classification

•phylum: the largest generally accepted groupings of animals and other living things

•Class: in the scientific classification of organisms in biology below phylum and above order.

•Order:The order as a distinctive rank of biological classification having its own distinctive name

•Family: Family, as a rank intermediate between order and genus, is a relatively recent invention.

•Genus: is a low-level taxonomic rank used in the classification of living and fossil organisms.

•Specie:a species is one of the basic units of biological classification

Taxonomy Object Taxonomy Object Properties Properties

Taxonomy Data type Taxonomy Data type PropertiesProperties

Data type Properties are to bind a value to an individual.

Web Site Features:Web Site Features:

Classification Layer PagesClassification Layer Pages Taxon detail pagesTaxon detail pages All entity page All entity page Statistics pageStatistics page

QueryQueryRead description:Read description:

SELECT ?xSELECT ?x WHERE ( nss:name, nss:hasDescription, ?x)WHERE ( nss:name, nss:hasDescription, ?x)Taxonomy parent:Taxonomy parent:

SELECT ?xSELECT ?x WHERE ( nss:name, nss:isPartOfKingdom, ?WHERE ( nss:name, nss:isPartOfKingdom, ?x)x)

Read all taxonomic data:Read all taxonomic data: SELECT ?xSELECT ?x WHERE ( ?x, ?a, ?b)WHERE ( ?x, ?a, ?b)

QUESTIONS?QUESTIONS?