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Pubcrawler Semantic Web “The Semantic Web will bring structure to the meaningful content of Web pages, creating an environment where software agents roaming from page to page can readily carry out sophisticated tasks for users.” Semantic Web Two major components: Agents-software designed to execute searches without direction from a human. • Flexible - server down, look for alternate resource. • Persistent - works without supervision, as needed. Ontology- structured language Ontology That department of metaphysics which investigates and explains the nature and essential properties and relations of all beings, as such, or the principles and causes of being. Webster's Revised Unabridged Dictionary Ontology Structured, hierarchical, controlled vocabulary that describes the concepts or knowledge regarding a particular domain. Why develop an ontology? To share common understanding of the structure of information. everyone agrees that the terms of the ontology describe the domain of knowledge Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html Why develop an ontology? To share common understanding of the structure of information. To allow reuse of domain knowledge. Ontologies describing gene functions can be combined with an ontology describing the sequence of genes. Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html Why develop an ontology? To share common understanding of the structure of information. To allow reuse of domain knowledge. To make domain assumptions explicit. Dehydrogenases ARE enzymes. Why develop an ontology? To share common understanding of the structure of information. To allow reuse of domain knowledge. To make domain assumptions explicit. Separate domain knowledge from operational knowledge. Domain knowledge about the function of enzymes from the reaction mechanisms of enzymes. Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. McGuinness http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html Why develop an ontology? To share common understanding of the structure of information. To allow reuse of domain knowledge. To make domain assumptions explicit. Separate domain knowledge from operational knowledge. Analyze domain knowledge. Formalizing knowledge into defined relationships of an ontology permits computer science to help analyze data. Adapted from: Ontology Development 101: A Guide to Creating Your First Ontology Natalya F. Noy and Deborah L. Ontology Describes the concepts or knowledge regarding a particular domain. An ontology is comprised of Classes • concepts that encompass the domain of interest. Function of a gene product Subclasses may exist-- enzyme Ontology An ontology is comprised of Classes • concepts that encompass the domain of interest. Function of a gene product Subclasses may exist-- enzyme Properties of the classes • specific properties dehydrogenase Ontology An ontology is comprised of Classes • concepts that encompass the domain of interest. Function of a gene product Subclasses may exist-- enzyme Properties of the classes • specific properties dehydrogenase Restrictions on the properties • only certain classes of dehydrogenases exist Ontology Typically, instances of the domain are kept separate from the ontology. Liver alcohol dehydrogenase is an instance. Combining an ontology with specific instances is a knowledge base (as distinct from a database). Taxonomy Taxonomy Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo sapiens * Gorilla * Gorilla gorilla (gorilla) * Gorilla gorilla beringei (mountain gorilla) * Gorilla gorilla gorilla (lowland gorilla) * Gorilla gorilla graueri * Homo * Homo sapiens (human) * Homo sapiens neanderthalensis * Pan (chimpanzees) * Pan paniscus (pygmy chimpanzee) * Pan troglodytes (chimpanzee) * Pan troglodytes schweinfurthii * Pan troglodytes troglodytes * Pan troglodytes vellerosus * Pan troglodytes verus * Pongo * Pongo pygmaeus (orangutan) * Pongo pygmaeus abelii (Sumatran orangutan) * Pongo pygmaeus pygmaeus (Bornean orangutan) * Pongo sp. Gene Ontology Gene Ontology Parent-Child Relationships Nucleus Nucleoplasm A child is a subset of a parent’s element s From: Karen Christie, Ceri Van Slyke and Petra Fey Nuclear envelope Nucleolus Chromosome Perinuclear space T he cell component t erm Nucleus has 5 children Gene Ontology “Tree” Relationships Derivation of Romance languages from Latin. From R.A. Hall Jr., Introductory Linguistics; originally published by Chilton Books, now distributed by Rand McNally & Co. From: Karen Christie, Ceri Van Slyke and Petra Fey Gene Ontology From: Karen Christie, Ceri Van Slyke and Petra Fey Gene Ontology Apoptosis •Utility: Microarray, want to know all genes involved in Apoptosis. • Determine fold change in gene expression for all genes involved in Apoptosis. •Report all genes, involved in apoptosis, that change at least 2 fold. MeSH Ontology Medical Subject Headings -provides indexing for PubMed. Can be used to generate complex queries in a simple fashion. Do not need to remember all these terms Food Food Fruits Vegetables Meats Food Fruits Apples Oranges Vegetables Meats Pears Food Fruits Apples Oranges Vegetables Meats Pears System would “know” that apples, oranges and pairs are all fruits, AND that they are edible. Food Fruits Apples Oranges Vegetables Pears Meats Chicken “Know” that chicken is not a fruit Food Fruits Apples Oranges Vegetables Pears Meats Chicken Additional subclasses Food Fruits Apples Oranges Vegetables Pears Meats Chicken Additional subclasses Instances