Pubcrawler

Semantic WebSemantic Web

““The Semantic Web will bring structure to The Semantic Web will bring structure to the meaningful content of Web pages, the meaningful content of Web pages, creating an environment where software creating an environment where software agents roaming from page to page can agents roaming from page to page can readily carry out sophisticated tasks for readily carry out sophisticated tasks for users.”users.”

Semantic WebSemantic Web

Two major components:Two major components: Agents-software designed to execute Agents-software designed to execute

searches without direction from a human.searches without direction from a human.• Flexible - server down, look for alternate resource.Flexible - server down, look for alternate resource.• Persistent - works without supervision, as needed.Persistent - works without supervision, as needed.

Ontology- structured languageOntology- structured language

OntologyOntology

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

OntologyOntology

Structured, hierarchical, controlled Structured, hierarchical, controlled vocabulary that describes the vocabulary that describes the concepts or concepts or knowledgeknowledge regarding a particular domain. regarding a particular domain.

Why develop an ontology?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.htmlhttp://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

Why develop an ontology?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.htmlhttp://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

Why develop an ontology?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.

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.htmlhttp://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

Why develop an ontology?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.htmlhttp://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

Why develop an ontology?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. McGuinness

http://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.htmlhttp://www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html

OntologyOntology

Describes the Describes the concepts or knowledgeconcepts or knowledge regarding a particular domain.regarding a particular domain.

An ontology is comprised ofAn ontology is comprised of ClassesClasses

• concepts that encompass the domain of interest.concepts that encompass the domain of interest. Function of a gene product -Function of a gene product - Subclasses may exist-- enzymeSubclasses may exist-- enzyme

OntologyOntology

An ontology is comprised ofAn ontology is comprised of Classes Classes

• concepts that encompass the domain of interest.concepts that encompass the domain of interest. Function of a gene product -Function of a gene product - Subclasses may exist-- enzymeSubclasses may exist-- enzyme

Properties of the classesProperties of the classes• specific propertiesspecific properties

dehydrogenasedehydrogenase

OntologyOntology

An ontology is comprised ofAn ontology is comprised of Classes Classes

• concepts that encompass the domain of interest.concepts that encompass the domain of interest. Function of a gene product -Function of a gene product - Subclasses may exist-- enzymeSubclasses may exist-- enzyme

Properties of the classesProperties of the classes• specific propertiesspecific properties

dehydrogenasedehydrogenase

Restrictions on the propertiesRestrictions on the properties• only certain classes of dehydrogenases existonly certain classes of dehydrogenases exist

OntologyOntology

Typically, instances of the domain are kept Typically, instances of the domain are kept separate from the ontology.separate from the ontology.

Liver alcohol dehydrogenase is an instance.Liver alcohol dehydrogenase is an instance. Combining an ontology with specific instances Combining an ontology with specific instances

is a knowledge base (as distinct from a is a knowledge base (as distinct from a database).database).

TaxonomyTaxonomy

TaxonomyTaxonomy

Eukaryota; Metazoa; Chordata; Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Mammalia; Eutheria; Primates; Catarrhini; Catarrhini; HominidaeHominidae;; Homo sapiens Homo sapiens

* Gorilla* Gorilla * Gorilla gorilla (gorilla)* Gorilla gorilla (gorilla) * Gorilla gorilla beringei (mountain gorilla)* Gorilla gorilla beringei (mountain gorilla) * Gorilla gorilla gorilla (lowland gorilla)* Gorilla gorilla gorilla (lowland gorilla) * Gorilla gorilla graueri* Gorilla gorilla graueri * Homo* Homo * Homo sapiens (human)* Homo sapiens (human) * Homo sapiens neanderthalensis* Homo sapiens neanderthalensis * Pan (chimpanzees)* Pan (chimpanzees) * Pan paniscus (pygmy chimpanzee)* Pan paniscus (pygmy chimpanzee) * Pan troglodytes (chimpanzee)* Pan troglodytes (chimpanzee) * Pan troglodytes schweinfurthii* Pan troglodytes schweinfurthii * Pan troglodytes troglodytes* Pan troglodytes troglodytes * Pan troglodytes vellerosus* Pan troglodytes vellerosus * Pan troglodytes verus* Pan troglodytes verus * Pongo* Pongo * Pongo pygmaeus (orangutan)* Pongo pygmaeus (orangutan) * Pongo pygmaeus abelii (Sumatran orangutan)* Pongo pygmaeus abelii (Sumatran orangutan) * Pongo pygmaeus pygmaeus (Bornean orangutan)* Pongo pygmaeus pygmaeus (Bornean orangutan) * Pongo sp.* Pongo sp.

Gene OntologyGene Ontology

Gene OntologyGene Ontology

Nucleus

Nucleoplasm Nuclearenvelope

Chromosome Perinuclear spaceNucleolus

A child is a subset ofa parent’s elements

The cell component term Nucleus has 5 children

Parent-Child Relationships

From: Karen Christie, Ceri Van Slyke and Petra Fey

Gene OntologyGene Ontology

Derivation of Romance languages from Latin. From R.A. Hall Jr., Introductory Linguistics; originally published by Chilton Books,now distributed by Rand McNally & Co.

“Tree” Relationships

From: Karen Christie, Ceri Van Slyke and Petra Fey

Gene OntologyGene 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 MeSH Ontology

Medical Subject Headings -provides indexing for Medical Subject Headings -provides indexing for PubMed.PubMed.

Can be used to generate complex queries in a Can be used to generate complex queries in a simple fashion.simple fashion.

Do not need to remember all these terms

Food

Food

Fruits

Vegetables

Meats

Food

Fruits

Oranges

Apples

PearsVegetables

Meats

Food

Fruits

Oranges

Apples

Pears

System would “know” that apples, oranges and pairs are all fruits, AND that they are edible.

Vegetables

Meats

Food

Fruits

Oranges

Apples

PearsVegetables

Meats

Chicken

“Know” that chicken is not a fruit

Food

Fruits

Oranges

Apples

PearsVegetables

Meats

Chicken

Additional subclasses

Food

Fruits

Oranges

Apples

PearsVegetables

Meats

Chicken

Additional subclasses

Instances