pubcrawler
DESCRIPTION
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: - PowerPoint PPT PresentationTRANSCRIPT
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