1 / 40

Pubcrawler

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:

linore
Download Presentation

Pubcrawler

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Pubcrawler

  2. 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.”

  3. 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

  4. 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

  5. Ontology • Structured, hierarchical, controlled vocabulary that describes the concepts or knowledge regarding a particular domain.

  6. 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

  7. 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

  8. 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.html

  9. 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

  10. 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.html

  11. 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

  12. 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

  13. 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

  14. 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).

  15. Taxonomy

  16. Taxonomy • Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo sapiens

  17. * 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.

  18. Gene Ontology

  19. Gene Ontology From: Karen Christie, Ceri Van Slyke and Petra Fey

  20. Gene Ontology From: Karen Christie, Ceri Van Slyke and Petra Fey

  21. Gene Ontology From: Karen Christie, Ceri Van Slyke and Petra Fey

  22. Gene Ontology Apoptosis

  23. 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.

  24. MeSH Ontology • Medical Subject Headings -provides indexing for PubMed. • Can be used to generate complex queries in a simple fashion.

  25. Do not need to remember all these terms

  26. Food

  27. Food Fruits Vegetables Meats

  28. Apples Oranges Pears Food Fruits Vegetables Meats

  29. Apples Oranges Pears Food Fruits Vegetables Meats System would “know” that apples, oranges and pairs are all fruits, AND that they are edible.

  30. Apples Oranges Pears Food Fruits Vegetables Meats “Know” that chicken is not a fruit Chicken

  31. Apples Oranges Pears Food Fruits Additional subclasses Vegetables Meats Chicken

  32. Apples Oranges Pears Food Fruits Additional subclasses Vegetables Instances Meats Chicken

More Related