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Simple Ontologies and the Applications that Use Them

Simple Ontologies and the Applications that Use Them. Cyndy Parr, Joel Sachs, Tim Finin parrc@si.edu, jsachs@cs.umbc.edu, finin@umbc.edu SPIRE (Semantic Prototypes in blah blah blah). Overview of Talk. Ontologies I hate Ontologies I like Tools for Citizen Science

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Simple Ontologies and the Applications that Use Them

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  1. Simple Ontologies and the Applications that Use Them Cyndy Parr, Joel Sachs, Tim Finin parrc@si.edu, jsachs@cs.umbc.edu, finin@umbc.edu SPIRE (Semantic Prototypes in blah blah blah)

  2. Overview of Talk • Ontologies I hate • Ontologies I like • Tools for Citizen Science (How we generate instance data) • Discovery and Integration (What we do with the instance data) • Linked Data (Lessons learned by the community)

  3. High Level Distinctions The first fundamental distinction is that between ‘Physical’ (things which have a position in space/time) and ‘Abstract’ (things which don’t)‏ Entity Physical Abstract

  4. High Level Distinctions Partition of ‘Physical’ into ‘Objects’ and ‘Processes’ Physical Object Process

  5. IntentionalProcess IntentionalPsychologicalProcess RecreationOrExercise OrganizationalProcess Guiding Keeping Maintaining Repairing Poking ContentDevelopment Making Searching SocialInteraction Maneuver Motion BodyMotion DirectionChange Transfer Transportation Radiating DualObjectProcess Substituting Transaction Comparing Attaching Detaching Combining Separating InternalChange BiologicalProcess QuantityChange Damaging ChemicalProcess SurfaceChange Creation StateChange ShapeChange Processes

  6. Lesson: Standard lower ontologies are more powerful than standard upper ontologies.

  7. Some Spire Ontologies • Rich’s ontologies • A collection of linked ontologies enabling highly detailed descriptions of ecological interaction. • Supports WoW - Webs on the Web • SpireEcoConcepts • Medium size. Used for expressing trophic links and related information, including bibliographic info on studies. • ETHAN • Evolutionary trees and natural history. • Huge. • Observation ontology • For semantic eco-blogging. • Tiny. • Invasives ontology • Lightweight and extensible in the most trivial of manners.

  8. Semantic Eco-Blogging: Motivation 1/3 of all new web content is user generated • Scientific data is increasingly a part of Web 2.0/3.0 • How easy can we make semantic annotation? Climate change drives ecological change • Alters species distribution Wuethrich, B. How Climate Change Alters Rhythms of the Wild Bernice Wuethrich (4 February 2000) Science 287 (5454), 793. • Drives evolution Bradshaw, W. E., and Holzapfel, C. M. 2001. Genetic shift in photoperiodic response correlated with global warming. Proc. Nat. Acad Sci. USA. 98:14509-14511

  9. Semantic Eco-blogging. • Eco-blogs are popping up all over the place. • Bloggers are both amateur nature-lovers, and working biologists. • “On April 24 in Washington DC, I saw a leopard slug. Here’s a picture.” • These observations are, potentially, an important part of the ecological record. • “What was the earliest sighting of a robin hatching?” • “What was the Northernmost sighting of the Asian Longhorn Beetle?” • Etc. • System concept: global human sensor net. • SPOTTER • A firefox plugin for creating OWL from field observations. • Spotter map lets you see all “spots” • Being tested at http://ebiquity.umbc.edu/fieldmarking/ and other blogs near you.

  10. The Blogger Bioblitz • Bioblitz: a 24 hour inventory of all living things in a given area. • Dual aims of establishing degree of biodiversity and popularizing science. • Last year’s blogger bioblitz. • 17 bloggers from: • Sitka, Alaska; Greece; Toronto; Santa Cruz; DC; etc. • 1200 observations. • Tripleshop was able, by combining the observations with background data, to respond to a number of ad-hoc queries.

  11. Integration • Swoogle • Google for the semantic web. • Crawls and indexes RDF documents. • Computes metadata, including “ontoRank”. • Tripleshop • A SPARQL query engine. • Leave out the FROM clause. • Data comes from Swoogle • Semi-automatic dataset constructor • Our main platform for integration

  12. Lesson: People want to be left alone.

  13. RDF123 A flexible and graphical means to map from spreadsheets to RDF The mapping is stored as an OWL file An RDF123 webservice takes a Google spreadsheet and a map as input, outputs RDF. So you can do all your work, collaboratively, in the spreadsheet, and you never have to export to RDF! This is important, because spreadsheets aren’t going anywhere anytime soon.

  14. A Few Words on Linked Data • “Linked Data on the Web” is a collection of best practices for publishing data on the semantic web. • Distinguishing between Information and non-information resources. • 303 redirects and content negotiation. • HTTP URIs for everything on Earth. • owl:sameAs • It is also, to an extent, a rebranding of the semantic web. • Much more emphasis on links amongst datasets. • Much less emphasis on formal semantics. • Linked data can be browsed, in much the same way we browse the traditional web. • So we can find data either by searching for it (with Swoogle/Tripleshop) or by surfing our way to it.

  15. Acknowledgements Andriy Parafiynyk Lushan Han Rong Pan Li Ding David Wang NSF NBII

  16. Some References Two relevant papers from our research group: Adding Semantics to Social Websites for Citizen Science http://ebiquity.umbc.edu/paper/html/id/365/Adding-Semantics-to-Social-Websites-for-Citizen-Science Using the Semantic Web to Support Ecoinformatics, http://ebiquity.umbc.edu/paper/html/id/319/Using-the-Semantic-Web-to-Support-Ecoinformatics 1. "The Machine is Us/ing Us", Mike Wesch, http://www.youtube.com/watch?v=6gmP4nk0EOEA vide on web 2.0. 2. "RDF Tutorial", Pierre-Antoine Champinhttp://bat710.univ-lyon1.fr/~champin/rdf-tutorial/An excellent RDF tutorial. 3. SPARQL: Web 2.0 Meet the Semantic Web, Kendall Clark http://www.oreillynet.com/xml/blog/2005/09/sparql_web_20_meet_the_semanti.htmlA somewhat breathless SPARQL pitch, but a good exposition of the semantic web vision. 4. "How to Publish Linked Data on the Web", Chris Bizer et al.http://www4.wiwiss.fu-berlin.de/bizer/pub/LinkedDataTutorial/An introduction and overview to Linked Data, includes many good references. 5. "URL Rewriting", Ross Shannon http://www.yourhtmlsource.com/sitemanagement/urlrewriting.htmlA great tutorial on using Apache's mod rewrite. It's also a nice exposition on some of the principles of RESTful web architecture. 6. http://ebiquity.umbc.edu/blogger/2007/09/14/semantic-eco-blogging-spotter-10-released/Blog post on semantic eco-blogging, with a link to the Firefox-plugin. Give it a try! 7. "Can the Internet be used the Support the Mission of a Healthy Puget Sound?", Mary McCafferyEPA report on the Puget Sound Information Challenge, including lessons learned.

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