Simple Ontologies and the Applications that Use Them

Cyndy Parr, Joel Sachs, Tim Fininparrc@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

(How we generate instance data)

• Discovery and Integration(What we do with the instance data)

• Linked Data(Lessons learned by the community)

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

High Level Distinctions

Partition of ‘Physical’ into ‘Objects’ and ‘Processes’

Physical

Object Process

ProcessesDualObjectProcess Substituting Transaction Comparing Attaching Detaching Combining SeparatingInternalChange BiologicalProcess QuantityChange Damaging ChemicalProcess SurfaceChange Creation StateChangeShapeChange

IntentionalProcess IntentionalPsychologicalProcess RecreationOrExercise OrganizationalProcess Guiding Keeping Maintaining Repairing Poking ContentDevelopment Making Searching SocialInteraction ManeuverMotion BodyMotion DirectionChange Transfer Transportation Radiating

Lesson:

Standard lower ontologies are more powerful than standard upper ontologies.

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.

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 evolutionBradshaw, W. E., and Holzapfel, C. M. 2001. Genetic shift in

photoperiodic response correlated with global warming. Proc. Nat. Acad Sci. USA. 98:14509-14511

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.

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.

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

Lesson:

People want to be left alone.

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.

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.

Acknowledgements

Andriy Parafiynyk

Lushan Han

Rong Pan

Li Ding

David Wang

NSF

NBII

Some ReferencesTwo 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.