Synthetic Biology:Semantic web ontology/RDF

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Overview

Resource Definition Framework - used for making statements about facts

<http://www.example.org/index.html>  has a creator whose value is John Smith

the RDF terms for the various parts of the statement are:

• the subject is the URL <http://www.example.org/index.html>
• the predicate is the word "creator"
• the object is the phrase "John Smith"

Beware of thinking of RDF as a format for serailizing objects. The semantic web is different - it is weblike.

• Any document can (potentially) say anything about anything. There is no set of "slots" or "attributes" for a class. The properties defined in a schema are not the only properties which one can use to describe something which is in that class.
• An object can be in many classes. When you create a semantic web document about something, others can deduce more things about it, in vocabularies you have never heard of.
• Entity-Relationship and UML diagrams are useful for describing RDF -- so long as you remember the above.

From http://www.w3.org/2000/10/swap/doc/formats.

N3

Notes:

• Comments start with # sign
• When you say what type of thing something is, you say a Class it belongs to.
• A property is something which is used to declare a relationship between two things.
• When the subject of any property must be in a class, that class is a domain of the property.
• When the object must be in a class, that class is called the range of a property.
• class identifiers start with capitals, properties with lower case letters
• a rdf:type
• => ?

References:

• A Rough Guide to N3
• Primer: Getting into RDF & Semantic Web using N3 from W3C
• Examples - Getting into RDF & Semantic Web using N3 from W3C
• Notation 3 - Ideas about Web Architecture from Design Issues
• Introduction to N3 Rules - slides
• N3 @ Wikipedia

Turtle

• Turtle - Terse RDF Triple Language - defines a text syntax for RDF called Turtle as an extension of the N-Triples test case format carefully taking the most useful and appropriate things added from Notation 3 while keeping the syntax describing only RDF graphs.

References

• RDF Primer at W3C
• Wikipedia page
• RDF @ W3C - a lot of links to resources
• RDF Made Easy - a short tutorial
• Intro to RDF and Jena RDP API
• RDF Tutorial @ W3C - a lengthy presentation
• Resource Description Framework @ logicerror.com
• RDF tutorial from w3schools.com
• Practical RDF - O'Reilly book, decent but not great
• RDF FAQ @ W3C
• RDF Data Access Use Cases and Requirements
• Relational Databases on the Semantic Web
• RDF Tutorial from the University of Lyon
• RDF model and syntax tutorial from RPI
• RDF Concepts and Abstract Syntax
• RDF semantics
• RDF Test Cases
• RDF/XML Syntax Specification
• RDF Vocabulary Reference
• Dave Beckett's Resource Description Framework (RDF) Resource Guide
• taubz.for.net - Resource Description Framework (RDF) for Networking Information on the Semantic Web by Joshua Tauberer
• RDF/A Primer 1.0: Embedding RDF in XHTML

Miscellaneous

• Fresnel - Display Vocabulary for RDF

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