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
• What Is RDF - xml.com article
• Wikipedia page
• RDF @ W3C - a lot of links to resources
• RDF Made Easy - a short tutorial
• Introduction to the RDF Model from XULPlanet
• Intro to RDF and Jena RDP API
• RDF Tutorial @ W3C - a lengthy presentation
• Resource Description Framework @ logicerror.com
• RDF tutorial from w3schools.com
• Bottoms Up RDF Tutorial @ burningbird.net
• 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
• Embedding RDF in XHTML
  • RDFa Primer 1.0
  • RDF In HTML

Miscellaneous

• Fresnel - Display Vocabulary for RDF
• Fresnel - SIMILE
• CBD - a Concise Bounded Description of the resource denoted by the starting node in the source graph, can be identified as follows:
  1. Include in the subgraph all statements in the source graph where the subject of the statement is the starting node;
  2. Recursively, for all statements identified in the subgraph thus far having a blank node object, include in the subgraph all statements in the source graph where the subject of the statement is the blank node in question and which are not already included in the subgraph.
  3. Recursively, for all statements included in the subgraph thus far, for all reifications of each statement in the source graph, include the concise bounded description beginning from the rdf:Statement node of each reification.
• Named Graphs - Semantic Web Activity (TriX, TriG, TriQL, RDFQ, NG4J)

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