Synthetic Biology:Semantic web ontology

This is a part of the effort to provide a standardized, extensible, scalable and machine-processable interface for the Registry of Standard Biological Parts. The idea of a Semantic Web data model seems to fit this goal. The success of developing a Synthetic Biology ontology depends in part on a good definition of the BioBricks abstraction hierarchy.

Semantic Web

RDF/XML, RDF Schema and OWL

"an initiative to enable cross-platform data exchange and reuse through well-defined ontologies and a common XML-based framework."

"The goal of the Semantic Web initiative is to create a universal medium for the exchange of data where data can be shared and processed by automated tools as well as by people." [10]

• allows to model real things, not just documents or database tables (knowledge representation)
• consists of statements about resources in the form of triples:

SUBJECT -> PROPERTY -> VALUE
-OR-
SUBJECT -> PREDICATE -> OBJECT

• identifies every resource with a globally unique URI: don't say "color", say <http://example.com/2005/std6#col>
• allows “serendipitous reuse”: integration with data sources in other fields (“web join”)

Resources

1. A No-Nonsense Guide to Semantic Web Specs for XML People Part I and Part II - good intro for those familiar with XML
2. W3C Semantic Web Activity (links to RDF, OWL, etc)
3. Semantic Web primer from 2000 at xml.com
4. Berners-Lee - Semantic Web Life Sciences - BioIT World
5. Web Services - Semantic Web by Tim-Berners Lee
6. Introduction to the Semantic Web and RDF by A.M. Kuchling
7. Wikipedia article on Semantic Web
8. Semantic Web tutorials from W3C
9. Semantic Web tutorial using N3
10. Primer: Getting into RDF & Semantic Web using N3
11. Semantic Web: interview with Tim Berners-Lee
12. W3C press release
13. Design Issues @ W3C - web architecture and metadata

Resource Description Framework (RDF)

Used for assertion of 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"

Resources

1. RDF Primer at W3C
2. Wikipedia page
3. RDF @ W3C - a lot of links to resources
4. RDF Made Easy - a short tutorial
5. Intro to RDF and Jena RDP API
6. RDF Tutorial @ W3C - a lengthy presentation
7. Practical RDF - O'Reilly book, decent but not great
8. RDF FAQ @ W3C
9. RDF Data Access Use Cases and Requirements
10. Relational Databases on the Semantic Web
11. RDF Tutorial from the University of Lyon
12. RDF Concepts and Abstract Syntax
13. RDF semantics
14. RDF Test Cases
15. RDF/XML Syntax Specification
16. RDF Vocabulary Reference

Software

• RDF Validator

RDF Schema

• ‘semantically extends’ RDF to enable us to talk about classes of resources, and the properties that will be used with them
• provides the means to describe application specific RDF vocabularies
• provides schema information as additional descriptions of resources, but does not prescribe how these descriptions should be used by an application
• describes classes (corresponds to the generic concept of a Type or Category) and properties

RDF schemas differ somewhat from XML schemas (such as DTDs or W3C XML Schemas) in that they do not define a permissible syntax but instead classes, properties, and their interrelation: they operate directly at the data model level, rather than the syntax level

Resources

1. RDF Vocabulary Description Language 1.0: RDF Schema - W3C Recommendation
2. RDF Schema Vocabulary Reference

Software

• RDF Schema formatter - extracts human readable information from a RDF Schema

Web Ontology Language (OWL)

Used to define relationships between vocabularies and other constraints. As the Semantic Web is inherently distributed, OWL must allow for information to be gathered from distributed sources.

OWL adds the ability to indicate when two classes or properties are identical. OWL declarations provide additional information to let rule-checking and theorem-proving systems work with RDF data.

• e.g. the 'ancestor' property is transitive.
• If (X ancestor Y) and (Y ancestor Z) are true, a system could infer that (X ancestor Z) is also true.

Resources

1. Wikipedia page
2. OWL @ W3C - links
3. OWL Web Ontology Language Guide
4. OWL Web Ontology Language Overview
5. OWL Web Ontology Language Reference
6. OWL Web Ontology Language Semantics and Abstract Syntax
7. OWL Vocabulary reference
8. OWL Implementations as of December 2003 (Historical)

Software

• OWL Ontology Browser and Editor

Ontologies

Controlled vocabulary of concepts and their relationships. Described using RDF Schema and OWL.

Examples:

1. Dublin Core
   • Namespace: http://purl.org/dc/elements/1.1/
   • Properties: title, creator, publisher, identifier
2. Gene Ontology
   • Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
   • Properties: name, definition, isa, association, evidence
3. Sequence Ontology: features on a nucleotide or protein sequence
4. BioPAX: biological pathway data
5. UniProt (planning)
6. SBML uses CellML metadata to describe its elements. See also a message on SBML forum.
7. BioModels database and Systems Biology Ontologies (SBO) project
8. Open Biomedical Ontologies
9. Bio-Ontologies
10. Ontologies for molecular biology and bioinformatics

Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the Registry website):

Resources

1. GO annotation wiki (from Sri)
2. RDF Schemas directory
3. Ontology Development 101: A Guide to Creating Your First Ontology

Software

• Ontology editors
  • Protégé is a free, open source ontology editor and knowledge-base framework
  • OilEd is an ontology editor allowing the user to build ontologies using DAML+OIL
  • Ontolingua
  • Chimaera is a software system that supports users in creating and maintaining distributed ontologies on the web

Contact: Ilya Sytchev