Synthetic Biology:Semantic web ontology: Difference between revisions
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====Software==== | ====Software==== | ||
*[http://www.w3.org/RDF/Validator RDF Validator] | *[http://www.w3.org/RDF/Validator RDF Validator] | ||
==RDF Schema== | ==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=== | ===Resources=== | ||
#[http://www.w3.org/TR/rdf-schema/ RDF Vocabulary Description Language 1.0: RDF Schema] - W3C Recommendation | |||
#[http://www.schemaweb.info/schema/SchemaInfo.aspx?id=2 RDF Schema Vocabulary Reference] | #[http://www.schemaweb.info/schema/SchemaInfo.aspx?id=2 RDF Schema Vocabulary Reference] | ||
====Software==== | |||
*[http://www.w3.org/2002/06/rdfs2html RDF Schema formatter] - extracts human readable information from a RDF Schema | |||
==Web Ontology Language (OWL)== | ==Web Ontology Language (OWL)== |
Revision as of 14:08, 16 September 2005
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
- A No-Nonsense Guide to Semantic Web Specs for XML People Part I and Part II - good intro for those familiar with XML
- W3C Semantic Web Activity (links to RDF, OWL, etc)
- Semantic Web primer from 2000 at xml.com
- Berners-Lee - Semantic Web Life Sciences - BioIT World
- Web Services - Semantic Web by Tim-Berners Lee
- Introduction to the Semantic Web and RDF by A.M. Kuchling
- Wikipedia article on Semantic Web
- Semantic Web tutorials from W3C
- Semantic Web tutorial using N3
- Primer: Getting into RDF & Semantic Web using N3
- Semantic Web: interview with Tim Berners-Lee
- W3C press release
- 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
- 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
- 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 Concepts and Abstract Syntax
- RDF semantics
- RDF Test Cases
- RDF/XML Syntax Specification
- RDF Vocabulary Reference
Software
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
- RDF Vocabulary Description Language 1.0: RDF Schema - W3C Recommendation
- RDF Schema Vocabulary Reference
Software
- RDF Schema formatter - extracts human readable information from a RDF Schema
Web Ontology Language (OWL)
Relationships between vocabularies and other constraints
Resources
Ontologies
Controlled vocabulary of concepts and their relationships. Described using RDF Schema and OWL.
Examples:
- Dublin Core
- Namespace: http://purl.org/dc/elements/1.1/
- Properties: title, creator, publisher, identifier
- Gene Ontology
- Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
- Properties: name, definition, isa, association, evidence
- Sequence Ontology: features on a nucleotide or protein sequence
- BioPAX: biological pathway data
- UniProt (planning)
- SBML uses CellML metadata to describe its elements. See also a message on SBML forum.
- BioModels database and Systems Biology Ontologies (SBO) project
Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the Registry website):
Resources
Contact: Ilya Sytchev