Synthetic Biology:Semantic web ontology: Difference between revisions

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*List of questions that the Registry should be able to handle (use cases)
*List of questions that the Registry should be able to handle (use cases)
Notes:
Notes:
*We should approach development of the term hierarchy working from bottom up (define basic terms and properties first, them move to classes and their relationships).
*Classes of standards: assembly standards, performance standards?
*Classes of standards: assembly standards, performance standards?
*Basic part: contains detailed specifications, DNA sequence.
*Part: piece of DNA with molecular function, combined by BioBricks assembly.
*Composite part: basic part plus assembly method; two composite parts are the same if they contain the same basic parts).
*Basic: contains detailed specifications, DNA sequence.
*Composite: basic part plus assembly method; two composite parts are the same if they contain the same basic parts).
*Device: may not be on a single piece of DNA.
*Device: may not be on a single piece of DNA.
*Separate spaces or sets of hierarchies:
*Separate spaces or sets of hierarchies:
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  #Systems rdf:type rdfs:Class .
  #Systems rdf:type rdfs:Class .
Other?
Other?
*We should approach development of the term hierarchy working from bottom up (define basic terms and properties first, them move on to classes and their relationships).


===Second meeting===
===Second meeting===

Revision as of 14:57, 20 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 ideas of the Semantic Web seem to provide a solution to this problem. The success of developing a Synthetic Biology ontology depends in part on a good definition of the BioBricks abstraction hierarchy.

Meetings

First meeting

Held on Tuesday (9/20/05) at 3pm, room 68-674
Participants (please put your name here):

To be discussed:

Notes:

  • Classes of standards: assembly standards, performance standards?
  • Part: piece of DNA with molecular function, combined by BioBricks assembly.
  • Basic: contains detailed specifications, DNA sequence.
  • Composite: basic part plus assembly method; two composite parts are the same if they contain the same basic parts).
  • Device: may not be on a single piece of DNA.
  • Separate spaces or sets of hierarchies:

Physical (DNA sequence, assembly methods): 

#BioBrick rdf:type rdfs:Class .
#Composite rdf:type #BioBrick .
#Basic rdf:type #BioBrick .
#Composite #contains #Basic .

Design (performance characteristics): 

#Parts rdf:type rdfs:Class .
#Devices rdf:type rdfs:Class .
#Systems rdf:type rdfs:Class .

Other?

  • We should approach development of the term hierarchy working from bottom up (define basic terms and properties first, them move on to classes and their relationships).

Second meeting

Proposed to be held on Friday (9/23/05) at 10am, room TBA
Participants:

To be discussed:
Basic terms for describing the biological parts and their properties.

Registry features

  • Registry_Wish_List
  • Subpart Search: search for parts that match a portion of this part or this sequence of parts
  • Superpart Search: search for parts that contain the given parts
  • ?

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
  14. Notions & Notations of the Semantic Web - MIT 6.898 Fall Seminar Course
  15. Semantic Web news aggregator

Resource Description Framework (RDF)

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:

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 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


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)
  9. OWL Web Ontology Language Semantics and Abstract Syntax

Software

Query

Resources

  1. RDF Query Survey - query language survey
  2. Redland Rasqal RDF Query Demonstration

RDQL

  1. RDQL - A Query Language for RDF
  2. RDQL Tutorial from phpxmlclasses project
  3. A Programmer's Introduction to RDQL - Jena tutorial

SPARQL

  1. SPARQL Query Language for RDF
  2. SPARQL Query Results XML Format

Ontologies

Essentially, a formal description of objects and their interrelationships Described using RDF Schema and/or OWL.

Examples:

  1. Dublin Core provides a vocabulary to describe bibliographic metadata
  2. Gene Ontology provides a controlled vocabulary to describe gene and gene product attributes in any organism
  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

Miscellaneous

Contact: Ilya Sytchev

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