Synthetic Biology:Semantic web ontology: Difference between revisions

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This is a part of the effort to provide a standardized, extensible, scalable and '''machine-processable''' interface for the [http://parts.mit.edu/ 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 | BioBricks abstraction hierarchy]].
{{Synthetic biology top}}


==Semantic Web==
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RDF/XML, RDF Schema and OWL


*allows to model real things, not just documents or database tables
==Overview==
*consists of statements about resources in the form of triples:
This is a part of the effort to provide a standardized, extensible, scalable and machine-processable interface for the [http://parts.mit.edu/ Registry of Standard Biological Parts]. Semantic Web technologies 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 [[Synthetic Biology:Abstraction hierarchy | BioBricks abstraction hierarchy]].
SUBJECT -> PROPERTY -> VALUE
*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===
==Meetings==
#[http://www.xml.com/lpt/a/2000/11/01/semanticweb/index.html Semantic Web primer] from 2000 at xml.com
*First meeting
#[http://www.w3.org/2005/Talks/0517-boit-tbl/ Berners-Lee - Semantic Web Life Sciences - BioIT World]
:Tuesday (9/20/05) at 3pm, room 68-674; [[Synthetic Biology:SWO1minutes|minutes]]
#[http://www.w3.org/2003/Talks/05-gartner-tbl/ Web Services - Semantic Web by Tim-Berners Lee]
*Second meeting
#[http://www.amk.ca/talks/2004-12-02/ Introduction to the Semantic Web and RDF by A.M. Kuchling]
:Friday (9/23/05) at 10am, room 68-121; [[Synthetic Biology:SWO2minutes|minutes]]


==Ontology==
==Resources==
Controlled vocabulary of concepts and their relationships.
*[[Synthetic_Biology:Semantic_web_ontology/Design|Design]]
*[[Synthetic_Biology:Semantic_web_ontology/Semantic_Web|Semantic Web]]
**[[Synthetic_Biology:Semantic_web_ontology/RDF|RDF]]
**[[Synthetic_Biology:Semantic_web_ontology/RDF_Schema|RDF Schema]]
**[[Synthetic_Biology:Semantic_web_ontology/OWL|OWL]]
**[[Synthetic_Biology:Semantic_web_ontology/Query|Query Languges]]
**[[Synthetic_Biology:Semantic_web_ontology/SWRL|Rule Languages (SWRL)]]
*[[Synthetic_Biology:Semantic_web_ontology/Web Services|Web Services]]
*[[Synthetic_Biology:Semantic_web_ontology/REST|REST]]
*[[Synthetic_Biology:Semantic_web_ontology/Agents|Agents]]
*[[Synthetic_Biology:Semantic_web_ontology/Examples|Examples]]
*[[Synthetic_Biology:Semantic_web_ontology/Software|Software]]
*[[Synthetic_Biology:Semantic_web_ontology/Knowledge_representation|Knowledge representation]]


Examples of ontologies:
==Miscellaneous==
#Dublin Core
*[http://www.w3.org/TR/webarch/ Architecture of the World Wide Web, Volume One]
#*Namespace: http://purl.org/dc/elements/1.1/
*[http://www.w3.org/DesignIssues/Overview.html Design Issues for the World Wide Web]
#*Properties: title, creator, publisher, identifier
**[http://www.w3.org/DesignIssues/HTTP-URI.html What do HTTP URIs Identify?]
#Gene Ontology
*[http://dig.csail.mit.edu/ Decentralized Information Group] @ CSAIL
#*Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
*[http://www.nodalpoint.org/node/1645 Object-oriented biology] - application of object-oriented paradigm to Gene (from nodalpoint.org)
#*Properties: name, definition, isa, association, evidence
*[http://www.synberc.org/ SynBERC]: [[SynBERC|Synthetic Biology Engineering Research Center]] is a multi-institution research effort to lay the foundation for synthetic biology, which aims to build biological components and assemble them into integrated systems to accomplish specific tasks
#[http://song.sourceforge.net/so.shtml Sequence Ontology]: features on a nucleotide or protein sequence
**[[SynBERC:MIT|MIT SynBERC]]
#[http://www.biopax.org/ BioPAX]: biological pathway data
*[[Registry_of_Standard_Biological_Models|Registry of Standard Biological Models]]
#[http://www.uniprot.org/ UniProt] (planning)
*[[DOI|DOI & LSID info]]
#[http://sbml.org/documents/ SBML] uses [http://www.cellml.org/specifications/archive/metadata/20011102/cellml_metadata_specification.html CellML metadata] to describe its elements. See also a [http://www.sbml.org/forums/index.php?t=msg&goto=1435&rid=0#msg_1435 message] on SBML forum.
*[http://researchweb.watson.ibm.com/journal/sj/402/haas.html IBM DiscoveryLink] provides users with a virtual database to which they can pose arbitrarily complex queries, even though the actual data needed to answer the query may originate from several different sources, and none of those sources, by itself, is capable of answering the query (data integration)
#[http://biomodels.net/ BioModels] database and Systems Biology Ontologies (SBO) project
*[http://mitdatacenter.org/ The Data Center at the Massachusetts Institute of Technology] is a new initiative charged with researching and developing the languages, protocols, and technologies to integrate data and models across global networks.


Resources:
Contact: [[User:Ilya|Ilya Sytchev]]
#[http://dimer.tamu.edu/GO/wiki GO annotation wiki] (from [[User:Skosuri|Sri]])
 
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{{Synthetic biology bottom}}

Latest revision as of 00:31, 26 September 2007

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Overview

This is a part of the effort to provide a standardized, extensible, scalable and machine-processable interface for the Registry of Standard Biological Parts. Semantic Web technologies 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
Tuesday (9/20/05) at 3pm, room 68-674; minutes
  • Second meeting
Friday (9/23/05) at 10am, room 68-121; minutes

Resources

Miscellaneous

Contact: Ilya Sytchev

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