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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}} |
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| ==Semantic Web== | | <div style="padding: 10px; color: #000000; background-color: #ccccff; width:730px" > |
| RDF/XML, RDF Schema and OWL
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| "an initiative to enable cross-platform data exchange and reuse through well-defined ontologies and a common XML-based framework."
| | ==Overview== |
| | 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]]. |
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| "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]
| | ==Meetings== |
| | *First meeting |
| | :Tuesday (9/20/05) at 3pm, room 68-674; [[Synthetic Biology:SWO1minutes|minutes]] |
| | *Second meeting |
| | :Friday (9/23/05) at 10am, room 68-121; [[Synthetic Biology:SWO2minutes|minutes]] |
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| *allows to model real things, not just documents or database tables (knowledge representation) | | ==Resources== |
| *consists of statements about resources in the form of triples: | | *[[Synthetic_Biology:Semantic_web_ontology/Design|Design]] |
| SUBJECT -> PROPERTY -> VALUE
| | *[[Synthetic_Biology:Semantic_web_ontology/Semantic_Web|Semantic Web]] |
| -OR-
| | **[[Synthetic_Biology:Semantic_web_ontology/RDF|RDF]] |
| SUBJECT -> PREDICATE -> OBJECT
| | **[[Synthetic_Biology:Semantic_web_ontology/RDF_Schema|RDF Schema]] |
| *identifies every resource with a globally unique URI: don't say "color", say <http://example.com/2005/std6#col> | | **[[Synthetic_Biology:Semantic_web_ontology/OWL|OWL]] |
| *allows “serendipitous reuse”: integration with data sources in other fields (“web join”) | | **[[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]] |
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| ===Resources=== | | ==Miscellaneous== |
| #A No-Nonsense Guide to Semantic Web Specs for XML People [http://www.betaversion.org/~stefano/linotype/news/57/ Part I] and [http://www.betaversion.org/~stefano/linotype/news/78/ Part II] - good intro for those familiar with XML
| | *[http://www.w3.org/TR/webarch/ Architecture of the World Wide Web, Volume One] |
| #[http://www.w3.org/2001/sw/ W3C Semantic Web Activity] (links to RDF, OWL, etc)
| | *[http://www.w3.org/DesignIssues/Overview.html Design Issues for the World Wide Web] |
| #[http://www.xml.com/lpt/a/2000/11/01/semanticweb/index.html Semantic Web primer] from 2000 at xml.com
| | **[http://www.w3.org/DesignIssues/HTTP-URI.html What do HTTP URIs Identify?] |
| #[http://www.w3.org/2005/Talks/0517-boit-tbl/ Berners-Lee - Semantic Web Life Sciences - BioIT World]
| | *[http://dig.csail.mit.edu/ Decentralized Information Group] @ CSAIL |
| #[http://www.w3.org/2003/Talks/05-gartner-tbl/ Web Services - Semantic Web by Tim-Berners Lee]
| | *[http://www.nodalpoint.org/node/1645 Object-oriented biology] - application of object-oriented paradigm to Gene (from nodalpoint.org) |
| #[http://www.amk.ca/talks/2004-12-02/ Introduction to the Semantic Web and RDF by A.M. Kuchling]
| | *[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 |
| #[[Wikipedia:Semantic_web | Wikipedia article on Semantic Web]]
| | **[[SynBERC:MIT|MIT SynBERC]] |
| #[http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web tutorials from W3C]
| | *[[Registry_of_Standard_Biological_Models|Registry of Standard Biological Models]] |
| #[http://www.w3.org/2000/10/swap/doc/ Semantic Web tutorial using N3]
| | *[[DOI|DOI & LSID info]] |
| #[http://www.w3.org/2000/10/swap/Primer Primer: Getting into RDF & Semantic Web using N3]
| | *[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://www.consortiuminfo.org/bulletins/semanticweb.php Semantic Web: interview with Tim Berners-Lee]
| | *[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. |
| #[http://www.w3.org/2004/01/sws-pressrelease W3C press release]
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| #[http://www.w3.org/DesignIssues/ Design Issues @ W3C] - web architecture and metadata
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| ==Resource Description Framework (RDF)==
| | Contact: [[User:Ilya|Ilya Sytchev]] |
| Used for assertion of facts
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| '''<http://www.example.org/index.html>''' has a '''creator''' whose value is '''John Smith'''
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| the RDF terms for the various parts of the statement are:
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| *the ''subject'' is the URL <http://www.example.org/index.html>
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| *the ''predicate'' is the word "creator"
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| *the ''object'' is the phrase "John Smith"
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| ===Resources===
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| #[http://www.w3.org/TR/rdf-primer/ RDF Primer at W3C]
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| #[http://en.wikipedia.org/wiki/Resource_Description_Framework Wikipedia page]
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| #[http://www.w3.org/RDF/ RDF @ W3C] - a lot of links to resources
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| #[http://www.xmltraining.com/rdf-made-easy.html RDF Made Easy] - a short tutorial
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| #[http://jena.sourceforge.net/tutorial/RDF_API Intro to RDF and Jena RDP API]
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| #[http://www.w3.org/Consortium/Offices/Presentations/RDFTutorial/ RDF Tutorial @ W3C] - a lengthy presentation
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| #[http://safari.oreilly.com/0596002637 Practical RDF] - O'Reilly book, decent but not great
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| #[http://www.w3.org/RDF/FAQ RDF FAQ @ W3C]
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| #[http://www.w3.org/TR/rdf-dawg-uc/ RDF Data Access Use Cases and Requirements]
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| #[http://www.w3.org/DesignIssues/RDB-RDF.html Relational Databases on the Semantic Web]
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| #[http://www710.univ-lyon1.fr/~champin/rdf-tutorial/ RDF Tutorial] from the University of Lyon
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| #[http://www.w3.org/TR/rdf-concepts/ RDF Concepts and Abstract Syntax]
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| #[http://www.w3.org/TR/rdf-mt/ RDF semantics]
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| #[http://www.w3.org/TR/rdf-testcases/ RDF Test Cases]
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| #[http://www.w3.org/TR/rdf-syntax-grammar/ RDF/XML Syntax Specification]
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| #[http://www.schemaweb.info/schema/SchemaInfo.aspx?id=1 RDF Vocabulary Reference]
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| ===Software===
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| *[http://www.w3.org/RDF/Validator RDF Validator]
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| ==RDF Schema==
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| *‘semantically extends’ RDF to enable us to talk about classes of resources, and the properties that will be used with them
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| *provides the means to describe application specific RDF vocabularies
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| *provides schema information as additional descriptions of resources, but does not prescribe how these descriptions should be used by an application
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| *describes classes (corresponds to the generic concept of a Type or Category) and properties
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| 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
| | </div> |
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| ===Resources===
| | {{Synthetic biology bottom}} |
| #[http://www.w3.org/TR/rdf-schema/ RDF Vocabulary Description Language 1.0: RDF Schema] - W3C Recommendation
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| #[http://www.schemaweb.info/schema/SchemaInfo.aspx?id=2 RDF Schema Vocabulary Reference]
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| ===Software===
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| *[http://www.w3.org/2002/06/rdfs2html RDF Schema formatter] - extracts human readable information from a RDF Schema
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| ==Web Ontology Language (OWL)==
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| 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.
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| OWL adds the ability to indicate when two classes or properties are identical.
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| OWL declarations provide additional information to let rule-checking and theorem-proving systems work with RDF data.
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| * e.g. the 'ancestor' property is transitive.
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| * If (X ancestor Y) and (Y ancestor Z) are true, a system could infer that (X ancestor Z) is also true.
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| ===Resources===
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| #[http://en.wikipedia.org/wiki/Web_Ontology_Language Wikipedia page]
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| #[http://www.w3.org/2004/OWL/ OWL @ W3C] - links
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| #[http://www.w3.org/TR/owl-guide/ OWL Web Ontology Language Guide]
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| #[http://www.w3.org/TR/owl-features/ OWL Web Ontology Language Overview]
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| #[http://www.w3.org/TR/owl-ref/ OWL Web Ontology Language Reference]
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| #[http://www.w3.org/TR/owl-semantics/ OWL Web Ontology Language Semantics and Abstract Syntax]
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| #[http://www.schemaweb.info/schema/SchemaInfo.aspx?id=60 OWL Vocabulary reference]
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| #[http://www.w3.org/2001/sw/WebOnt/impls OWL Implementations as of December 2003 (Historical)]
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| ===Software===
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| *[http://www.mindswap.org/2004/SWOOP/ OWL Ontology Browser and Editor]
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| ==Ontologies==
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| Essentially, a formal description of objects and their interrelationships
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| Described using RDF Schema and/or OWL.
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| Examples:
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| #[http://dublincore.org/ Dublin Core]
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| #*Namespace: http://purl.org/dc/elements/1.1/
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| #*Properties: title, creator, publisher, identifier
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| #[http://geneontology.org/ Gene Ontology]
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| #*Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
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| #*Properties: name, definition, isa, association, evidence
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| #[http://song.sourceforge.net/so.shtml Sequence Ontology]: features on a nucleotide or protein sequence
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| #[http://www.biopax.org/ BioPAX]: biological pathway data
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| #[http://www.uniprot.org/ UniProt] (planning)
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| #[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.
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| #[http://biomodels.net/ BioModels] database and Systems Biology Ontologies (SBO) project
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| #[http://obo.sourceforge.net/ Open Biomedical Ontologies]
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| #[http://anil.cchmc.org/Bio-Ontologies.html Bio-Ontologies]
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| #[http://www.bioinfo.de/isb/2002/02/0017/main.html Ontologies for molecular biology and bioinformatics]
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| Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the [http://parts2.mit.edu/r/parts/partsdb/index.cgi Registry website]):
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| [[Image:SBOv0.01.png]]
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| ===Resources===
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| #[http://dimer.tamu.edu/GO/wiki GO annotation wiki] (from [[User:Skosuri|Sri]])
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| #[http://www.schemaweb.info/ RDF Schemas directory]
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| #[http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html Ontology Development 101: A Guide to Creating Your First Ontology]
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| ===Software===
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| *Ontology editors
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| **[http://protege.stanford.edu Protégé] is a free, open source ontology editor and knowledge-base framework
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| **[http://oiled.man.ac.uk/ OilEd] is an ontology editor allowing the user to build ontologies using DAML+OIL
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| **[http://ontolingua.stanford.edu/ Ontolingua]
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| **[http://www.ksl.stanford.edu/software/chimaera/ Chimaera] is a software system that supports users in creating and maintaining distributed ontologies on the web
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| Contact: [[User:Ilya|Ilya Sytchev]]
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