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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 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 | BioBricks abstraction hierarchy]].
| | {{Synthetic biology top}} |
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| ==Meetings== | | <div style="padding: 10px; color: #000000; background-color: #ccccff; width:730px" > |
| ===First meeting===
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| Held on Tuesday (9/20/05) at 3pm, room 68-674<br/>
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| Participants (please put your name here):
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| *[[User:Ilya|IS]]
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| *[[User:Jasonk|JK]]
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| *[[Sriram Kosuri|SK]]
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| *[[Reshma Shetty|RS]]
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| *[[User:Randy|Randy Rettberg]]
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| To be discussed:
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| *[[BioBricks_abstraction_hierarchy | BioBricks abstraction hierarchy]]
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| *List of questions that the Registry should be able to handle (use cases)
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| Notes:
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| *Classes of standards: assembly standards, performance standards?
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| *Part: piece of DNA with molecular function, combined by BioBricks assembly.
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| *Basic: contains detailed specifications, DNA sequence.
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| *Composite: basic part plus assembly method; two composite parts are the same if they contain the same basic parts).
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| *Device: may not be on a single piece of DNA.
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| *Separate spaces or sets of hierarchies:
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| Physical (DNA sequence, assembly methods):
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| #BioBrick rdf:type rdfs:Class .
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| #Composite rdf:type #BioBrick .
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| #Basic rdf:type #BioBrick .
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| #Composite #contains #Basic .
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| Design (performance characteristics):
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| #Parts rdf:type rdfs:Class .
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| #Devices rdf:type rdfs:Class .
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| #Systems rdf:type rdfs:Class .
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| Other?
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| *We should approach development of the abstraction hierarchy working from bottom up (define basic terms and properties first, then move on to classes and their relationships).
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| ===Second meeting=== | | ==Overview== |
| Proposed to be held on Friday (9/23/05) at 10am, room 68-121.<br/>
| | 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]]. |
| Participants:
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| *[[User:Ilya|IS]]
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| *[[Reshma Shetty | RS]]
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| *[[Jason Kelly|JK]]
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| *[[Sriram Kosuri|SK]]
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| To be discussed:<br/>
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| Basic terms for describing the biological parts and their properties.
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| ==Registry features== | | ==Meetings== |
| *[[Registry_Wish_List]] | | *First meeting |
| *Subpart Search: search for parts that match a portion of this part or this sequence of parts. Software agent would take a part name and using the ontology definitions would query other registries via their semantic web interfaces (no need to know about schema: e.g., just say "need all <#part>s that match a <#component> of the given <#part>"). Software agent can search anyone's registry if they use a common ontology: simply follow URLs (or use query language) and add triples to the local RDF store. | | :Tuesday (9/20/05) at 3pm, room 68-674; [[Synthetic Biology:SWO1minutes|minutes]] |
| *Superpart Search: search for parts that contain the given parts
| | *Second meeting |
| *What about sub- and superpart searches in distributed registries?
| | :Friday (9/23/05) at 10am, room 68-121; [[Synthetic Biology:SWO2minutes|minutes]] |
| *Search for function (case insensitive): repressor, reporter, inverter, etc.
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| *What are the available (instances of) parts? Are they used in any devices already? (saves time for constructing expression device). Problem: different names for exactly same DNA sequence
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| *What kinds of devices/systems have been built?
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| *?
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| ==Semantic Web== | | ==Resources== |
| RDF/XML, RDF Schema and OWL | | *[[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]] |
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| "an initiative to enable cross-platform data exchange and reuse through well-defined ontologies and a common XML-based framework."
| | ==Miscellaneous== |
| | *[http://www.w3.org/TR/webarch/ Architecture of the World Wide Web, Volume One] |
| | *[http://www.w3.org/DesignIssues/Overview.html Design Issues for the World Wide Web] |
| | **[http://www.w3.org/DesignIssues/HTTP-URI.html What do HTTP URIs Identify?] |
| | *[http://dig.csail.mit.edu/ Decentralized Information Group] @ CSAIL |
| | *[http://www.nodalpoint.org/node/1645 Object-oriented biology] - application of object-oriented paradigm to Gene (from nodalpoint.org) |
| | *[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 |
| | **[[SynBERC:MIT|MIT SynBERC]] |
| | *[[Registry_of_Standard_Biological_Models|Registry of Standard Biological Models]] |
| | *[[DOI|DOI & LSID info]] |
| | *[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://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. |
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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]
| | Contact: [[User:Ilya|Ilya Sytchev]] |
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| *allows to model real things, not just documents or database tables (knowledge representation)
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| *consists of statements about resources in the form of triples:
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| SUBJECT -> PROPERTY -> VALUE
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| -OR-
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| SUBJECT -> PREDICATE -> OBJECT
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| *identifies every resource with a globally unique URI: don't say "color", say <http://example.com/2005/std6#col>
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| *allows “serendipitous reuse”: integration with data sources in other fields (“web join”)
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| ===Resources===
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| #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
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| #[http://www.w3.org/2001/sw/ W3C Semantic Web Activity] (links to RDF, OWL, etc)
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| #[http://www.xml.com/lpt/a/2000/11/01/semanticweb/index.html Semantic Web primer] from 2000 at xml.com
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| #[http://www.w3.org/2005/Talks/0517-boit-tbl/ Berners-Lee - Semantic Web Life Sciences - BioIT World]
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| #[http://www.w3.org/2003/Talks/05-gartner-tbl/ Web Services - Semantic Web by Tim-Berners Lee]
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| #[http://www.amk.ca/talks/2004-12-02/ Introduction to the Semantic Web and RDF by A.M. Kuchling]
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| #[[Wikipedia:Semantic_web | Wikipedia article on Semantic Web]]
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| #[http://www.w3.org/2001/sw/BestPractices/Tutorials Semantic Web tutorials from W3C]
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| #[http://www.w3.org/2000/10/swap/doc/ Semantic Web tutorial using N3]
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| #[http://www.w3.org/2000/10/swap/Primer Primer: Getting into RDF & Semantic Web using N3]
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| #[http://www.consortiuminfo.org/bulletins/semanticweb.php Semantic Web: interview with Tim Berners-Lee]
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| #[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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| #[http://groups.csail.mit.edu/dig/2005/09/6.898/ Notions & Notations of the Semantic Web] - MIT 6.898 Fall Seminar Course
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| #[http://www.rundom.com/extensibility/?feed=96 Semantic Web news aggregator]
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| ==Resource Description Framework (RDF)==
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| Used for making statements about 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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| *[http://4suite.org/ 4Suite™]: an open-source platform for XML and RDF processing
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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
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| ===Resources===
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| #[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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| #[http://www.w3.org/TR/owl-absyn/ OWL Web Ontology Language Semantics and Abstract Syntax]
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| ===Software===
| | </div> |
| *[http://www.mindswap.org/2004/SWOOP/ OWL Ontology Browser and Editor]
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| ==Query==
| | {{Synthetic biology bottom}} |
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| ===Resources===
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| #[http://www.w3.org/2001/11/13-RDF-Query-Rules/ RDF Query Survey] - query language survey
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| #[http://librdf.org/query Redland Rasqal RDF Query Demonstration]
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| ====RDQL====
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| #[http://www.w3.org/Submission/RDQL/ RDQL - A Query Language for RDF]
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| #[http://phpxmlclasses.sourceforge.net/rdql.html RDQL Tutorial] from phpxmlclasses project
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| #[http://jena.sourceforge.net/tutorial/RDQL/index.html A Programmer's Introduction to RDQL] - Jena tutorial
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| ====SPARQL====
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| #[http://www.w3.org/TR/rdf-sparql-query/ SPARQL Query Language for RDF]
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| #[http://www.w3.org/TR/rdf-sparql-XMLres/ SPARQL Query Results XML Format]
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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] provides a vocabulary to describe bibliographic metadata
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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] provides a controlled vocabulary to describe gene and gene product attributes in any organism. GO terms are organized in directed acyclic graphs (DAGs), which differ from hierarchies in that a 'child' (more specialized term) can have many 'parents' (less specialized terms). GO terms are connected by 'is a' (generalizations) and 'part of' (composition) relationships.
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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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| ==Implementation==
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| *Persistent RDF store (MySQL + Jena)
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| *Possible architecture of the Registry: http://www.w3.org/2005/Talks/0517-boit-tbl/#[19]
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| ==Miscellaneous==
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| *[http://www.w3.org/TR/webarch/ Architecture of the World Wide Web, Volume One]
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| *[http://www.nodalpoint.org/node/1645 Object-oriented biology] - application of object-oriented paradigm to Gene Ontology
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| *[[BioBricks|BioBricks]]: protocols and standards.
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| Contact: [[User:Ilya|Ilya Sytchev]]
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