Semantic web technologies applied to bioinformatics and laboratory data management

Semantic web technologies applied to bioinformatics and laboratory data management ,[object Object]

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CSS (in content or as external files) Robert Cailliau WWW fomer logo Tim Berners-Lee, Robert Cailiau. CERN (1990)

[object Object],> Buzz word. First coinage associated to Tim O'Reilly. > The term "Web 2.0" (2004–present) is commonly associated with web applications that facilitate interactive information sharing, interoperability, user-centered design, and collaboration on the World Wide Web. > Examples of Web 2.0 include web-based communities, hosted services, web applications, social-networking sites, video-sharing sites, wikis, blogs, mashups, and folksonomies. ,[object Object]

wikis are intended to be easy to use

wikis support tracking of all changes

wikis may allow upload different media Wiki – Wiki ! WikiWikiWeb. Ward Cunningham - 1994

[object Object],> Most popular wiki software > Behind Wikimedia Foundation. > The most know implementation is: Wikipedia http://www.wikipedia.org First version 2002. Wikipedia before UseModWiki (Perl Wiki)

[object Object],http://en.wikipedia.org/wiki/Portal:Gene_Wiki > Approach rellevant human genes information to end-users > Manual collaborative annotation & automated external reference thanks to robot software ,[object Object],Published September 2009

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[object Object],> To get information from a HTML source (wiki included) Download tools: ,[object Object]

[object Object],> Processing content. (example, EC: 3.4.21.-) ,[object Object]

[object Object],> http://en.wikipedia.org/w/api.php

[object Object],> Common scripting with Python or Perl: MediaWiki::Bot > You can get / store information from/in wiki.

[object Object],> Easier to extract data: ,[object Object]

Useful when templates are used

Can retrieve all pages from a category

[object Object],> The Semantic Web is not a separate Web but an extension of the current one, in which information is given well-defined meaning, better enabling computers and people to work in collaboration. Sir Tim Berners-Lee

The Berners-Lee Semantic Web ‘Birthday Cake’ http://www.mkbergman.com/231/from-data-federation-pyramid-to-the-semantic-web-birthday-cake/

[object Object],> http://www.snpedia.com (starts from 2007) > Semantic MediaWiki (first releases 2005) > Database of SNP (Single Nucleotide Polymorphisms) > In September 2009, website claimed 7,938 SNPs in their database. > Predictive medicine report against SNPedia using Promethease: An application to query SNPedia against your genotyping

[object Object],* Type:Page : links to pages (the default) * Type:String : text strings that are not longer than 250 letters * Type:Number : integer and decimal numbers with optional exponent * Type:Boolean : restricts the value of a property to true/false (also 1/0 and yes/no) * Type:Date: specifies particular points in time * Type:Text: like Type:String but can have unlimited length; the trade-off is values of this type cannot be selection or sort criteria in queries. * Type:Code: like Type:Text but with additional precautions to preserve special formatting as used for technical texts. The value displays as regular text everywhere else (query results, factbox, "Pages using the property", etc.). * Type:Temperature: variation of Type:Number that supports uits of temperature (cannot be user-defined since converting temperature units is more complicated than multiplying by a conversion factor). * Type:Telephone number: validates and stores international telephone numbers based on the RFC 3966 standard * Type:Record: type for compound property values that consists of a short list of values with fixed type and order

[object Object],For specifying URLs and emails, there are some special variations of the string data type: * Type:URL: displays an external link to its URL object * Type:Email: displays an e-mail address as a link (with mailto:) * Type:Annotation URI: similar to Type:URL but with some technical differences in SMW's RDF export Some extension provide further types: * Type:Geographic coordinate (provided by Semantic Maps ): describes geographic locations. Different forms of geographic coordinates are supported. http://semantic-mediawiki.org/wiki/Help:Properties_and_types

[object Object],Triple {subject, property/predicate, object} Defining & describing data and relations among data Suitable to attach metadata to certain resources Understood by machines (not so much by humans…) Normally in XML format Alternative: RDFa (in XHTML pages directly)

[object Object],RDF query language; its name is a recursive acronym that stands for SPARQL Protocol and RDF Query Language . ,[object Object]

Example query of biological resources:

http://www.semantic-systems-biology.org/biogateway/querying

[object Object],Semantic MediaWiki (and other semantic addons) is an extension of MediaWiki. At least as much as with MediaWiki. Better and more specific search capabilities Not only free text search on pages It resembles relational database searching SPARQL =~ SQL

[object Object],Better browsing interface (browsing through properties, not only categories) Importing and exporting of logical mesh. Easier exchange of information with 3 rd party applications (through RDF)

Protein-Wiki Semantic wiki-based system for the management of a protein production service. Currently in testing phase In collaboration with CRG Protein Service Customisation built up after study of their present workflow and actual needs. Intended for internal use

[object Object],> Cheaper approach than most commercial similar solutions > Open-source technology. Blooming comunity behind. ,[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Design: Guglielmo Roma

Protein-Wiki : Users roles S ubmit requests to the service using pre-defined templates, view the status of his/her requests at any time, and retrieve the study reports when experiments are complete Can add, edit experimental data, cannot create or delete experiments. Can create, edit, delete new experiments, associated to submitted requests, using pre-defined templates C reation of new templates, users management and their training

Protein-Wiki : permissions & security Login & role permissions. Done automatically or via administrator Namespaces specific permissions: Experiment:: (only lab members/managers) Template:: (only administrators) Page specific permissions By using user and parse functions extensions Network?

Semantic web technologies applied to bioinformatics and laboratory data management

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