Schema.org extension for biological database @ Biohackathon2013
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Schema.org extension for biological database @ Biohackathon2013

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Schema.org extension for biological database and database entry. It will make database developers happy in the future.

Schema.org extension for biological database and database entry. It will make database developers happy in the future.

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Schema.org extension for biological database @ Biohackathon2013 Schema.org extension for biological database @ Biohackathon2013 Presentation Transcript

  • Schema.org extenstionMaori ItoNational Institute of Biomedical Innovation
  • What is schema.org?• "Schema.org is a set of extensible schemas thatenables webmasters to embed structured data ontheir web pages for use by search engines and otherapplications.”• "Search engines including Bing, Google, Yahoo! andYandex rely on this markup to improve the display ofsearch results, making it easier for people to find theright web pages.”(http://schema.org/)
  • Microdata“You use the schema.org vocabulary, alongwith the microdata format, to add information toyour HTML content.”(http://schema.org/docs/gs.html)• Finalizing the proposal of schema.orgextension is a requirement to show “rich”results for major search engines.
  • If you mark up with microdata,• You can reveal more rich search results andimportant keywords.• These search results may result in moreclicks to your pages.
  • Goal 1• To finalize the proposal of schema.orgextension “BiologicalDatabaseEntry” and“BiologicalDatabase”.– http://www.w3.org/wiki/WebSchemas/BioDatabases (W3C Wiki)
  • How to mark up and reflect theresults?【HTML】<div itemscope itemtype="http://schema.org/BiologicalDatabaseEntry"><span >2012-10-24</span></div>【Result】Declare scope itemtype with normal html tagSelect propery Content
  • Why microdata?• Reasonable• Flexibility– RDFa > microdata > microformats• Simple– Microformats > microdata ≒ RDFa• Standardization– Microdata > RDFa > microformats• Yield to the powerful..– Major search engine decided to use it.
  • Advantage and Disadvantage• Advantage– Get better results– If we can translate microdata property intopredicate, we can convert them to RDF– Easy to use web application– Microdata can coexist with html• Disadvantage– Need some time and some more efforts to markup– Tag > Graph
  • Current Situation• Define original "property"(entryID, isEntryOf, taxon, seeAlso, reference) and "how to mark up" forbiological database and its entries.• Reflect search results for ourdeveloping search engine.– Sagace : http://sagace.nibio.go.jp
  • 5 DBs, 1 catalog and 1 DBarchive applied microdata!• DoBISCUIT(Database Of BIoSynthesis clustersCUrated and InTegrated)• JCRB Cell Bank• Functional Glycomics with KO mice database• Glyco-Disease Genes Database• JCGGDB Report• Integbio Database Catalog• Life Science Database ArchiveThank you very much!!
  • Goal 2• Making valuable web application withmicrodata.
  • RDFXMLand allStructured datamicrodataStructured HTMLWe can make webapplication easily!
  • Example of web application
  • How to use -11. Paste css and Javascript into html<link rel="stylesheet"href="http://sagace.nibio.go.jp/publication/micropop/micropop.css" /><script type="text/javascript"src="http://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script type="text/javascript"src="http://sagace.nibio.go.jp/publication/micropop/micropop.js"></script>
  • How to use -22.Mark up with MicrodataE.g.:<ul itemscope itemtype="http://schema.org/ScholarlyArticle"><li>Computational design, construction, and characterization of a set ofspecificity determining residues in protein-protein interactions<span itemprop=’reference content=pmid:22674858 >PubMed:22674858</span></li></ul> Javascript can find ID easilyDeclare scope itemtype with normal html tag
  • Advantage• We can make many web applicationsin the same way easily.• Database developers can feel benefitimmediately.• We can get data on the fly, the datacan be updated continually andautomatically by reference structureddata.
  • To achieve these goals,• “Need more people who think it is a goodidea.” (by organizers @ schema.org)– public-vocabs@w3.org (<- ML Let’s join !)• We need more databases and web pagesthat are marked up with microdata.• I want your opinion on microdata.• Lets talk!