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Department of Bioinformatics - BiGCaT 1
The Web – What is the Issue?
Egon Willighagen (@egonwillighagen)
21 Oct 2014, What's in a Name, Burlington House, London, UK
Department of Bioinformatics - BiGCaT 2
Web → <html></html>
• World Wide Web– hyperlinked web pages
• Web Browser• Nowadays:
– dynamically created– Interactive
• Is there an issue?
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Data in HTML
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What is HTML?
• Aimed at human– “Hypertext”– later applets, flash, javascript, HTML5's canvas
• Terminology– title, paragraph, link, list, …
• Visualization– bold, italic, …
• CSS: separate content from looks
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Where are the semantics?
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Where are the semantics?
<p lang=”nl”>Mama, die, die, die...</p>
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Solution #1: <head> + mime types
<head><link rel="alternate" type="application/rss+xml" title="RSS" href="http://some.website.org/rss/" />
</head>
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Murray-Rust, P., Rzepa, H.S., Williamson, M.J. & Willighagen, E.L. Chemical markup, XML, and the world wide web. 5. applications of chemical metadata in RSS aggregators. J Chem Inf Comput Sci 44, 462-469 (2004)
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Solution #1: <head> + mime types
• <head><link rel="meta" type="application/rdf+xml" href="meta.rdf"/>
</head>
• Any format. Yes, also JSON.• Any Chemical MIME type!
H. S. Rzepa, P. Murray-Rust and B. J. Whitaker, J. Chem. Inf. Comp. Sci., 1998, 38, 976-982.
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Also JavaScript Object Notation (JSON)
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Solution #2: microformats
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Solution #2: microformats
<html xmlns="http://www.w3.org/1999/xhtml"
xmlns:chem="http://www.blueobelisk.org/chemistryblogs/">
<head>
<title>m1</title>
<script type="text/javascript" src="sechemtic.js" /></head>
<body onload="addGoogleAndPubChemLinks(1,1)"> <h1>The Output</h1>
<p>This article is about <span class="chem:compound">m1</span>
(SMILES:<span class="chem:smiles">CCCOC</span>).</p>
</body>
</html>
Willighagen, E. et al. Userscripts for the life sciences. BMC Bioinformatics 8, 487+ (2007)
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Solution #3: schema.org
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Solution #4: HTML+RDFa
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Solution #4: HTML+RDFa
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Orion Jankowski, SPARQL to Chart, 2010http://www.pharmash.com/posts/2010-09-27-sparql-to-chart.html
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Solution #5: Semantic MediaWiki
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Solution #6: RDF/XML + XSLT
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More about the Semantic Web
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The Web – What is the issue?
We're not using these innovative solutions enough.
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Acknowledgments
• People whom I worked with on solutions– H. Rzepa, P. Murray-Rust, P. Maas, N. Jeliazkova,
N. O'Boyle, R. Guha, C. Steinbeck, D. Wild, ...
• Projects that allow(ed) me to continue adoption of these methods– Open PHACTS (IMI-funded)– eNanoMapper (EC-funded)
• WikiPedia contributors (for images)
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