Schema.org extension for biological database @ Biohackathon2013

Schema.org extenstion

Maori ItoNational Institute of Biomedical Innovation

What is schema.org?

• "Schema.org is a set of extensible schemas that enables webmasters to embed structured data on their web pages for use by search engines and other applications.”

• "Search engines including Bing, Google, Yahoo! and Yandex rely on this markup to improve the display of search results, making it easier for people to find the right web pages.”

(http://schema.org/)

Microdata

“You use the schema.org vocabulary, along with the microdata format, to add information to your HTML content.”

(http://schema.org/docs/gs.html)• Finalizing the proposal of schema.org

extension is a requirement to show “rich” results for major search engines.

If you mark up with microdata,

• You can reveal more rich search results and important keywords.

• These search results may result in more clicks to your pages.

Goal 1

• To finalize the proposal of schema.org extension “BiologicalDatabaseEntry” and “BiologicalDatabase”.– http://www.w3.org/wiki/WebSchemas/

BioDatabases (W3C Wiki)

How to mark up and reflect the results?

【 HTML 】

<div itemscope itemtype="http://schema.org/BiologicalDatabaseEntry"> <span itemprop="dateModified">2012-10-24</span></div>

【 Result 】

Declare scope itemtype with normal html tag

Select 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 into

predicate, 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

mark up– Tag > Graph

Current Situation

• Define original "property" (entryID, isEntryOf, taxon, seeAlso, reference) and "how to mark up" for biological database and its entries.

• Reflect search results for our developing search engine.– Sagace : http://sagace.nibio.go.jp

5 DBs, 1 catalog and 1 DB archive applied microdata!

• DoBISCUIT(Database Of BIoSynthesis clusters CUrated and InTegrated)

• JCRB Cell Bank • Functional Glycomics with KO mice database • Glyco-Disease Genes Database• JCGGDB Report• Integbio Database Catalog• Life Science Database Archive

Thank you very much!!

Goal 2

• Making valuable web application with microdata.

RDFXML

and all

Structured data

microdata

Structured HTMLWe can make web application easily!

Example of web application

How to use -1

1. 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 -2

２． Mark up with MicrodataE.g. ：

<ul itemscope itemtype="http://schema.org/ScholarlyArticle"><li>Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions<span itemprop=’reference' content='pmid:22674858' \>PubMed:22674858</span></li> </ul> Javascript can find ID easily

Declare scope itemtype with normal html tag

Advantage

• We can make many web applications in the same way easily.

• Database developers can feel benefit immediately.

• We can get data on the fly, the data can be updated continually and automatically by reference structured data.

To achieve these goals,

• “Need more people who think it is a good idea.” (by organizers @ schema.org)– public-vocabs@w3.org (<- ML Let’s join !)

• We need more databases and web pages that are marked up with microdata.

• I want your opinion on microdata.• Let's talk!