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

1. Schema.org extenstion
Maori Ito
National Institute of Biomedical Innovation

2. 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/)

3. 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.

4. 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.

5. Goal 1
• To finalize the proposal of schema.org
extension “BiologicalDatabaseEntry” and
“BiologicalDatabase”.
– http://www.w3.org/wiki/WebSchemas/BioDatabas
es (W3C Wiki)

6. How to mark up and reflect the
results?
【HTML】
<div itemscope itemtype="http://schema.org/BiologicalDatabaseEntry">
<span >2012-10-24</span>
</div>
【Result】
Declare scope itemtype with normal html tag
Select propery Content

7. 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.

8. 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

9. Current Situation
• Define original "property"
(entryID, isEntryOf, taxon, seeAlso, r
eference) 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

10. 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!!

11. Goal 2
• Making valuable web application with
microdata.

12. RDF
XML
and all
Structured data
microdata
Structured HTML
We can make web
application easily!

13. Example of web application

14. 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>

15. How to use -2
２．Mark up with Microdata
E.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

16. 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.

17. 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!