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Slides from #scio12 #SemanticWeb session bit.ly/x28qHL by @kristiholmes & @ChemConnector
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The Semantic Web
Science OnlineKristi Holmes & Antony Williams
January 20, 2012
We humans have always applied tools to our work to make things
work better…
Simple Machines
Semantic Web Value Proposition
• At its heart, the Semantic Web is really about extending standard Web technologies to better deal with data on the Web.
• Its fundamental approach is to create a uniform data model and a simple grammar that are realized through a Web language known as the RDF standard which provide a means to give Web addresses to data elements.
George Thomas and Jim Hendler, http://www.data.gov/communities/node/116/blogs/142
Semantic Web Value Proposition
• Resources associated with subjects, predicates (properties and objects & all get HTTP dereferenceable URI's, with different serialized representations to suit machine (apps) and human (browser) user preferences.
• By normalizing the way we access, process, persist, and visualize data across domains, we simplify mashups and maintenance and unleash more innovation powered by democratized data.
George Thomas and Jim Hendler, http://www.data.gov/communities/node/116/blogs/142
Using languages designed for data
RDF | OWL | XML
Semantic web: describes methods and technologies to allow machines to understand the meaning or "semantics” of information on the web. -- W3C director Sir Tim Berners-Lee
Ontology: a formal representation of the knowledge by a set of concepts within a domain and the relationships between those concepts.-- Wikipedia
The semantic advantage
Data modeled as bidirectional relationships
All data has standard formatEv
eryt
hing
has
its o
wn
URI
Data are structured as “triples” as subject-predicate-object and information is stored using the Resource Description Framework (RDF) .
Concepts and their relationships use a shared ontology to facilitate the harvesting of data from multiple sources.
Jane Smith
is member of
author of
has affiliations with
Dept. of Genetics
College of Medicine
Journal article
Book chapter
Book
Genetics Institute
Subject Predicate Object
Storing data: People as an example
Detailed Data Relationships
David Nelson
Mike Conlon
Biomedical Informatics
Gene Anderson
Clinical Translational Science Institute (CTSI)
Ed Tech Magazine
Development of an Observational Instrument to Measure Mother-Infant Separation Post Birth
has research areais research area of
featured in
has position in
features
organization with position for
has authorauthor of
organization with position for
has position in
author of
has author
Connections among scientists illustrated
Current and accurate data revealed
Inverse relationships are created
SemWeb Elevator Pitch by David Wood
http://www.youtube.com/watch?v=VzguipSLUYc
The 5 Stars of Linked Open Data
★★★★★★★★★★★★★★★
http://lab.linkeddata.deri.ie/2010/star-scheme-by-example/
AVAILABILITY & VALUE
Datasets published in Linked Data form (2011)http://richard.cyganiak.de/2007/10/lod/
Ok! Now let’s dig into a few good examples of how we can put
these things to work
Civil War Data
http://www.civilwardata150.net/
OpenPHACTS
Open PHACTS Project• Develop a set of robust standards…• Implement the standards in a semantic integration hub• Deliver services to support drug discovery programs in
pharma and public domain• 22 partners, 8 pharmaceutical companies, 3 biotechs• 36 months project
Guiding principle is open access, open usage, open source- Key to standards adoption -
http://www.openphacts.org/
Complex to navigate…
What’s the structure?
Are they in our file?
What’s similar?
What’s the target?Pharmacology
data?
Known Pathways?
Working On Now?Connections to
disease?
Expressed in right cell type?
Competitors?
IP?
VIVO
http://vivosearch.org/ http://vivosearchlight.org/ http://vivo.cns.iu.edu/gallery.html
Are you using Linked Data?
What are your hopes for this collection of technologies?
AcknowledgementsFunding:• Royal Society of Chemistry• Innovative Medicines Initiative
Questions:• [email protected]• Twitter: @ChemConnector• http://www.openphacts.org/• http://www.chemspider.com• http://www.chemconnector.com
Thank you!
Funding:• VIVO, NIH award U24 RR029822• Washington University Institute
of Clinical and Translational Sciences, NIH award UL1 RR024992
Questions:• [email protected] • Twitter: @kristiholmes• http://vivo.wustl.edu/display/n4754
CreditsSites:• http://www.youtube.com/watch?v=VzguipSLUYc• http://lab.linkeddata.deri.ie/2010/star-scheme-by-example/• http://richard.cyganiak.de/2007/10/lod/• http://www.deri.ie/about/press/coverage/details/?uid=194&ref=214• http://logd.tw.rpi.edu/• http://www.data.gov/• http://www.civilwardata150.net/• http://www.data.gov/communities/node/116/blogs/142• http://vivosearch.org/ • http://vivosearchlight.org/• http://vivo.cns.iu.edu/gallery.html
Images: • http://cardillowiki.pbworks.com/f/SimpleMachinesImages.jpg • http://www.promo-wholesale.com/Upfiles/Prod_k/Classic-Corkscrew_20090741553.jpg• http://www.whitegadget.com/attachments/pc-wallpapers/68644d1313647290-macbook-
air-macbook-air-wallpapers.jpg