Scio12 sem web_final


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Slides from #scio12 #SemanticWeb session by @kristiholmes & @ChemConnector

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  • My favorite tool…
  • Here were talking about different machines – computers.Describe typical web page, limitations of HTMLConnecting documents, not concepts; not easy to traverse across disparate data sourcesFrom DERI ( The semantic web is a term coined by world wide web inventor and Deri advisory board member Tim Berners-Lee, to describe the “web of data” that enables machines to understand the semantics, or meaning, of information on the web. It involves the insertion of machine-readable metadata into web pages to give information on how they are related to each other, enabling automated agents to access the web more intelligently and perform tasks on behalf of users. Berners-Lee has defined the semantic web as “a web of data that can be processed directly and indirectly by machines”.
  • This slide is meant for reference, post conference
  • This slide is meant for reference, post conference
  • From DERI ( The Semantic Web involves publishing in languages specifically designed for data: Resource Description Framework (RDF), Web Ontology Language (OWL), and Extensible Markup Language (XML). HTML describes documents and the links between them. RDF, OWL, and XML, by contrast, can describe arbitrary things such as people, meetings, or airplane parts.
  • Semantic/ontology definitions (below RDF), Elly in RDF example for visual, point out links.content from the VIVO team –
  • Simple semantic advantage, content from the VIVO team –
  • content from the VIVO team –
  • Slide content from the VIVO team ( and James King (NIH Library)
  • Image hyperlinked to movie – 1 minute, 45 seconds long
  • ★ make your stuff available on the Web (whatever format) under an open license ★★ make it available as structured data (e.g., Excel instead of image scan of a table)★★★ use non-proprietary formats (e.g., CSV instead of Excel)★★★★ use URIs to identify things, so that people can point at your stuff★★★★★ link your data to other data to provide contextGo to (linked on arrow) and view data levels and examples – emphasize costs and benefits
  • Live demo of VIVO Searchlight Across institutions VIVO provides a uniform semantic structure to enable a new class of tools using the data to advance science. visualizations, search, discovery, etc
  • Scio12 sem web_final

    1. 1. The Semantic Web Science OnlineKristi Holmes & Antony Williams January 20, 2012
    2. 2. We humans have always appliedtools to our work to make things work better…
    3. 3. Simple Machines
    4. 4. 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,
    5. 5. Semantic Web Value Proposition• Resources associated with subjects, predicates (properties and objects &all get HTTP dereferenceable URIs, 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,
    6. 6. Using languages designed for data RDF | OWL | XML
    7. 7. 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-LeeOntology: a formal representation of the knowledge by a set of concepts within a domain and the relationships between those concepts. -- Wikipedia
    8. 8. The semantic advantage Data modeled as bidirectional relationships
    9. 9. Storing data: People as an example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. Dept. of Genetics College of is member of Medicine Jane Genetics Smith has affiliations with Institute author of Journal article Book Book chapter Subject Predicate Object
    10. 10. Detailed Data Relationships Connections among scientists illustrated Inverse relationships are created David Nelson Biomedical Informatics has position in organization with position for is research area of has research area has position in Clinical Translational featured in Mike Conlon Science Institute (CTSI) organization with position for Ed Tech Magazine features has author author of Gene Anderson author of Development of an Observational Instrument to has author Measure Mother-Infant Separation Post BirthCurrent and accurate data revealed
    11. 11. SemWeb Elevator Pitch by David Wood
    12. 12. The 5 Stars of Linked Open Data AVAILABILITY & VALUE ★ ★★ ★★★ ★★★★ ★★★★★
    13. 13. Datasets published in Linked Data form (2011)
    14. 14. Ok! Now let’s dig into a few good examples of how we can put these things to work
    15. 15. Linking government data
    16. 16. Linking government data
    17. 17. Civil War Data
    18. 18. OpenPHACTSOpen 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 -
    19. 19. Complex to navigate… IP? What’s the structure? Are they in our file? What’s similar? What’s the Pharmacology target? data? Known Pathways? Competitors? Working On Connections to Now? disease? Expressed in right cell type?
    20. 20. VIVO
    21. 21. VIVO
    22. 22. Are you using Linked Data?What are your hopes for thiscollection of technologies?
    23. 23. AcknowledgementsFunding: Funding:• Royal Society of Chemistry • VIVO, NIH award U24 RR029822• Innovative Medicines Initiative • Washington University Institute of Clinical and Translational Sciences, NIH award UL1 RR024992Questions: Questions:• •• Twitter: @ChemConnector • Twitter: @kristiholmes• ••• Thank you!
    24. 24. CreditsSites:••••••••••••• Corkscrew_20090741553.jpg• macbook-air-macbook-air-wallpapers.jpg