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  • 1. RDFISING Research DocumentsThe Research Article Use Case
    Alexander Garcia-Castro, UAMS, PhD
    Jael Garcia, UniversitätderBundeswehr
  • 2. Goals and Motivation
    Semantic Web in action
    Network of interconnected documents
    Relationship between data repositories and research documents
    Opening research documents to the Web
  • 3. Research Documents
    Research Papers
    Laboratory information
    Lab Notebooks
    Information Scraps
    LIMS records
    Personal Information Management Systems
  • 4. The Research Article Use Case
    Generate RDF for research papers
    Facilitate the annotation -AO
    Metadata enrichment
    Semiautomatic analysis for “ Materials and Methods”
    • 100 Research articles from FEBS –not an open accesss journal
    • 5. The American Journal of Translational Research –open access: Volume 2(2010), Volume 3 (2011)
  • Network of Interconnected Documents
    Biblio + Content + References
    BIBO
    Publisher XML
  • 6. RDFising Research Documents Metadata and Content
    Biblio + Content + References
    RDF Generation
    BIBO
    Data Enrichment
    Publisher XML
  • 7. Indentification
    Basic Data
    S0014-5793(02)03578-0
    12586329
    T-0901317, a synthetic liver X receptor ligand, inhibits development of atherosclerosis in LDL receptor-deficient mice
    bibo:doi / dc:identifier
    pmid:12586329
    Liver X receptors (LXRa and LXRß) are nuclear receptors, which are important regulators of cholesterol and lipid …
    Liver X receptor
    dc:title
    Macrophage
    bibo:abstract
    dc:subject
    bibo:AcademicArticle
    rdf:type
    http://dx.doi.org/10.1016/S0014-5793(02)03578-0
    bibo:authorList
    owl:sameAs
    Authors
    http://www.ncbi.nlm.nih.gov/pubmed/12586329
    rdfs:Seq
    rdfs:member
    dc:publisher
    dc:issued
    bibo:volume
    Publication Data
    foaf:Person
    bibo:Journal
    536
    2003
    dc:title
    bibo:issn
    bibo:pageEnd
    bibo:pageStart
    FEBS Lettters
    RDFised Document
    6
    11
    0014-5793
  • 8. Content
    Liver X receptors (LXRs), LXRa and LXRß, are members …
    rdfs:comment
    dc:title
    pattern:contains
    doco:Paragraph
    doco:Section
    Introduction
    pattern:contains
    http://dx.doi.org/10.1016/S0014-5793(02)03578-0
    bibo:cites
    bibo:cites
    References
    http://www.ncbi.nlm.nih.gov/pubmed/8878485
    dc:publisher
    rdf:type
    bibo:Journal
    bibo:Article
    dc:title
    bibo:issn
    pmid:8878485
    8878485
    bibo:pageStart
    Nature
    bibo:pageEnd
    dc:title
    dc:issued
    bibo:volume
    728
    731
    An oxysterol signalling pathway mediated by the nuclear receptor LXR alpha
    383
    1996
    0028-0836
  • 9. Research Document RDFSample View
    Biblio + Content + References
  • 10. RDFising Research Documents – Annotated Content
    RDF Generation
    Automatically Annotated XML
    Automatic Annotation
    Publisher XML
  • 11. RDFised Annotations
    Provenance
    foaf:Agent
    rdf:type
    June 1, 2010
    whatizitChebiDict
    pav:createdBy
    pav:createdOn
    http://dx.doi.org/10.1016/S0014-5793(03)00051-6#Introduction
    ao:annotatesResource
    ao:Qualifier
    ao:Annotation
    rdfs:subClassOf
    ao:hasTopic
    ao:body
    Annotation Topic
    chebi:CHEBI_16113
    cholesterol
  • 12. Annotated Content RDFSample View
  • 13. Retrieval on RDFised Documents
    http://dx.doi.org/10.1016/S0014-5793(03)00034-6
    One URI
    Single
    Result
    Another SPARQL
    Same URI
    RDFs for one URI, one unified result
    Biblio + Content + References
  • 14. Final Remarks
    Identifying and representing valid semantic units in research articles is possible –orchestration of existing ontologies
    Representing and delivering the Interconnectedness of RDFised documents is difficult
    The added value is visible when having large volumes of RDF data
    Visualization is very difficult, user experience beyond SPARQL is HARD
  • 15. Future Work
    Focus on “Materials and Methods”
    Tables and Figures, how to best represent them?
    Interactive tables plugged to data repositories?
    Real time table-dependent figures?
    Data Repositories and Research Papers, how are they related?
  • 16. Acknowledgments
    Protechsolutions.com for their HPC facilities