Monday presentation 1336-may23

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Monday presentation 1336-may23

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

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