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Rubber Hits the Road: Why NEMO needs RDF

Rubber Hits the Road: Why NEMO needs RDF. Paea LePendu Stanford Center for Biomedical Informatics Research National Center for Biomedical Ontology (NCBO) Stanford University February 26, 2010. Information Processing (Where I Come In). Ontology. F ormal knowledge representation

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Rubber Hits the Road: Why NEMO needs RDF

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  1. Rubber Hits the Road:Why NEMO needs RDF PaeaLePendu Stanford Center for Biomedical Informatics Research National Center for Biomedical Ontology (NCBO) Stanford University February 26, 2010 NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  2. Information Processing(Where I Come In) NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  3. Ontology • Formal knowledge representation • Logic + XML = OWL • Structure & Relationships • Unique names for unique terms (URIs) • Overlap? (Mappings) • Linked via the Web • Tools • Protégé • BioPortal • Pellet Reasoner NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  4. NCBO BioPortal NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  5. RDF – Resource Description FrameworkWho is Eric Miller?(http://en.wikipedia.org/wiki/Resource_Description_Framework) NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  6. NEMO Annotation Task Force(http://nemo.nic.uoregon.edu/wiki/Data_Annotation) • Key Personnel: • Haishan Liu, Bob Frank, Jason Sydes • Gwen Frishkoff & Dejing Dou • Goals (3 phases): • Prototyping Annotations • Finessing Annotations (term selection) • Databasing the Annotations (RDF) NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  7. Simulated ERP Summary Metrics • Data- format, labels, meaning? NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  8. Web of Knowledge(http://www.iskouk.org/presentations/miles_web_and_skos_200807.pdf) NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  9. Web of Knowledge(http://www.iskouk.org/presentations/miles_web_and_skos_200807.pdf) NEMO:Stimulus#SimWord Dataset#10001 Unit#microSeconds Latency Method#tPCA PeakLatency PeakLatency#484 Observation#5 ROI#BillatParietal NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  10. Annotation at NCBO(http://www.bioontology.org/resources-index) • Resource Index • PubMed, PubChem, ClinicalTrials, Gene Expression Omnibus, DrugBank, etc. • Data is a publication or article • Resource is a supplier of data • Index associates data to ontology terms • 20 resources (going on 100) • Over 5 BILLION annotations! NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  11. Annotation at NEMO • Tagged Datasets • Search & Retrieval • Mining datasets: • Co-occurrences • Cross-correlations • Frequent items • Tag clouds • Minimal inference P100 Language Reading N100 NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  12. Deep Annotation at NEMO • Tagged records within datasets • Rich semantics • Detailed queries (SPARQL) • Aggregations • Mining data instances • Fine-grained analysis • NEMO is novel! NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  13. Linked Open Data(http://linkeddata.org/) NIF BioPortal NEMO NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

  14. Thank you. • Questions? NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

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