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Advancing Biomedical Research: The Role of RDF in NEMO

This presentation from the NEMO All-Hands Meeting at Stanford University discusses the integration of Resource Description Framework (RDF) in biomedical informatics. It covers topics like ontology, formal knowledge representation, unique identifiers for terms, and tools such as Protégé and BioPortal. The presentation outlines the goals of the NEMO Annotation Task Force, including prototyping and databasing annotations. Additionally, it highlights the importance of linked data in enhancing the search and retrieval of biomedical datasets, thus advancing research in the field.

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Advancing Biomedical Research: The Role of RDF in NEMO

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Presentation Transcript

  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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