Rubber Hits the Road: Why NEMO needs RDF Paea LePendu Stanford Center for Biomedical Informatics Research National Center for Biomedical Ontology (NCBO)

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Presentation transcript:

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

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

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,

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

RDF – Resource Description Framework Who is Eric Miller? ( 5NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

NEMO Annotation Task Force ( 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) 6NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

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

Web of Knowledge ( 8NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, Dataset# Stimulus#SimWord Observation#5 Method#tPCA PeakLatency#484 PeakLatency Latency Unit#milliSeconds ROI#BillatParietal

Annotation at NCBO ( 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! 9NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

Annotation at NEMO Tagged Datasets ◦ Search & Retrieval ◦ Mining datasets:  Co-occurrences  Cross-correlations  Frequent items  Tag clouds  Minimal inference P100 N100 Auditory Visual 10NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

Deep Annotation at NEMO Tagged records within datasets ◦ Rich semantics ◦ Detailed queries (SPARQL)  Aggregations  Mining data instances ◦ Fine-grained analysis NEMO is novel! 11NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

Linked Open Data ( BioPortal NIF NEMO 12NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

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