1. 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 1NEMO 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, 2010.2

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, 2010.3

4. NCBO BioPortal NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.4

5. RDF – Resource Description Framework Who is Eric Miller? (http://en.wikipedia.org/wiki/Resource_Description_Framework) 5NEMO 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) 6NEMO 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, 2010.7

8. Web of Knowledge (http://www.iskouk.org/presentations/miles_web_and_skos_200807.pdf) 8NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010. Dataset#1000 1 Stimulus#SimWord Observation#5 Method#tPCA PeakLatency#484 PeakLatency Latency Unit#milliSeconds ROI#BillatParietal

9. 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! 9NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

10. 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.

11. 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.

12. Linked Open Data (http://linkeddata.org/) BioPortal NIF NEMO 12NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.

13. Thank you. Questions? NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.13