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

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Rubber Hits the Road: Why NEMO needs RDF

Paea LePenduStanford Center for Biomedical Informatics ResearchNational Center for Biomedical Ontology (NCBO)Stanford UniversityFebruary 26, 2010

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

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Information Processing(Where I Come In)

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

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OntologyFormal 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.

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NCBO BioPortal

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

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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.

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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.

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Simulated ERP Summary MetricsData- format, labels, meaning?

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

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Web of Knowledge(http://www.iskouk.org/presentations/miles_web_and_skos_200807.pdf)

Dataset#10001

Stimulus#SimWord

Observation#5

Method#tPCA

PeakLatency#484

PeakLatency

Latency

Unit#milliSeconds

ROI#BillatParietal

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

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Annotation at NCBO(http://www.bioontology.org/resources-index)

Resource Index◦PubMed, PubChem, ClinicalTrials,

Gene Expression Omnibus, DrugBank, etc.

Data is a publication or articleResource is a supplier of dataIndex associates data to ontology

terms◦20 resources (going on 100)◦Over 5 BILLION annotations!

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

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Annotation at NEMOTagged Datasets

◦Search & Retrieval◦Mining datasets:

Co-occurrences Cross-correlations Frequent items

Tag clouds Minimal inference

P100

N100

Auditory

Visual

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

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Deep Annotation at NEMOTagged 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.

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Linked Open Data(http://linkeddata.org/)

BioPortal

NIF

NEMO

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

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Thank you.Questions?