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