Rubber Hits the Road: Why NEMO needs RDF
description
Transcript of Rubber Hits the Road: Why NEMO needs RDF
![Page 1: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/1.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
1
Rubber Hits the Road: Why NEMO needs RDFPaea LePenduStanford Center for Biomedical Informatics ResearchNational Center for Biomedical Ontology (NCBO)Stanford UniversityFebruary 26, 2010
![Page 2: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/2.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
2
Information Processing(Where I Come In)
![Page 3: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/3.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
3
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
![Page 4: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/4.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
4
NCBO BioPortal
![Page 5: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/5.jpg)
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)
![Page 6: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/6.jpg)
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)
![Page 7: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/7.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
7
Simulated ERP Summary MetricsData- format, labels, meaning?
![Page 8: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/8.jpg)
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)
Dataset#10001
Stimulus#SimWord
Observation#5
Method#tPCA
PeakLatency#484
PeakLatency
LatencyUnit#milliSeconds
ROI#BillatParietal
![Page 9: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/9.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
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 articleResource is a supplier of dataIndex associates data to ontology
terms◦20 resources (going on 100)◦Over 5 BILLION annotations!
![Page 10: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/10.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
10
Annotation at NEMOTagged Datasets
◦Search & Retrieval◦Mining datasets:
Co-occurrences Cross-correlations Frequent items
Tag clouds Minimal inference
P100
N100
Auditory
Visual
![Page 11: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/11.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
11
Deep Annotation at NEMOTagged records within datasets
◦Rich semantics◦Detailed queries (SPARQL)
Aggregations Mining data instances
◦Fine-grained analysis
NEMO is novel!
![Page 12: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/12.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
12
Linked Open Data(http://linkeddata.org/)
BioPortalNIF
NEMO
![Page 13: Rubber Hits the Road: Why NEMO needs RDF](https://reader035.fdocuments.in/reader035/viewer/2022062812/568162b2550346895dd33aa3/html5/thumbnails/13.jpg)
NEMO All-hands Meeting. Atlanta, GA. Feb. 26-8, 2010.
13
Thank you.Questions?