Transcript NCBO Services Project Mtg

BioPortal and
NCBO Web services
Trish Whetzel
Outreach Coordinator
THE NATIONAL CENTER FOR
BIOMEDICAL ONTOLOGY
National Center for
Biomedical Ontology
• Mission
– To create software for the application of
ontologies in biomedical science and clinical
care
• NCBO Partners
– Mark Musen, Stanford University
– Christopher Chute, Mayo Clinic
– Barry Smith, University at Buffalo
– Margaret-Anne Storey, University of Victoria
National Centers for Biomedical Computing
(http://www.ncbcs.org)
NCBO Key Activities
• We create and maintain a library of
biomedical ontologies
• We build tools and Web services to
enable the use of ontologies
• We collaborate with scientific
communities that develop and use
ontologies
www.bioontology.or
http://bioportal.bioontology.org
Ontology
Services
http://rest.bioontology.org
Views
•
•
•
•
Search
Traverse
Comment
Download
Mapping
Services
• Create
• Upload
• Download
Widgets
•
•
•
Annotation
Term recognition
Data Access
Tree-view
Auto-complete
Graph-view
Fetch “data”
annotated with a
given term
http://bioportal.bioontology.org
Browse ontologies
Search for terms
Widgets
Term auto-complete
Tree widget
Visualization
Tag text with ontology terms
Generation of tagged data
Text clinical note
BioPortal – knowledge graph
Creating clean lexicons
Term – 1
:
:
:
Term – n
Frequency
Diseases
Procedures
Syntactic types
Term recognition
tool NCBO Annotator
NCBO Annotator
NegEx
Patterns
Drugs
P1
ICD9
P1
T1,
T2,
no T4
ICD9
…
T5,
T4,
T3
…
ICD9
ICD9
T4,
T3,
T1
T8,
T9,
T4
…
ICD9
ICD9
T6,
T8,
T10
T1,
T2,
no T4
NegEx Rules – Negation
detection
P2
P2
Cohort
of
Interest
Further Analysis
Terms Recognized
Negation detection
P3
P3
:
:
Pn
Pn
Terms form a temporal series of tags 
Adverse drug events
ROR of 2.058, CI of [1.804, 2.349]
PRR of 1.828, CI of [1.645, 2.032]
The uncorrected X2 statistic has p-value < 10-7.
ROR=1.524, CI=[0.872, 2.666]
PRR=1.508, CI=[0.8768, 2.594]
X2 p-value=0.06816.
Search ontology-based index
Who is using our Web services?
BioPortal SPARQL Endpoint
http://sparql.bioontology.org/
Links of Interest
• Web service documentation
http://www.bioontology.org/wiki/index.php/NC
BO_REST_services
• Software questions
– Software support: [email protected]
• Social media
– Twitter: @bioontology
– Facebook: http://on.fb.me/bioontology
– LinkedIn: http://linkd.in/ncbo-group