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Mapping to Ontologies. Nigam Shah nigam@stanford.edu. NCBO: Key activities. We create and maintain a library of biomedical ontologies. We build tools and Web services to enable the use of ontologies and their derivatives. - PowerPoint PPT Presentation
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Mapping to Ontologies
Nigam Shahnigam@stanford.edu
NCBO: Key activities
• We create and maintain a library of biomedical ontologies.
• We build tools and Web services to enable the use of ontologies and their derivatives.
• We collaborate with scientific communities that develop and use ontologies.
www.bioontology.org
Total Monthly Visits to BioPortal
http:
//re
st.b
ioon
tolo
gy.o
rgOntology Services
• Download• Traverse• Search• Comment
Widgets• Tree-view• Auto-complete• Graph-view
Annotation
Data Access
Mapping Services
• Create• Download• Upload
Views
Term recognition
Fetch “data” annotated with a given term
http://bioportal.bioontology.org
Mappings
Root
Term-1 Term-2
Term-3 Term-4
Term-5
R
t1 t2
t4
t5 t6 t7
t3
Term-2 t1
Term-5 t5
Ontology A Upload or Download mapping subsets
Ontology B
Annotation as a Web service
Process textual metadata to automatically tag text with as many ontology terms as possible.
Code
Annotator service
Multiple ways to access
Specific UI
Excel
98 million calls, ~900 GB of data
Elsevier
UIMA platform
ANNOTATION ANALYTICS - I
Analysis of semantically tagged data
Mining Annotations of Grants, Publications
Grants from 1972 to 2007 30 funding agencies
Publications from MedlineOnly “Journal articles”
BioPortal + Protégé are tools for collaborative, shared development of such
hierarchies (ontologies).
Degree of Sponsorship
Allocation of Funding
Who funds what
15
CreditsMark Musen, PIThe team @ www.bioontology.org/project-team
NIH Roadmap grant U54 HG004028
ANNOTATION ANALYTICS - II
Analysis of semantically tagged data
Term – 1:::Term – nSyntactic types
Frequency
Term recognition tool NCBO Annotator
NegEx Patterns
NegEx Rules – Negation detection
P1 ICD9 ICD9 ICD9 ICD9 ICD9 ICD9
P1 T1, T2, no T4
… T5, T4, T3
… T4, T3, T1
T8, T9, T4
… T6, T8, T10
T1, T2, no T4
P2
P2
P3
P3
:
:
Pn
Pn Terms form a temporal series of tags
Coh
ort
of
Inte
rest
Diseases
Procedures
Drugs
BioPortal – knowledge graph
Creating clean lexicons
Annotation Workflow
Furt
her A
naly
sis
Text clinical note
Terms Recognized
Negation detection
Generation of tagged data
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.
Adverse drug events
Recommended