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:

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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