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Mapping to Ontologies. Nigam Shah [email protected] 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.

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Ncbo key activities
NCBO: Key activities

  • We create and maintain a library of biomedical ontologies.

  • We buildtools and Web services to enable the use of ontologies and their derivatives.

  • We collaborate with scientific communities that develop and use ontologies.




Ontology Services

Views

  • Create

  • Download

  • Upload

Mapping Services

http://rest.bioontology.org

  • Tree-view

  • Auto-complete

  • Graph-view

Widgets

Annotation

Term recognition

Fetch “data” annotated with a given term

Data Access

http://bioportal.bioontology.org


Mappings
Mappings

R

Root

Term-1

Term-2

t1

t2

Term-2

t1

Term-3

Term-4

t3

Term-5

t5

t4

t5

t7

Term-5

t6

Ontology B

Ontology A

Upload or Download mapping subsets


Annotation as a web service
Annotation as a Web service

Process textual metadata to automatically tag text with as many ontology terms as possible.


Multiple ways to access
Multiple ways to access

Code

Excel

Elsevier

UIMA platform

Specific UI

98 million calls, ~900 GB of data

Annotator service


Annotation analytics i
Annotation Analytics - I

Analysis of semantically tagged data


Mining annotations of grants publications
Mining Annotations of Grants, Publications

  • Publications from Medline

    • Only “Journal articles”

Grants from 1972 to 2007

30 funding agencies


BioPortal + Protégé are tools for collaborative, shared development of such hierarchies (ontologies).





Credits

Mark Musen, PI

  • The team @ www.bioontology.org/project-team

    NIH Roadmap grant U54 HG004028


Annotation analytics ii
Annotation Analytics - II

Analysis of semantically tagged data


Generation of tagged data
Generation of tagged data

Text clinical note

BioPortal – knowledge graph

Creating clean lexicons

Term – 1

:

:

:

Term – n

Frequency

Diseases

Annotation Workflow

Term recognition tool NCBO Annotator

NegEx Patterns

Procedures

Syntactic types

Drugs

Terms Recognized

NegExRules – Negation detection

Further Analysis

Negation detection

Cohort of Interest

Terms form a temporal series of tags 


Adverse drug events
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.


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