Mapping to ontologies
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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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Mapping to Ontologies

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Mapping to Ontologies

Nigam Shah

[email protected]


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.


www.bioontology.org


Total Monthly Visits to BioPortal


  • Download

  • Traverse

  • Search

  • Comment

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

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

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


Multiple ways to access

Code

Excel

Elsevier

UIMA platform

Specific UI

98 million calls, ~900 GB of data

Annotator service


Annotation Analytics - I

Analysis of semantically tagged data


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).


Degree of Sponsorship


Allocation of Funding


Who funds what


Credits

Mark Musen, PI

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

    NIH Roadmap grant U54 HG004028


Annotation Analytics - II

Analysis of semantically 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

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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