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

Mapping to Ontologies

Nigam Shah

[email protected]


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.


Mapping to ontologies

www.bioontology.org


Total monthly visits to bioportal

Total Monthly Visits to BioPortal


Mapping to ontologies

  • 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

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


Mapping to ontologies

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


Degree of sponsorship

Degree of Sponsorship


Allocation of funding

Allocation of Funding


Who funds what

Who funds what


Mapping to 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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