BioPortal and NCBO Web services

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BioPortal and NCBO Web services

• Trish Whetzel
• Outreach Coordinator

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National Center for Biomedical Ontology

• Mission
• To create software for the application of
  ontologies in biomedical science and clinical
  care
• NCBO Partners
• Mark Musen, Stanford University
• Christopher Chute, Mayo Clinic
• Barry Smith, University at Buffalo
• Margaret-Anne Storey, University of Victoria

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National Centers for Biomedical Computing
(http//www.ncbcs.org)
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NCBO Key Activities

• We create and maintain a library of biomedical
  ontologies
• We build tools and Web services to enable the use
  of ontologies
• We collaborate with scientific communities that
  develop and use ontologies

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www.bioontology.org
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http//bioportal.bioontology.org
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• Search
• Traverse
• Comment
• Download

Ontology Services
Views

• Create
• Upload
• Download

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
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Browse ontologies
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Search for terms
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Widgets
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Tag text with ontology terms
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Generation of tagged data
Text clinical note
BioPortal knowledge graph
Creating clean lexicons
Term 1 Term n
Frequency
Diseases
NCBO Annotator
Term recognition tool NCBO Annotator
NegEx Patterns
Procedures
Syntactic types
Drugs
Terms Recognized
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
NegEx Rules Negation detection
Further Analysis
Negation detection
Cohort of Interest
Terms form a temporal series of tags ?
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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 lt 10-7.
ROR1.524, CI0.872, 2.666 PRR1.508,
CI0.8768, 2.594 X2 p-value0.06816.
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Search ontology-based index
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Who is using our Web services?
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BioPortal SPARQL Endpoint
http//sparql.bioontology.org/
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Links of Interest

• Web service documentation
• http//www.bioontology.org/wiki/index.php/NCBO_RES
  T_services
• Software questions
• Software support support_at_bioontology.org
• Social media
• Twitter _at_bioontology
• Facebook http//on.fb.me/bioontology
• LinkedIn http//linkd.in/ncbo-group