Ontology Generation Based on a UserSpecified Ontology Seed

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Ontology Generation Based on a User-Specified
Ontology Seed

• Cui Tao
• Data Extraction Research Group
• Department of Computer Science
• Brigham Young University

Supported by NSF
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Introduction

• Motivation
• Traditional search engines return documents
• Ontology-based data extraction return
  information
• Problem
• Build extraction ontology that meet users needs
• Goal
• Automatically build ontologies for users needs

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Example

• Example a biologist is interested in information
  about large proteins in humans and their
  functions
• Possible queries
• Find proteins in humans that are gt20 kDa
• Find all the proteins in humans that serve as
  receptors
• ...
• Information sources --- various online databases
• NCBI
• Gene Cards
• The Gene Ontology
• GPM Proteomics Database

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Extraction Ontology
Molecular Weight

• Regular Expression \d1,5(\.\d1,2)?
• Unit kilodaltons?kdas?kds?das?daltons?

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User Interface
Select a title for the forms
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User InterfaceBinary Relationship
Protein
Name

Name
Protein
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User InterfaceBinary Relationship
Protein
Name
Name
Protein

Molecular weight
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User InterfaceN-ary Relationship
Start
End
Orientation
Chromosome number
Chromosome location
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User InterfaceN-ary Relationship
GO phrase
GO
GO ID
Go ID
Go term

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Overall Form
Go ID
Go term

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Ontology View
Start
End
Orientation
Chromosome number
Chromosome location
GO phrase
Name
Protein
GO
GO ID
Molecular weight
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Fill in the Form
Go ID
Go term

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Protein
Fill in the Form
Name
14-3-3 protein epsilon Mitochondrial import
stimulation factor Lsubunit Protein kinase C
inhibitor protein-1 KCIP-1 14-3-3E
Molecular Weight
29175 Daltons
Chromosome location
Go ID
Go term

GO0019899 GO0019904
enzyme binding protein domain specific binding
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Mapping
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Mapping
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Mapping
Name
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Data Frame Generation

• Choose from data frame library
• Data frames for basic values
• Numbers within different ranges
• Integers, floats, etc
• Emails, phone numbers, addresses, etc
• Domain specific values (DNA sequences)
• Units
• Build lexicon files

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Data Frame Generation

• Find the best matched data frame from the
  library
• Find the correct units

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Build Lexicon Files
Name
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Contribution

• Automatically generates ontologies depending on
  users requests
• Provides a tool for users to easily provide
  ontology seeds
• Automatically generates ontology views from
  ontology seeds
• Automatically map ontology concepts to source
  databases