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Data Integration and Extraction over Molecular Biological Data

Cui Tao

supported by NSF

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Motivation

Online biological data: Highly diverse in granularity and

variety Various formats Different terminologies, ID systems,

units

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How to Build a Gene Extraction Ontology? Concepts Relationship sets Constraints Data Frames

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How to Build a Gene Extraction Ontology?

(G*A*U*C*)*

(G*A*T*C*)*

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Knowledge Sources Gene Ontology

Thousands of terms

All Species Toolkit 1,231,935 species names

Protein Databases Thousands of protein names

(Molecular Function, Biological Process, Cellular Component)

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Extraction Rules Statistical NLP Machine learning

Naïve Bayes Hidden Markov Models Decision Trees

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Integration

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Integration Information Hidden behind Links

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Query-based Extraction

Query the gene extraction ontology

Find applicable resources Fill out forms Extract information

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Query-based Extraction

Example: “Find the alfR gene, its sequence, its protein's function, and any mutant that inhibits this gene.”

Gene NameGene Sequence

Gene

Mutant

Protein FunctionMutant Function

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Contribution Provides a way to automatically

integrate online biological data from different sources

Provides an approach that can find proper online resources, fill out online forms and extract data depending on user’s query