Faculty of Computer Science

Towards Applying Text Mining and Natural Language Processing for Biomedical Ontology Acquisition
Inniss T., Light M., Thomas G., Lee J., Grassi M., Williams A.
TMBIO(2006)

John G

CMPUT 605

March 31, 2013

2006

Department of Computing Science

Focus
Ontology for describing age-related macular degeneration (AMD) Comparison of the accuracy of three methods for Ontology
Natural Language Processing (NLP) Text Mining (SAS Text Miner) Human Expert

Manual and adhoc knowledge acquisition IDOCS (Intelligent Distributed Ontology Consensus System)

CMPUT 605

2006

Department of Computing Science

Introduction
No existing common and standardized vocabulary for classification of disease types for certain eyediseases
Clinicians, dispersed geographically, may use different terms to describe the same condition Research aimed at extracting the feature and attribute descriptions for the vocabulary of AMD, and build an Ontology from that.

CMPUT 605

2006

Department of Computing Science

Related Work
Lot of research done, since 1990s, for applying NLP techniques in medicine, bio-medicine etc.
NLP & Text Data Mining have been recognized to play an important role in this endeavor Research focused on online repositories such as Medline & PubMed

NLP systems developed: MedLee, UMLS, GENIES etc.

CMPUT 605

2006

Department of Computing Science

IDOCS

CMPUT 605

2006

Department of Computing Science

Methodology
Four clinical experts in retinal diseases enlisted to view 100 eye sample images of AMD
Experts in different geographic locations Described the observations using digital voice recorders no artificially imposed vocabulary constraints Another retinal expert for manual parsing of the transcribed text extracting key words, organization of key-words into categories etc.

CMPUT 605

2006

Department of Computing Science

Methodology: NLP
NLP: Used for information extraction and automatic summarization.
Identify short sequences of words having meaning over and above a meaning composed directly from their parts extreme programming Ngram Statistics Package (NSP) used for collocation discovery in case of bi-grams

Word-pair associations measured by PMI

CMPUT 605

2006

Department of Computing Science

Methodology: NLP

Large PMI for larger degree of association between the words s

CMPUT 605

2006

Department of Computing Science

Methodology:Text Mining (SAS Text Miner)

Collection of documents (corpus) used as input to any text mining algorithm
Corpus broken into tokens or terms (tokens in a particular language) Term weighting Measures: Entropy, Inverse Document Frequency (IDF), Global Frequency (GF) IDF, None (Global weight of 1) & Normal term wt.

CMPUT 605

2006

Department of Computing Science

Results: Human Experts

CMPUT 605

2006

Department of Computing Science

Results: NLP

CMPUT 605

2006

Department of Computing Science

Results: Text Miner

Frequency wt. None
Term wt. Normal

CMPUT 605

2006

Department of Computing Science

Comparison
sss

CMPUT 605

2006

Department of Computing Science

Comparison

Thus text mining is a viable and effective method for determining vocabulary to describe a particular disease
Text Mining found a lot of terms that NLP found Human Expert is the best Ground Truth

CMPUT 605

2006

Department of Computing Science

Ontology Generation

CMPUT 605

2006

Department of Computing Science

Conclusion and Future Work

Human experts are the best, but they did miss some key descriptors
Text Mining and NLP can enhance the generation of feature generations, by preventing the above case As a consequence more robust vocabulary can be generated Extension evaluate the effectiveness of the automated tools, text mining & NLP Different weighting schemes will be tried in the future
CMPUT 605

2006

Department of Computing Science

Thank You For Your Attention!

CMPUT 605

2006