Enriching Biomedical Events with Meta-knowledge A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Engineering and Physical Sciences March 2013 Raheel Nawaz School of Computer Science List of Contents List of Contents ......................................................................................................... 2 List of Figures ............................................................................................................ 8 List of Tables ............................................................................................................ 10 Abstract .................................................................................................................... 12 Publications ............................................................................................................. 13 Declaration............................................................................................................... 16 Copyright ................................................................................................................. 17 Dedication ................................................................................................................ 17 Acknowledgements ................................................................................................. 20 Thesis Outline .......................................................................................................... 21 Chapter 1: Introduction ......................................................................................... 23 1.1 Problem Domain and Motivation .................................................................. 23 1.2 Aims and Objectives ..................................................................................... 26 1.2.1 Research Aims ..................................................................................... 26 1.2.2 Hypotheses ........................................................................................... 27 1.2.3 Research Objectives ............................................................................ 27 1.2.4 Research Evaluation ............................................................................ 28 1.3 Summary of Contributions ............................................................................ 28 Chapter 2: Event-based Biomedical Text Mining ................................................ 29 2.1 Introduction to Bio-events ............................................................................ 29 2.1.1 Textual Events ..................................................................................... 29 2.1.2 Bio-events ............................................................................................ 32 2.1.3 Bio-event Corpora ............................................................................... 34 2.2 Bio-event Extraction ..................................................................................... 37 2.2.1 Shared Tasks ........................................................................................ 37 2.2.1.1 BioNLP’09 Shared Task on Event Extraction .............................. 37 2.2.1.2 BioNLP’11 Shared Task on Event Extraction .............................. 39 2.2.1.3 BioNLP’13 Shared Task on Event Extraction .............................. 39 2.2.2 State-of-the-Art Systems ..................................................................... 40 2.3 Applications of Bio-event Extraction............................................................ 41 2.3.1 Information Retrieval .......................................................................... 42 2.3.2 Linking Pathways to Literature ........................................................... 46 2.3.3 Other Applications ............................................................................... 48 2.4 Interpretation of Bio-events .......................................................................... 49 Chapter 3: Meta-knowledge ................................................................................... 52 2 3.1 Need for Meta-knowledge Annotation .......................................................... 52 3.2 Analysis of Related Work .............................................................................. 56 3.2.1 Lexical Markers of Meta-Knowledge .................................................. 56 3.2.2 Existing Corpora with Meta-Knowledge Annotations ......................... 59 3.2.2.1 Corpora with Meta-Knowledge Annotations at the Text Span Level ....................................................................................................... 59 3.2.2.2 Corpora with Meta-Knowledge Annotations at the Event Level .. 61 3.3 Meta-knowledge Annotation Scheme ............................................................ 62 3.3.1 Knowledge Type................................................................................... 63 3.3.1.1 Investigation .................................................................................. 64 3.3.1.2 Observation ................................................................................... 66 3.3.1.3 Analysis ......................................................................................... 68 3.3.1.4 Method .......................................................................................... 72 3.3.1.5 Fact ................................................................................................ 73 3.3.1.6 Other .............................................................................................. 74 3.3.2 Certainty Level ..................................................................................... 76 3.3.2.1 L3 .................................................................................................. 77 3.3.2.2 L2 .................................................................................................. 78 3.3.2.3 L1 .................................................................................................. 79 3.3.3 Polarity ................................................................................................. 80 3.3.3.1 Positive .......................................................................................... 80 3.3.3.2 Negative ........................................................................................ 80 3.3.4 Manner ................................................................................................. 82 3.3.4.1 High ............................................................................................... 83 3.3.4.2 Low ............................................................................................... 84 3.3.4.3 Neutral ........................................................................................... 85 3.3.5 Knowledge Source ............................................................................... 86 3.3.5.1 Current ........................................................................................... 86 3.3.5.2 Other .............................................................................................. 88 3.3.6 Hyper-Dimensions ............................................................................... 90 3.3.6.1 New Knowledge ............................................................................ 90 3.3.6.2 Hypothesis ..................................................................................... 91 3.4 Hypothetical Annotation Examples ............................................................... 92 Chapter 4: Meta-Knowledge Annotation .............................................................. 97 4.1 Evaluation of the Annotation Scheme ........................................................... 97 4.2 Annotators and Training ................................................................................ 97 4.3 Annotation of Abstracts ................................................................................. 99 4.3.1 General Corpus Characteristics ............................................................ 99 4.3.1.1 Knowledge Type ......................................................................... 100 4.3.1.2 Certainty Level ............................................................................ 102 4.3.1.3 Polarity ........................................................................................ 106 3 4.3.1.4 Manner ......................................................................................... 111 4.3.1.5 Knowledge Source ....................................................................... 114 4.3.1.6 Hyper-dimensions ........................................................................ 115 4.3.2 Inter-Annotator Agreement ................................................................. 116 4.3.3 Annotation Discrepancies ................................................................... 118 4.4 Annotation of Full Papers ........................................................................... 122 4.4.1 Knowledge Type ................................................................................ 126 4.4.2 Certainty Level .................................................................................. 128 4.4.3 Polarity ............................................................................................... 129 4.4.4 Manner ............................................................................................... 130 4.4.5 Knowledge Source ............................................................................