1. ANALYSIS OF INTER-ANNOTATOR AGREEMENT (TEXT MINING & REG. ANNOTATION) RegCreative Jamboree, Friday, December, 1st, (2006) MARTIN KRALLINGER, 2006 TEXT MINING & REG. ANNOTATION

2. MAIN ASPECTS  Explore annotation overlap  Discuss variability in annotation  Text mining and regulatory element annotation: needs, limits, tasks MARTIN KRALLINGER, 2006 TEXT MINING & REG. ANNOTATION

3. SOCIOLOGY OF GENOME ANNOTATION (Lincoln Stein 2001) MARTIN KRALLINGER, 2006  Models of annotation  Museum model: small group of specialized curators  Jamboree model: a group of biologists and bioinformaticians come together for a short intensive annotation workshop  Cottage industry: decentralized effort of annotators among the recruited community  Factory model: highly automated methods (Elsik et al, 2006) TEXT MINING & REG. ANNOTATION

4. MARTIN KRALLINGER, 2006 WHY PRE-JAMBOREE QUEUE?  Get familiar with annotation system (before jamboree)!  Understand content and annotation strategy of Oreganno  Detect aspects which require improvements such as incompleteness, ambiguity or wrong structures in annotation strategy, guidelines or documentation -> active Feedback (Questionnaire and wiki)  Assess consistency of the current annotation procedures  Explore which aspects affect annotation agreement  Estimate difficulty of task (alternative interpretation, uncertainty, etc,..) TEXT MINING & REG. ANNOTATION

5. SIMILARITY MEASURES MARTIN KRALLINGER, 2006  Similarity calculation popular subject in computer science  Different entities considered:  Feature vectors: Alignment, Cosine, Dice, Euclidean, …  Strings or sequences of strings (text): averaged String Matching, TFIDF  Sets: Jaccard, Loss of Information, Resembalance  Sequences: Levensthein Edit Distance  Trees: Bottom-up/Top-down Maximum Common Subtree, Tree Edit Distance  Graphs: Conceptual Similarity, Graph Isomorphism, Subgraph Isomorphism, Maximum Common Subgraph Isomorphism, Graph Isomorphism Covering, Shortest Path  Information theory: Jiang & Conrath, Lin, Resnik  Bioinformatics: sequence similarity, structural similarity, similarity of gene expression  Here similarity between human annotations ( refer to SimPack project examples) TEXT MINING & REG. ANNOTATION

6. MEASUREMENT OF OBSERVER AGREEMENT MARTIN KRALLINGER, 2006  Assumption when independent annotators agree they are correct ?!  Statistical agreement measures for categorical data  Overall proportion of agreement  Pairwise comparison; Cohen’s kappa; Pearson Chi-square  Weighted kappa for multiple categories  High accuracy implies high agreement  Kappa sometimes is inconsistent with accuracy measured as AROC Measurement of Observer agreement Kundel and Polansky, Statistical concepts Series (2003) Kappa coefficient TEXT MINING & REG. ANNOTATION

7. ANNOTATOR AGREEMENT FOR WSD MARTIN KRALLINGER, 2006 A case Study on Inter-Annotator Agreement for Word Sense Disambiguation, Ng et al  Word Sense Disambiguation (WSD) a central problem in NLP  WSD: discerning the meaning of a word in context  Two human annotators may disagree in their sense assignment  Agreement of human annotators often the baseline for evaluation of automated approaches  Case study using more than 30,000 instances of the most frequently occurring nouns and verbs in English  Sense tagged word in sentences manually by two groups of annotator to WordNet  Used the Kappa score to measure inter-annotator agreement considering effect of chance agreement  Difficult to achieve high agreement when they have to assign refined sense tags  Importance of example sentences for the usage of each word sense TEXT MINING & REG. ANNOTATION

8. AGREEMENT OF SPEECH CORPORA MARTIN KRALLINGER, 2006  Phonetically annotated speech corpora  Quality of manual annotations affected by:  Implicit incoherence: labeling incoherent due to human variability in perceptual capacities and other factors  Lack of consensus on coding schema: manual annotations reflect the variability of the interpretation and application of the coding schema by the annotators  Annotator characteristics: individual characteristics of coders such as familiarity with the material, amount of former training, motivation, interest and fatigue induced errors Measuring the reliability of Manual annotations of Speech corpora, Gut and Bayerl TEXT MINING & REG. ANNOTATION

9. CHALLENGES FOR OREGANNO ANNOTATION MARTIN KRALLINGER, 2006  Complexity of gene regulation  Need of ontologies and lexical resources  Deep inference of domain expert curators  Spatial, temporal, experimental conditions  Range of entity types: genes, regulatory sequences, proteins  Gene family and individual gene member distinction  TF binding site sequence extraction and mapping to genome  TF mapping to normalized database entries (NCBI, Ensembl)  Archeology-like annotation: annotation of old papers  BUT GENE REGULATION IS ONE OF THE MAIN BIOLOGICAL INFORMATION (ANNOTATION) ASPECTS! TEXT MINING & REG. ANNOTATION

10. SOURCES FOR ANNOTATION VARIABILITY (1) MARTIN KRALLINGER, 2006  Curator background (biologist, bioinformatician,...)  Familiarity with the annotation system  Number of previously annotated papers or proteins  Prior knowledge on the regulated gene or TF  Prior knowledge (experience) on the experimental types  Sub-domain knowledge (e.g. developmental biology or OS)  Publication date (reflect the state of knowledge) TEXT MINING & REG. ANNOTATION

11. SOURCES FOR ANNOTATION VARIABILITY (2) MARTIN KRALLINGER, 2006  Nr. of papers annotated the same day (fatigue effect)  Unclear or partial documentation of certain annotation aspects  Annotation type (ontology of annotation types?, CV?)  Nr. of pages, figures, tables, references,…  Consultation of additional resources (material, databases, web)  Different degrees of granularity in annotation  Differences in the recall of manually extracted annotations (all ?)  Sequence (paper/database, strand, typos, length) TEXT MINING & REG. ANNOTATION

12. REGCREATIVE CASE STUDY: PREJAMBOREE (1) MARTIN KRALLINGER, 2006  Relatively few articles -> only exploratory examination  Annotation type: 9/11 ( 2071609, 10674400: RR vs. TFBS)  Considerable difference in average nr. of annotations/paper  Some only extracted a single annotation others basically every annotation mentioned in the paper  Almost perfect agreement in organism source (1 case of human and mouse disagreement), but genes correct!  Very high agreement on the gene names, only few user defined cases (which are difficult to evaluate) TEXT MINING & REG. ANNOTATION

13. REGCREATIVE CASE STUDY: PREJAMBOREE (2) MARTIN KRALLINGER, 2006  Certain disagreement in TF names, many are user defined!  Evidence class: high agreement many Transcription regulator site, and unknown  Evidence type: high agreement, some more complete than others, (again, some annotate all the types others only some of them)  Evidence sub-type: similar to evidence types, but in general a little lower agreement than for the evidence type. TEXT MINING & REG. ANNOTATION

14. Transcription names factor: PREJAMBOREE MARTIN KRALLINGER, 2006 TEXT MINING & REG. ANNOTATION

15. MARTIN KRALLINGER, 2006 Example case 1: TF annotation variance TEXT MINING & REG. ANNOTATION 7534794 Curator B UNKNOWN USER DEFINED Curator B AP-1 USER DEFINED Curator A c-Rel/p65 heterodimer USER DEFINED Curator A UNKNOWN USER DEFINED A B

16. MARTIN KRALLINGER, 2006 Example case 2: TF annotation variance TEXT MINING & REG. ANNOTATION 1718972 Curator A Tcf1 NCBI Curator B Tcf1 NCBI Curator B C\EBP family USER DEFINED Curator B C\EBP and NF-1 USER DEFINED Curator B Tcf1 NCBI Curator B UNKNOWN USER DEFINED

17. MARTIN KRALLINGER, 2006 Example case: difference in evidence types A B A B 10674400 Curator A REGULATORY REGION Curator B TRANSCRIPTION FACTOR BINDING SITE 2071609 Curator A REGULATORY REGION Curator B TRANSCRIPTION FACTOR BINDING SITE TEXT MINING & REG. ANNOTATION

18. MARTIN KRALLINGER, 2006 3038906 Curator A TRANSCRIPTION FACTOR BINDING SITE Col1a2 UNKNOWN TCCAAACTTGGCAAGGGCGAGA CLASS:OREGEC00001 TYPE: OREGET00003 SUBTYPE:OREGES00015 CLASS:OREGEC00001 TYPE: OREGET00001 SUBTYPE:OREGES00003 Curator B 1->TRANSCRIPTION FACTOR BINDING SITE Col1a2 Nfia TTCCAAACTTGGCAAGGGCGAGAGAGGGCGA CLASS:OREGEC00001 TYPE: OREGET00003 SUBTYPE:OREGES00033 CLASS:OREGEC00001 TYPE: OREGET00003 SUBTYPE:OREGES00015 CLASS:OREGEC00002 TYPE: OREGET00001 SUBTYPE:OREGES00003 Different amount of annotation extracted A B A B TEXT MINING & REG. ANNOTATION

19. REGCREATIVE CASE STUDY: JAMBOREE MARTIN KRALLINGER, 2006  Intensive annotation strategy: face to face with other curators and expert annotators  Get direct feedback and provide suggestions  Promote integration of additional aspects in the annotation structure as well as annotated information types  Populate the database with new annotation records  Explore efficient curation training strategies  Create Gold Standard collection of annotation records, maybe useful to allow example-based annotation training/evaluation  Explore demands of biologists / curators to text mining community - > where it would be useful TEXT MINING & REG. ANNOTATION

20. REGCREATIVE CASE STUDY: POST-JAMBOREE MARTIN KRALLINGER, 2006  Monitor improvements in the annotation consistency  Allow consistent community-based annotation  Promote integration of additional aspects in the annotation structure as well as annotated information types  Increase efficiency in populating the database  Construction for text mining training collection TEXT MINING & REG. ANNOTATION

21. ANNOTATION CONSISTENCY MARTIN KRALLINGER, 2006 TEXT MINING & REG. ANNOTATION For selection as relevant paper for curation For the evidence class For the evidence types For the evidence subtypes For the regulated genes For the transcription factors For cell types How to structure comments Other aspects:...

22. TEXT MINING TASKS FOR GENE REGULATION EXTRACTION MARTIN KRALLINGER, 2006 TEXT MINING & REG. ANNOTATION  Detection of relevant articles: abstracts or full text  Extraction of ranked list of regulated genes: mention or normalized gene (database entries)  Extraction of ranked list if TF  Extraction of ranked list of evidence type IDs together with name and text passage (sentence)  Extraction of ranked associations between these genes and TF  Extraction of associations to other controlled vocabularies or ontologies