Ontology-driven discourse analysis for information extraction
Data & Knowledge EngineeringPublished 22 December 2004
Philipp Cimiano, Uwe Reyle, Jasmin Šarić
Citations39
SJR quartileQ2
SJR score0.68
SNIP1.41
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
A novel approach to discourse analysis within information extraction systems that makes use of DRT as formal representation of the linguistic context as well as of a domain-specific ontology as a basis to compute conceptual relations between extracted events thus establishing discourse coherence.
Abstract
This paper presents a novel approach to discourse analysis within information extraction systems. It makes use of DRT as formal representation of the linguistic context as well as of a domain-specific ontology as a basis to compute conceptual relations between extracted events thus establishing discourse coherence. The approach has been implemented within GenIE, an information extraction system with the aim of extracting information about biochemical pathways, about sequences, structures and functions of genomes and proteins. The approach is evaluated against a semantically hand-annotated set of Swiss-Prot protein function descriptions and shows very promising results.
Keywords
Computer ScienceBiochemistry, Genetics and Molecular Biology
BiometricsThe Measurement of Observer Agreement for Categorical Data
78,934 Citations1977J. Richard Landis, Gary G. Koch
A general statistical methodology for the analysis of multivariate categorical data arising from observer reliability studies is presented and tests for interobserver bias are presented in terms of first-order marginal homogeneity and measures of interob server agreement are developed as generalized kappa-type statistics.
International Journal of Human-Computer StudiesToward principles for the design of ontologies used for knowledge sharing?
7,656 Citations1995Thomas Gruber
The role of ontology in supporting knowledge sharing activities is described, and a set of criteria to guide the development of ontologies for these purposes are presented, and it is shown how these criteria are applied in case studies from the design ofOntologies for engineering mathematics and bibliographic data.
Nucleic Acids ResearchThe SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999
3,238 Citations1999Amos Bairoch, Rolf Apweiler
Current developments of the database include: cross-references to additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT.
Nucleic Acids ResearchThe SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
3,133 Citations2000Amos Bairoch
The Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT, is described.
arXiv (Cornell University)Assessing agreement on classification tasks: the kappa statistic
2,092 Citations1996Jean Carletta
Handbook of Formal Languages
1,947 Citations1997Grzegorz Rozenberg, Arto Salomaa
This first handbook of formal languages gives a comprehensive up-to-date coverage of all important aspects and subareas of the field.
Journal of SemanticsPresupposition Projection as Anaphora Resolution
1,147 Citations1992R.A. van der Sandt
It is argued that presuppositional expressions should not be seen as referring expressions, nor is presupposition to be explicated in terms of some non-standard logic, while the theory is elaborated in the framework of discourse representation theory.
The Logical Form of Action Sentences
1,041 Citations2001Donald Davidson
Genome ResearchCreating the Gene Ontology Resource: Design and Implementation
963 Citations2001The Gene Ontology Consortium
The Gene Ontology project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism, which includes building three extensive ontologies to describe molecular function, biological process, and cellular component.
The Mouseion at the JAXlibrary (Jackson Laboratory)Creating the gene ontology resource: design and implementation.
829 Citations2001Judith A. Blake, John Corradi +4 more
Tree-Adjoining Grammars
715 Citations1997Aravind K. Joshi, Yves Schabes
A tree generating system called tree-adjoining grammar (TAG) is described and a number of formal results have been established for TAGs, which are of interest to researchers in formal languages and automata, including those interested in tree grammars and tree automata.
PubMedToward information extraction: identifying protein names from biological papers.
494 Citations1998Ken Fukuda, Akihiro Tamura +2 more
A new method of extracting material names, PROPER, using surface clue on character strings is proposed, which extracts material names in the sentence with 94.70% precision and 98.84% recall, regardless of whether it is already known or newly defined.
Natural Language EngineeringPartial parsing via finite-state cascades
480 Citations1996Steven Abney
Deterministic parsers specified by finite state cascades may be more accurate than exhaustive search stochastic context free parsers and extended at modest cost to construct parse trees with finite feature structures.
PubMedAutomatic extraction of biological information from scientific text: protein-protein interactions.
433 Citations1999Christian Blaschke, Miguel A. Andrade‐Navarro +2 more
The basic design of a system for automatic detection of protein-protein interactions extracted from scientific abstracts is described and the feasibility of developing a fully automated system able to describe networks of protein interactions with sufficient accuracy is demonstrated.
The Philosophical QuarterlyThe Logic of Decision and Action.
343 Citations1970Kit Fine, Nicholas Rescher
Journal of SemanticsDealing with Ambiguities by Underspecification: Construction, Representation and Deduction
337 Citations1993Uwe Reyle
A theory of language meaning that represents scope ambiguities by underspecified structures that relates these structures directly, without considering cases is provided.
International Joint Conference on Artificial IntelligenceFASTUS: A Finite-state Processor for Information Extraction from Real-world Text.
256 Citations1993Douglas E. Appelt, Jerry R. Hobbs +3 more
FASTUS has been evaluated on several blind tests that demonstrate that state-of-the-art performance on information-extraction tasks is obtainable with surprisingly little computational effort.
Selectional Preference and Sense Disambiguation
225 Citations1997Philip Resnik
EVENT EXTRACTION FROM BIOMEDICAL PAPERS USING A FULL PARSER
223 Citations2000Akane Yakushiji, Yuka Tateisi +2 more
An information extraction system using a full parser to investigate the plausibility of full analysis of text using general-purpose parser and grammar applied to biomedical domain and the use of modules that handles partial results of parsing is proposed for further improvement.
Computational LinguisticsRepresentation and Inference for Natural Language: A First Course in Computational Semantics
219 Citations2006Francis Jeffry Pelletier
This book introduces fundamental techniques for computing semantic representations for fragments of natural language and performing inference with the result by using first-order logic and lambda calculus.
Robust Relational Parsing over Biomedical Literature: Extracting Inhibit Relation
211 Citations2001James Pustejovsky, José M. Castaño +3 more
The design of a robust parser for identifying and extracting biomolecular relations from the biomedical literature is described, and the use of text-based anaphora resolution to enhance the results of argument binding in relational extraction is used.
BioinformaticsAn ontology for biological function based on molecular interactions
184 Citations2000Peter D. Karp
The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics, and presents the functional ontology developed for the EcoCyc database.
University of Sheffield
165 Citations1995Robert Gaizauskas, Kevin Humphreys +2 more
The LaSIE (Large Scale Information Extraction) system has been developed at the University of Sheffield as part of an ongoing research effort into information extraction and, more generally, natural language engineering.
Discourse relations and defeasible knowledge
151 Citations1991Alex Lascarides, Nicholas Asher
Extracting molecular binding relationships from biomedical text
110 Citations2000Thomas C. Rindflesch, Jayant V. Rajan +1 more
The domain knowledge and the underspecified linguistic analyses that support the identification of predications about macromolecular binding relationships from biomedical text are described and reported on.
Journal of SemanticsBridging
90 Citations1998Nicholas Asher
This paper model the processing of given information as a byproduct of computing rhetorical structure in a framework known as SDRT (Asher, 1993), which formalises the interaction between discourse structure and compositional and lexical semantics in determining semantic content.
BioinformaticsA knowledge model for analysis and simulation of regulatory networks
75 Citations2000Andrey Rzhetsky, Tomohiro Koike +7 more
An ontological model for the representation of biological knowledge related to regulatory networks in vertebrates is introduced and is partially realized in a computer system designed to aid researchers in biology and medicine in visualizing and editing a representation of a signal transduction system.
Journal of Logic Language and InformationA calculus for first order Discourse Representation Structures
51 Citations1996Hans Kamp, Uwe Reyle
This paper presents a sound and complete proof system for the first order fragment of Discourse Representation Theory, and considers the distinctive architecture of DRS-like semantic representation in a sublanguage of the one defined in Section 2, which differs from the full language in that it lacks identity and disjunction.
Terminology-driven mining of biomedical literature
50 Citations2003Goran Nenadić, Irena Spasić +1 more
An overview of an integrated framework for terminology-driven mining from biomedical literature is presented, which addresses acronyms as a common way of introducing term variants in biomedical papers.
Inferring discourse relations in context
48 Citations1992Alex Lascarides, Nicholas Asher +1 more
Some general conclusions are drawn about the role of domain-specific information, top-down and bottom-up discourse information flow, and the usefulness of formalisation in discourse theory.
Talking about trees
45 Citations1993Patrick Blackburn, Claire Gardent +1 more
The motivation for introducing these languages is to provide tools for formalising grammatical frameworks perspicuously, and the paper illustrates this by showing how the leading ideas of GPSG can be captured in LT (LF).
Journal of Chemical Information and Computer SciencesName=Struct: A Practical Approach to the Sorry State of Real-Life Chemical Nomenclature
42 Citations1999Jonathan Brecher
The design of Name=Struct, an automated system for the conversion of chemical names to their corresponding structures, is described and the nomenclature interpretation problems addressed in its development are discussed.
BioinformaticsTerminology-driven mining of biomedical literature
33 Citations2003Goran Nenadić, Irena Spasić +1 more
Annotating anaphoric and bridging relations with MMAX
29 Citations2001Christoph Müller, Michael Strube
Annotation of anaphoric and bridging relations in a corpus of written texts is presented and an annotation scheme is defined based on differences as well as similarities between these phenomena.
Journal of Logic Language and InformationTalking about Trees and Truth-Conditions
29 Citations2001Reinhard Muskens
Logical Description Grammar (LDG), a model ofgrammar and the syntax-semantics interface based on descriptions inelementary logic, offers a natural way of dealing with underspecification in natural language syntax andsemantics.
Lecture notes in computer scienceORAKEL: A Natural Language Interface to an F-Logic Knowledge Base
28 Citations2004Philipp Cimiano
RAKEL is a natural language interface which translates wh-questions into logical queries and evaluates them with respect to a given knowledge base and makes use of a compositional approach in order to construct the semantics of a wh-question.
Extracting regulatory gene expression networks from PubMed
24 Citations2004Jasmin Šarić, Lars Juhl Jensen +3 more
From abstracts related to baker's yeast, a regulatory network comprised of 441 pairwise relations from 58,664 abstracts is extracted with an accuracy of 83-90%.
Comparative and Functional GenomicsDeveloping a protein‐interactions ontology
22 Citations2003Esther Ratsch, Jörg Schultz +5 more
The approach for developing a formal ontology dealing with the interactions of a protein with other biomolecules and rules governing these definitions and relations should be incorporated whenever necessary are described.
Exploiting Syntax when Detecting Protein Names in Text
22 Citations2002Gunnar Eriksson, Kristofer Franzén +3 more
The different steps involved in the approach to protein tagging are presented, and it is shown how combinations of them influence recall and precision.
Language Resources and EvaluationDiversity of scenarios in information extraction
21 Citations2002Silja Huttunen, Roman Yangarber +1 more
It is proposed that these kinds of event relationships can be better described with a modular, hierarchical model, and traditional views on event structure and template design are not adequate for the more complex scenarios.
Talking about trees, scope and concepts
2 Citations2005Philipp Cimiano, Uwe Reyle
The ultimate task for both computational and theoretical linguistics must not only be to describe the sources of ambiguity but also to identify the ways in which ambiguities can be eliminated again.