Karin Verspoor

Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis.

Hamed Hassanzadeh, Anthony Nguyen, Karin Verspoor

Journal article  |  2019  |  Journal of Biomedical Informatics

OBJECTIVE: Published clinical trials and high quality peer reviewed medical publications are considered as the main sources of evi..

The current scope of healthcare-associated infection surveillance activities in hospitalized immunocompromised patients: a systematic review.

Jake C Valentine, Lisa Hall, Karin M Verspoor, Leon J Worth

Journal article  |  2019  |  International Journal of Epidemiology

BACKGROUND: Immunocompromised patients are at increased risk of acquiring healthcare-associated infections (HAIs) and often requir..

Exploring effective approaches for haplotype block phasing.

Ziad Al Bkhetan, Justin Zobel, Adam Kowalczyk, Karin Verspoor, Benjamin Goudey

Journal article  |  2019  |  BMC Bioinformatics

BACKGROUND: Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as..

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases

Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor

Journal article  |  2019

Abstract The volume of biological database records is growing rapidly, populated by complex records drawn from heterogeneous sourc..

Characterizing the Scope of Exposome Research Through Topic Modeling and Ontology Analysis.

Guillermo Lopez-Campos, Philip Kiossoglou, Ann Borda, Christopher Hawthorne, Kathleen Gray, Karin Verspoor

Journal article  |  2019  |  Studies in Health Technology and Informatics

Exposomics is a field of research which is receiving growing attention. In this work, we characterize the exposome research landsc..

Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings

Zenan Zhai, Dat Quoc Nguyen, Saber Akhondi, Camilo Thorne, Christian Druckenbrodt, Trevor Cohn, Michelle Gregory, Karin Verspoor

Conference Proceedings  |  2019  |  Proceedings of the 18th BioNLP Workshop and Shared Task

Chemical patents are an important resource for chemical information. However, few chemical Named Entity Recognition (NER) systems ..

Using natural language processing and VetCompass to understand antimicrobial usage patterns in Australia

B Hur, LY Hardefeldt, K Verspoor, T Baldwin, JR Gilkerson

Conference Proceedings  |  2019  |  Australian Veterinary Journal

Background Currently there is an incomplete understanding of antimicrobial usage patterns in veterinary clinics in Australia, but ..

Automated assessment of biological database assertions using the scientific literature

Mohamed Reda Bouadjenek, Justin Zobel, Karin Verspoor

Journal article  |  2019  |  BMC Bioinformatics

Background The large biological databases such as GenBank contain vast numbers of records, the content of which is substantively b..

From POS tagging to dependency parsing for biomedical event extraction

Quoc Nguyen Dat, Karin Verspoor

Journal article  |  2019  |  BMC Bioinformatics

Given the importance of relation or event extraction from biomedical research publications to support knowledge capture and synthe..

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine

Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sergio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Husunbeyi, Arzucan Ozgur, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, et al.

Journal article  |  2019  |  Database

The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual p..

End-to-end neural relation extraction using deep biaffine attention

DQ Nguyen, K Verspoor

Conference Proceedings  |  2019  |  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

© Springer Nature Switzerland AG 2019. We propose a neural network model for joint extraction of named entities and relations betw..

Parallel corpora for the biomedical domain

A Névéol, AJ Yepes, M Neves, K Verspoor

Conference Proceedings  |  2019  |  LREC 2018 - 11th International Conference on Language Resources and Evaluation

© LREC 2018 - 11th International Conference on Language Resources and Evaluation. All rights reserved. A vast amount of biomedical..

Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.

Qingyu Chen, Xiuzhen Zhang, Yu Wan, Justin Zobel, Karin Verspoor

Journal article  |  2018  |  Journal of Computational Biology

Duplicate sequence records-that is, records having similar or identical sequences-are a challenge in search of biological sequence..

BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics

Qingyu Chen, Nagesh C Panyam, Aparna Elangovan, Karin Verspoor

Journal article  |  2018  |  Database

Crowdsourcing critical appraisal of research evidence (CrowdCARE) was found to be a valid approach to assessing clinical research quality

Michael J Pianta, Eve Makrai, Karin M Verspoor, Trevor A Cohn, Laura E Downie

Journal article  |  2018  |  Journal of Clinical Epidemiology

The Use of Web-Based Technologies in Health Research Participation: Qualitative Study of Consumer and Researcher Experiences

Patrick Cheong-Iao Pang, Shanton Chang, Karin Verspoor, Ornella Clavisi

Journal article  |  2018  |  Journal of Medical Internet Research

An Improved Neural Network Model for Joint POS Tagging and Dependency Parsing

Dat Quoc Nguyen, Karin Verspoor

Conference Proceedings  |  2018  |  Proceedings of the

We propose a novel neural network model for joint part-of-speech (POS) tagging and dependency parsing. Our model extends the well-..

Semantic-Based Policy Composition for Privacy-Demanding Data Linkage

Y Lu, RO Sinnott, K Verspoor

Conference Proceedings  |  2018  |  2018 17th IEEE International Conference On Trust, Security And Privacy In Computing And Communications/ 12th IEEE International Conference On Big Data Science And Engineering (TrustCom/BigDataSE)

© 2018 IEEE. Record linkage can be used to support current and future health research across populations however such approaches g..

Privacy-Preserving Access Control in Electronic Health Record Linkage

Y Lu, RO Sinnott, K Verspoor, U Parampalli

Conference Proceedings  |  2018  |  2018 17th IEEE International Conference On Trust, Security And Privacy In Computing And Communications/ 12th IEEE International Conference On Big Data Science And Engineering (TrustCom/BigDataSE)

© 2018 IEEE. Sharing aggregated electronic health records (EHRs) for integrated health care and public health studies is increasin..

Appraising the Quality of Systematic Reviews for Age-Related Macular Degeneration Interventions A Systematic Review

Laura E Downie, Eve Makrai, Yokim Bonggotgetsakul, Lucy J Dirito, Kresimir Kristo, Minh-An N Pham, Mina You, Karin Verspoor, Michael J Pianta

Journal article  |  2018  |  JAMA Ophthalmology

Convolutional neural networks for chemical-disease relation extraction are improved with character-based word embeddings

Dat Quoc Nguyen, Karin Verspoor

Conference Proceedings  |  2018  |  Proceedings of the BioNLP 2018 workshop

We investigate the incorporation of character-based word representations into a standard CNN-based relation extraction model. We e..

A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration

Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman Halgamuge

Journal article  |  2018  |  BMC Bioinformatics

The randomized information coefficient: assessing dependencies in noisy data

Simone Romano, Nguyen Xuan Vinh, Karin Verspoor, James Bailey

Journal article  |  2018  |  Machine Learning

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases

Qingyu Chen, Yu Wan, Xiuzhen Zhang, Yang Lei, Justin Zobel, Karin Verspoor

Journal article  |  2018  |  Journal of Data and Information Quality

Exploiting graph kernels for high performance biomedical relation extraction

Nagesh C Panyam, Karin Verspoor, Trevor Cohn, Kotagiri Ramamohanarao

Journal article  |  2018  |  J. Biomedical Semantics

Web forum retrieval and text analytics: A survey

D Hoogeveen, L Wang, T Baldwin, KM Verspoor

Journal article  |  2018  |  Foundations and Trends® in Information Retrieval

DrKnow: A Diagnostic Learning Tool with Feedback from Automated Clinical Decision Support.

Piyapong Khumrin, Anna Ryan, Terry Juddy, Karin Verspoor

Conference Proceedings  |  2018  |  AMIA ... Annual Symposium proceedings. AMIA Symposium

Providing medical trainees with effective feedback is critical to the successful development of their diagnostic reasoning skills...

CommViz: Visualization of semantic patterns in large social communication networks

Karin Verspoor, Bahadorreza Ofoghi, Marlene Robles Granda

Journal article  |  2018  |  Information Visualization

Detecting misflagged duplicate questions in community question-answering archives

D Hoogeveen, A Bennett, Y Li, KM Verspoor, T Baldwin

Conference Proceedings  |  2018  |  12th International AAAI Conference on Web and Social Media, ICWSM 2018

Copyright © 2018, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved. In this paper we..

Multi-field query expansion is effective for biomedical dataset retrieval

Mohamed Reda Bouadjenek, Karin Verspoor

Journal article  |  2017  |  Database

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

K Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-Young Choi, Michael Bada, William A Baumgartner, Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E Hunter

Journal article  |  2017  |  BMC Bioinformatics

Automated detection of records in biological sequence databases that are inconsistent with the literature

Mohamed Reda Bouadjenek, Karin Verspoor, Justin Zobel

Journal article  |  2017  |  Journal of Biomedical Informatics

Literature consistency of bioinformatics sequence databases is effective for assessing record quality

Mohamed Reda Bouadjenek, Karin Verspoor, Justin Zobel

Journal article  |  2017  |  Database

Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman Halgamuge

Journal article  |  2017  |  BMC Bioinformatics

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study

Qingyu Chen, Justin Zobel, Karin Verspoor

Journal article  |  2017  |  Database

Benchmarks for measurement of duplicate detection methods in nucleotide databases.

Qingyu Chen, Justin Zobel, Karin Verspoor

Journal article  |  2017  |  Database

Duplication of information in databases is a major data quality challenge. The presence of duplicates, implying either redundancy ..

A Semantic-Based K-Anonymity Scheme for Health Record Linkage

Yang Lu, Richard O Sinnott, Karin Verspoor

Journal article  |  2017  |  Studies in Health Technology and Informatics

From Evaluating to Forecasting Performance: How to Turn Information Retrieval, Natural Language Processing and Recommender Systems into Predictive Sciences

Justin Zobel, Nicola Ferro, Norbert Fuhr, Gregory Grefenstette, Joseph A Konstan, Pablo Castells, Elizabeth M Daly, Thierry Declerck, Michael D Ekstrand, Werner Geyer, Julio Gonzalo, Tsvi Kuflik, Krister Lindén, Bernardo Magnini, Jian-Yun Nie, Raffaele Perego, Bracha Shapira, Ian Soboroff, Nava Tintarev, Karin Verspoor, et al.

Conference Proceedings  |  2017

We describe the state-of-the-art in performance modeling and prediction for Information Retrieval (IR), Natural Language Processin..

Understanding the Context of Learning in an Online Social Network for Health Professionals' Informal Learning

X Li, K Gray, K Verspoor, S Barnett

Journal article  |  2017  |  Studies in Health Technology and Informatics

© 2017 European Federation for Medical Informatics (EFMI) and IOS Press. Online social networks (OSN) enable health professionals ..

The Colorado Richly Annotated Full Text (CRAFT) Corpus: Multi-Model Annotation in the Biomedical Domain

KB Cohen, C VERSPOOR, K Fort, M Bada, M Palmer, L Hunter

Book Chapter  |  2017

Learning Biological Sequence Types Using the Literature

Mohamed Reda Bouadjenek, Karin Verspoor, Justin Zobel

Conference Proceedings  |  2017  |  Proceedings of the 2017 ACM on Conference on Information and Knowledge Management - CIKM '17

Diagnostic Machine Learning Models for Acute Abdominal Pain: Towards an e-Learning Tool for Medical Students

Piyapong Khumrin, Anna Ryan, Terry Judd, Karin Verspoor

Conference Proceedings  |  2017  |  Studies in Health Technology and Informatics

Characterising the Scope of Exposome Research: A Generalisable Approach

Philip Kiossoglou, Ann Borda, Kathleen Gray, Fernando Martin-Sanchez, Karin Verspoor, Guillermo Lopez-Campos

Conference Proceedings  |  2017  |  Studies in Health Technology and Informatics

Developing a Manually Annotated Corpus of Clinical Letters for Breast Cancer Patients on Routine Follow-Up

Graham Pitson, Patricia Banks, Lawrence Cavedon, Karin Verspoor

Journal article  |  2017  |  Studies in Health Technology and Informatics

Textual emotion classification: An interoperability study on cross-genre data sets

B Ofoghi, K Verspoor

Conference Proceedings  |  2017  |  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

© Springer International Publishing AG 2017. This paper describes the application and analysis of a previously developed textual e..

Understanding Health Professionals' Informal Learning in Online Social Networks: A Cross-Sectional Survey

Xin Li, Karin Verspoor, Kathleen Gray, Stephen Barnett

Conference Proceedings  |  2017  |  Studies in Health Technology and Informatics

A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning

Yahui Sun, Pathima Nusrath Hameed, Karin Verspoor, Saman Halgamuge

Conference Proceedings  |  2016  |  BMC Systems Biology

Text mining electronic hospital records to automatically classify admissions against disease: Measuring the impact of linking data sources

Simon Kocbek, Lawrence Cavedon, David Martinez, Christopher Bain, Chris Mac Manus, Gholamreza Haffari, Ingrid Zukerman, Karin Verspoor

Journal article  |  2016  |  Journal of Biomedical Informatics

Benchmarks for Measurement of Duplicate Detection Methods in Nucleotide Databases

Qingyu Chen, Justin Zobel, Karin Verspoor

Journal article  |  2016

Abstract Duplication of information in databases is a major data quality challenge. The presence of duplicates, implying either re..

Duplicates, redundancies, and inconsistencies in the primary nucleotide databases: a descriptive study

Qingyu Chen, Justin Zobel, Karin Verspoor

Journal article  |  2016

Abstract GenBank, the EMBL European Nucleotide Archive, and the DNA DataBank of Japan, known collectively as the International Nuc..

The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia

Satoshi Mizuno, Soichi Ogishima, Hidekazu Nishigori, Daniel G Jamieson, Karin Verspoor, Hiroshi Tanaka, Nobuo Yaegashi, Jun Nakaya

Journal article  |  2016  |  PLOS ONE

Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition

Christopher S Funk, K Bretonnel Cohen, Lawrence E Hunter, Karin M Verspoor

Journal article  |  2016  |  Journal of Biomedical Semantics

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark, Asma R Bankapur, Daniel D'Andrea, Rosalba Lepore, Christopher S Funk, Indika Kahanda, Karin M Verspoor, Asa Ben-Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin, Sayed ME Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, et al.

Journal article  |  2016  |  Genome Biology

Supervised Learning for Detection of Duplicates in Genomic Sequence Databases

Qingyu Chen, Justin Zobel, Xiuzhen Zhang, Karin Verspoor

Journal article  |  2016  |  PLOS ONE

Coreference resolution improves extraction of Biological Expression Language statements from texts

Miji Choi, Haibin Liu, William Baumgartner, Justin Zobel, Karin Verspoor

Journal article  |  2016  |  Database

Designing Health Websites Based on Users' Web-Based Information-Seeking Behaviors: A Mixed-Method Observational Study

Patrick Cheong-Iao Pang, Shanton Chang, Karin Verspoor, Jon Pearce

Journal article  |  2016  |  Journal of Medical Internet Research

A posteriori ontology engineering for data-driven science

DDG Gessler, C Joslyn, K Verspoor

Book Chapter  |  2016

A categorical analysis of coreference resolution errors in biomedical texts

Miji Choi, Justin Zobel, Karin Verspoor

Journal article  |  2016  |  Journal of Biomedical Informatics

Towards a Methodology for Nursing-Specific Clinical Decision Support Systems (CDSS)

Tanvir Ahamed, Reeva Lederman, Rachelle Bosua, Karin Verspoor, Wray Buntine, Graeme Hart

Journal article  |  2016  |  Journal of Decision Systems

Adjusting for Chance Clustering Comparison Measures

Simone Romano, Xuan Vinh Nguyen, James Bailey, Karin Verspoor

Journal article  |  2016  |  Journal of Machine Learning Research

Evaluation of CD-HIT for constructing non-redundant databases

Q Chen, Y Wan, Y Lei, J Zobel, C VERSPOOR

Conference Proceedings  |  2016  |  2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Rev at SemEval-2016 task 2: Aligning chunks by lexical, part of speech and semantic equivalence

TP Ping, K Verspoor, T Miller

Conference Proceedings  |  2016  |  SemEval 2016 - 10th International Workshop on Semantic Evaluation, Proceedings

Syndromic surveillance on the victorian chief complaint data set using a hybrid statistical and machine learning technique

H Aamer, B Ofoghi, K Verspoor

Conference Proceedings  |  2016  |  CEUR Workshop Proceedings

Emergency Department Chief Complaints have been used to detect the size and the spread of disease outbreaks in the past. Chief com..

Analysing Health Professionals' Learning Interactions in an Online Social Network: A Longitudinal Study

Xin Li, Karin Verspoor, Kathleen Gray, Stephen Barnett

Conference Proceedings  |  2016  |  Studies in Health Technology and Informatics

SeeDev Binary Event Extraction using SVMs and a Rich Feature Set

NC Panyam, G Khirbat, K Verspoor, T Cohn, K Ramamohanarao

Conference Proceedings  |  2016  |  BioNLP-ST

Exploiting Tree Kernels for high performance Chemical Induced Disease relation extraction

NC Panyam, K Verspoor, T Cohn, K Ramamohanarao

Conference Proceedings  |  2016  |  CEUR Workshop Proceedings

Towards early discovery of salient health threats: a social media emotion classification technique

Bahadorreza Ofoghi, Meghan Mann, Karin Verspoor

Conference Proceedings  |  2016  |  Pacific Symposium on Biocomputing

Finding and Exploring Health Information with a Slider-Based User Interface

Patrick Cheong-Iao Pang, Karin Verspoor, Jon Pearce, Shanton Chang

Journal article  |  2016  |  Studies in Health Technology and Informatics

Establishing a baseline for literature mining human genetic variants and their relationships to disease cohorts

Karin M Verspoor, Go Eun Heo, Keun Young Kang, Min Song

Conference Proceedings  |  2016  |  BMC Medical Informatics and Decision Making

A framework to adjust dependency measure estimates for chance

S Romano, XV Nguyen, J Bailey, K Verspoor

Conference Proceedings  |  2016  |  16th SIAM International Conference on Data Mining 2016, SDM 2016

Copyright © by SIAM. Estimating the strength of dependency between two variables is fundamental for exploratory analysis and many ..

Innovation in designing health information websites: Results from a quantitative study

PCI Pang, S Chang, K Verspoor, J Pearce

Conference Proceedings  |  2016  |  Pacific Asia Conference on Information Systems, PACIS 2016 - Proceedings

A wealth of health information exists on the Internet, but successfully finding that information is not easy. One of the issues ca..

What Are Health Website Visitors Doing: Insights from Visualisations Towards Exploratory Search

PC-I Pang, M Harrop, K Verspoor, J Pearce, S Chang

Conference Proceedings  |  2016  |  Proceedings of the 28th Australian Conference on Computer-Human Interaction - OzCHI '16

Findings of the 2016 Conference on Machine Translation

O Bojar, R Chatterjee, C Federmann, Y Graham, B Haddow, M Huck, A Jimeno Yepes, P Koehn, V Logacheva, C Monz, M Negri, A N´ev´eol, M Neves, M Popel, M Post, R Rubino, C Scarton, L Specia, M Turchi, C VERSPOOR, et al.

Conference Proceedings  |  2016

Discovery of learning topics in an online social network for health professionals

X Li, K Verspoor, K Gray, S Barnett

Conference Proceedings  |  2016  |  CEUR Workshop Proceedings

Online social networking provides support to health professionals' learning and professional development. To understand their lear..

CQADupStack: Gold or Silver?

D Hoogeveen, K Verspoor, T BALDWIN

Conference Proceedings  |  2016

Special issue on bio-ontologies and phenotypes

Larisa N Soldatova, Nigel Collier, Anika Oellrich, Tudor Groza, Karin Verspoor, Philippe Rocca-Serra, Michel Dumontier, Nigam H Shah

Journal article  |  2015  |  Journal of Biomedical Semantics

CQADupStack: A benchmark data set for community question-answering research

D Hoogeveen, KM Verspoor, T Baldwin

Conference Proceedings  |  2015  |  Proceedings of the 20th Australasian Document Computing Symposium

Better health information exploration

PCI Pang, K Verspoor, S Chang, J Pearce

Conference Proceedings  |  2015  |  Proceedings of the Asia Pacific HCI and UX Design Symposium on - APCHIUX '15

Optimizing graph-based patterns to extract biomedical events from the literature

Haibin Liu, Karin Verspoor, Donald C Comeau, Andrew D MacKinlay, W John Wilbur

Journal article  |  2015  |  BMC Bioinformatics

A close look at protein function prediction evaluation protocols

Indika Kahanda, Christopher S Funk, Fahad Ullah, Karin M Verspoor, Asa Ben-Hur

Journal article  |  2015  |  GigaScience

Assessing the Impact of Case Sensitivity and Term Information Gain on Biomedical Concept Recognition

Tudor Groza, Karin Verspoor

Journal article  |  2015  |  PLOS ONE

CHEMDNER: The drugs and chemical names extraction challenge

Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Alfonso Valencia

Journal article  |  2015  |  Journal of Cheminformatics

Better Health Explorer: Designing for Health Information Seekers

C-I Pang, C VERSPOOR, J Pearce, S Chang

Conference Proceedings  |  2015  |  Proceedings of the Annual Meeting of the Australian Special Interest Group for Computer Human Interaction on - OzCHI '15

Analysing health professionals' learning interactions in online social networks: A social network analysis approach

X Li, K Gray, C VERSPOOR, S Barnett

Conference Proceedings  |  2015

Evaluation of a Machine Learning Duplicate Detection Method for Bioinformatics Databases

Q Chen, J Zobel, K Verspoor

Conference Proceedings  |  2015  |  Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics - DTMBIO '15

Conceptualising health information seeking behaviours and exploratory search: result of a qualitative study

PCI Pang, K Verspoor, S CHANG, J Pearce

Journal article  |  2015  |  Health and Technology

PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources.

Indika Kahanda, Christopher Funk, Karin Verspoor, Asa Ben-Hur

Journal article  |  2015  |  F1000Research

The human phenotype ontology (HPO) was recently developed as a standardized vocabulary for describing the phenotype abnormalities ..

Interoperability of text corpus annotations with the semantic web.

Karin Verspoor, Jin-Dong Kim, Michel Dumontier

Journal article  |  2015  |  BMC Proceedings

Domain Adaption of Named Entity Recognition to Support Credit Risk Assessment

JC Salinas Alvarado, K Verpsoor, T BALDWIN

Conference Proceedings  |  2015

International workshop on data and text mining in biomedical informatics (DTMBIO)

Editorship  |  2015

Evaluating classification power of linked admission data sources with text mining

S Kocbek, L Cavedon, D Martinez, C Bain, C MacManus, G Haffari, I Zukerman, K Verspoor

Conference Proceedings  |  2015  |  CEUR Workshop Proceedings

Lung cancer is a leading cause of death in developed countries. This paper presents a text mining system using Support Vector Mach..

Assessing the performance of American chief complaint classifiers on Victorian syndromic surveillance data

B Ofoghi, K Verspoor

Conference Proceedings  |  2015  |  CEUR Workshop Proceedings

Syndromic surveillance systems aim to support early detection of salient disease outbreaks, and to shed timely light on the size a..

Structural Alignment as the Basis to Improve Significant Change Detection in Versioned Sentences

T Ping, C VERSPOOR, T Miller

Conference Proceedings  |  2015

The CHEMDNER corpus of chemicals and drugs and its annotation principles

M Krallinger, O Rabal, F Leitner, M Vazquez, D Salgado, Z Lu, R Leaman, Y Lu, D Ji, DM Lowe, RA Sayle, RT Batista-Navarro, R Rak, T Huber, T Rocktäschel, S Matos, D Campos, B Tang, H Xu, T Munkhdalai, et al.

Journal article  |  2015  |  Journal of Cheminformatics

Copyright © 2015 Krallinger et al. The automatic extraction of chemical information from text requires the recognition of chemical..

Evaluating a variety of text-mined features for automatic protein function prediction

C Funk, I Kahanda, A Ben-Hur, CM VERSPOOR

Journal article  |  2015  |  Journal of Biomedical Semantics

Drawing on Millions of Biomedical Journal Publications to do Predictive Biology

Karin M Verspoor

Conference Proceedings  |  2015  |  2015 International Conference on Big Data and Smart Computing (BIGCOMP)

Associating disease-related genetic variants in intergenic regions to the genes they impact

Geoff Macintyre, Antonio Jimeno Yepes, Cheng Soon Ong, Karin Verspoor

Journal article  |  2014  |  PeerJ

Big data in medicine is driving big changes.

F Martin-Sanchez, K Verspoor

Journal article  |  2014  |  Yearbook of Medical Informatics

OBJECTIVES: To summarise current research that takes advantage of "Big Data" in health and biomedical informatics applications. ME..

BioC interoperability track overview

Donald C Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Dogan, Antonio Jimeno Yepes, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J Mattingly, Mariana Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C Wiegers, Cathy H Wu, W John Wilbur

Journal article  |  2014  |  Database: the journal of biological databases and curation

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters

Christopher Funk, William Baumgartner, Benjamin Garcia, Christophe Roeder, Michael Bada, K Bretonnel Cohen, Lawrence E Hunter, Karin Verspoor

Journal article  |  2014  |  BMC Bioinformatics

Literature mining of genetic variants for curation: quantifying the importance of supplementary material

Antonio Jimeno Yepes, Karin Verspoor

Journal article  |  2014  |  Database: the journal of biological databases and curation

Online Health Information Seeking Behaviour: Understanding Different Search Approaches

CI PANG, S Chang, J Pearce, K Verspoor

Conference Proceedings  |  2014  |  Proceedings of the 18th Pacific Asia Conference on Information Systems (PACIS 2014)

Mapping Biomedical Vocabularies: A Semi-Automated Term Matching Approach

Bahadorreza Ofoghi, Guillermo H Lopez-Campos, Fernando Jose Martin Sanchez, Karin Verspoor

Book Chapter  |  2014  |  Studies in Health Technology and Informatics

Mutation extraction tools can be combined for robust recognition of genetic variants in the literature.

Antonio Jimeno Yepes, Karin Verspoor

Journal article  |  2014  |  F1000Research

As the cost of genomic sequencing continues to fall, the amount of data being collected and studied for the purpose of understandi..

Two Platforms for Research in Human Communication Science: The AusTalk Corpus and the Alveo Virtual Laboratory

D Burnham, D Estival, S Cassidy, P Sefton, CM VERSPOOR

Conference Proceedings  |  2014  |  2014 17th Oriental Chapter of the International Committee for the Co-ordination and Standardization of Speech Databases and Assessment Techniques (COCOSDA)

What Can We Get From 1000 Tokens? A Case Study of Multilingual POS Tagging For Resource-Poor Languages

L Duong, T Cohn, CM VERSPOOR, S Bird, P Cook

Conference Proceedings  |  2014  |  Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP)

Biomedical Text Mining: State-of-the-Art, Open Problems and Future Challenges

A Holzinger, J Schantl, M Schroettner, C Seifert, K Verspoor

Book Chapter  |  2014  |  Lecture Notes in Artificial Intelligence

Semantic Precision and Recall for Concept Annotation of Text

M Bada, WA Baumgartner, C Funk, LE Hunter, CM VERSPOOR

Conference Proceedings  |  2014

Analysis of Coreference Relations in the Biomedical Literature

M Choi, CM VERSPOOR, J Zobel

Conference Proceedings  |  2014

BiomRKRS: A Biomarker Retrieval and Knowledge Reasoning System

B Ofoghi, J Warren, GH Lopez Campos, K Gray, CM Verspoor, F Martin Sanchez

Conference Proceedings  |  2014  |  Proceedings of the Seventh Australasian Workshop on Health Informatics and Knowledge Management

Standardized mutual information for clustering comparisons: Why Normalization Should Not Be The Standard

S Romano, J Bailey, NX Vinh, K Verspoor

Conference Proceedings  |  2014  |  31st International Conference on Machine Learning, ICML 2014

Evaluation of coreference resolution for biomedical text

M Choi, K Verspoor, J Zobel

Conference Proceedings  |  2014  |  CEUR Workshop Proceedings

Roles for Text Mining in Protein Function Prediction

K Verspoor

Book Chapter  |  2014  |  Methods in Molecular Biology

Designing for health exploratory seeking behaviour

PC-I Pang, K Verspoor, S Chang, J Pearce

Conference Proceedings  |  2014  |  CEUR Workshop Proceedings

Diving deep into data to crack the gene code on disease

K Verspoor

Original Creative Work - Textual Work  |  2014

Automated Generation of Test Suites for Error Analysis of Concept Recognition Systems

T Groza, CM VERSPOOR

Conference Proceedings  |  2014

Exploring Temporal Patterns in Emergency Department Triage Notes with Topic Models

S Kocbek, CM VERSPOOR, W Buntine

Conference Proceedings  |  2014

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database.

Daniel J Park, Tú Nguyen-Dumont, Sori Kang, Karin Verspoor, Bernard J Pope

Journal article  |  2014  |  Source Code for Biology and Medicine

BackgroundThe NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different or..

Integrating UIMA with Alveo, a human communication science virtual laboratory

D Estival, S Cassidy, CM VERSPOOR, A MacKinlay, D Burnham

Conference Proceedings  |  2014

Representing annotation compositionality and provenance for the Semantic Web

Kevin M Livingston, Michael Bada, Lawrence E Hunter, Karin Verspoor

Journal article  |  2013  |  Journal of Biomedical Semantics

BioC: a minimalist approach to interoperability for biomedical text processing

Donald C Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C Wiegers, Cathy H Wu, W John Wilbur

Journal article  |  2013  |  Database: the journal of biological databases and curation

Approximate Subgraph Matching-Based Literature Mining for Biomedical Events and Relations

Haibin Liu, Lawrence Hunter, Vlado Keselj, Karin Verspoor

Journal article  |  2013  |  PLoS One

Annotating the biomedical literature for the human variome

Karin Verspoor, Antonio Jimeno Yepes, Lawrence Cavedon, Tara McIntosh, Asha Herten-Crabb, Zoe Thomas, John-Paul Plazzer

Journal article  |  2013  |  Database: the journal of biological databases and curation

Acquisition and evaluation of verb subcategorization resources for biomedicine

Laura Rimell, Thomas Lippincott, Karin Verspoor, Helen L Johnson, Anna Korhonen

Journal article  |  2013  |  Journal of Biomedical Informatics

Approaches to verb subcategorization for biomedicine

Thomas Lippincott, Laura Rimell, Karin Verspoor, Anna Korhonen

Journal article  |  2013  |  Journal of Biomedical Informatics

A large-scale evaluation of computational protein function prediction

Predrag Radivojac, Wyatt T Clark, Tal Ronnen Oron, Alexandra M Schnoes, Tobias Wittkop, Artem Sokolov, Kiley Graim, Christopher Funk, Karin Verspoor, Asa Ben-Hur, Gaurav Pandey, Jeffrey M Yunes, Ameet S Talwalkar, Susanna Repo, Michael L Souza, Damiano Piovesan, Rita Casadio, Zheng Wang, Jianlin Cheng, Hai Fang, et al.

Journal article  |  2013  |  Nature Methods

Combining heterogeneous data sources for accurate functional annotation of proteins

Artem Sokolov, Christopher Funk, Kiley Graim, Karin Verspoor, Asa Ben-Hur

Journal article  |  2013  |  BMC Bioinformatics

Impact of Corpus Diversity and Complexity on NER Performance

T Shmanina, I Zukerman, AJ Jimeno Yepes, L Cavedon, CM Verspoor

Conference Proceedings  |  2013  |  Proceedings of the Australasian Language Technology Association Workshop 2013

e-Learning with Kaggle in Class: Adapting the ALTA Shared Task 2013 to a Class Project

CM Verspoor, J Nicholson

Conference Proceedings  |  2013  |  Proceedings of the Australasian Language Technology Association Workshop 2013

Information Extraction from Medication Prescriptions Within Drug Administration Data

A MacKinlay, K Verspoor

Conference Proceedings  |  2013  |  Proceedings of the 4th International Louhi Workshop on Health Document Text Mining and Information Analysis

Towards automatic large-scale curation of genomic variation: improving coverage based on supplementary material

AJ Yepes, K Verspoor

Conference Proceedings  |  2013  |  Proceedings of BioLINK SIG 2013

Earlier Identification of Epilepsy Surgery Candidates Using Natural Language Processing

P MatyKiewicz, KB Cohen, KD Holland, TA Glauser, SM Standridge, CM Verspoor, J Pestian

Conference Proceedings  |  2013  |  Proceedings of the 2013 Workshop on Biomedical Natural Language Processing

Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data

A MACKINLAY, D Martinez, AJ Jimeno Yepes, H Liu, WJ Wilbur, CM Verspoor

Conference Proceedings  |  2013  |  Proceedings of the BioNLP Shared Task 2013 Workshop

Detection of protein catalytic sites in the biomedical literature.

K Verspoor, A Mackinlay, JD Cohn, ME Wall

Conference Proceedings  |  2013  |  Proceedings of the Pacific Symposium on Biocomputing

Generalizing an Approximate Subgraph Matching-based System to Extract Events in Molecular Biology and Cancer Genetics

H Liu, K Verspoor, DC Comeau, A MacKinlay, WJ Wilbur

Conference Proceedings  |  2013  |  Proceedings of the BioNLP Shared Task 2013 Workshop

Natural Language Processing

Karin Verspoor, Kevin Bretonnel Cohen

Book Chapter  |  2013

Subgraph matching-based literature mining for biomedical relations and events

H Liu, V Kešelj, C Blouin, K Verspoor

Conference Proceedings  |  2012  |  AAAI Fall Symposium - Technical Report

Towards adaptation of Linguistic Annotations to scholarly annotation formalisms on the Semantic Web

K Verspoor, K Livingston

Conference Proceedings  |  2012  |  Proceedings of the Sixth Linguistic Annotation Workshop

Literature mining of protein-residue associations with graph rules learned through distant supervision.

Ke Ravikumar, Haibin Liu, Judith D Cohn, Michael E Wall, Karin Verspoor

Journal article  |  2012  |  Journal of Biomedical Semantics

BACKGROUND: We propose a method for automatic extraction of protein-specific residue mentions from the biomedical literature. The ..

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L Johnson, Christophe Roeder, Jinho D Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A Baumgartner, Michael Bada, Martha Palmer, Lawrence E Hunter

Journal article  |  2012  |  BMC Bioinformatics

Concept annotation in the CRAFT corpus

Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, K Bretonnel Cohen, Karin Verspoor, Judith A Blake, Lawrence E Hunter

Journal article  |  2012  |  BMC Bioinformatics

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text

Haibin Liu, Tom Christiansen, William A Baumgartner, Karin Verspoor

Journal article  |  2012  |  Journal of Biomedical Semantics

Text Mining Improves Prediction of Protein Functional Sites

Karin M Verspoor, Judith D Cohn, Komandur E Ravikumar, Michael E Wall

Journal article  |  2012  |  PLoS One

Extracting Structured Information from Free-Text Medication Prescriptions Using Dependencies

Andrew MacKinlay, Karin Verspoor

Conference Proceedings  |  2012  |  Proceedings of the Sixth ACM International Workshop on Data and Text Mining in Biomedical Informatics

Simple similarity-based question answering strategies for biomedical text

D Martinez, A MacKinlay, D Molla-Aliod, L Cavedon, K Verspoor

Conference Proceedings  |  2012  |  CEUR Workshop Proceedings

U-Compare bio-event meta-service: compatible BioNLP event extraction services

Yoshinobu Kano, Jari Bjoerne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana Neves, Alberto Pascual-Montano, Arzucan Ozgur, et al.

Journal article  |  2011  |  BMC Bioinformatics

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA

K Bretonnel Cohen, Karin Verspoor, Helen L Johnson, Chris Roeder, Philip V Ogren, William A Baumgartner, Elizabeth White, Hannah Tipney, Lawrence Hunter

Journal article  |  2011  |  Computational Intelligence

The gene normalization task in BioCreative III

Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illes Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, et al.

Journal article  |  2011  |  BMC Bioinformatics

Fast and simple semantic class assignment for biomedical text

KB Cohen, T Christiansen, WA Baumgartner Jnr., K Verspoor, LE Hunter

Conference Proceedings  |  2011  |  Proceedings of BioNLP Shared Task 2011 Workshop

From graphs to events: a subgraph matching approach for information extraction from biomedical text

H Liu, R Komandur, K Verspoor

Conference Proceedings  |  2011  |  Proceedings of BioNLP Shared Task 2011 Workshop

Pattern learning through distant supervision for extraction of protein-residue associations in the biomedical literature

KE Ravikumar, H Liu, JD Cohn, ME Wall, K Verspoor

Conference Proceedings  |  2011  |  Proceedings of the 2011 10th International Conference on Machine Learning and Applications and Workshops

The structural and content aspects of abstracts versus bodies of full text journal articles are different

K Bretonnel Cohen, Helen L Johnson, Karin Verspoor, Christophe Roeder, Lawrence E Hunter

Journal article  |  2010  |  BMC Bioinformatics

A UIMA wrapper for the NCBO annotator

Christophe Roeder, Clement Jonquet, Nigam H Shah, William A Baumgartner, Karin Verspoor, Lawrence Hunter

Journal article  |  2010  |  Bioinformatics

Exploring Species-Based Strategies for Gene Normalization

Karin Verspoor, Christophe Roeder, Helen L Johnson, K Bretonnel Cohen, William A Baumgartner, Lawrence E Hunter

Journal article  |  2010  |  IEEE - ACM Transactions on Computational Biology and Bioinformatics

Test suite design for ontology concept recognition systems

K Bretonnel Cohen, Christophe Roeder, William A Baumgartner, Lawrence E Hunter, Karin Verspoor

Conference Proceedings  |  2010  |  Proceedings of the 7th Language Resources and Evaluation Conference

Leveraging Gene Ontology Annotations to Improve a Memory-Based Language Understanding System

Kevin M Livingston, Helen L Johnson, Karin Verspoor, Lawrence E Hunter

Conference Proceedings  |  2010  |  Proceedings of the 2010 IEEE Fourth International Conference on Semantic Computing

Visualization and Language Processing for Supporting Analysis across the Biomedical Literature

Carsten Goerg, Hannah Tipney, Karin Verspoor, William A Baumgartner, K Bretonnel Cohen, John Stasko, Lawrence E Hunter

Conference Proceedings  |  2010  |  Knowledge-Based and Intelligent Information and Engineering Systems

Ontology quality assurance through analysis of term transformations

Karin Verspoor, Daniel Dvorkin, K Bretonnel Cohen, Lawrence Hunter

Journal article  |  2009  |  Bioinformatics

The textual characteristics of traditional and Open Access scientific journals are similar

Karin Verspoor, K Bretonnel Cohen, Lawrence Hunter

Journal article  |  2009  |  BMC Bioinformatics

Natural Language Processing with Python

S BIRD, undefined Loper, undefined Klein

Book  |  2009

Exploiting term relations for semantic hierarchy construction

C Joslyn, P Paulson, K Verspoor

Conference Proceedings  |  2008  |  Proceedings of the 2008 IEEE International Conference on Semantic Computing

A semantics-enhanced language model for unsupervised word sense disambiguation

Shou-De Lin, Karin Verspoor

Conference Proceedings  |  2008  |  Computational Linguistics and Intelligent Text Processing

Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

Alaa Abi-Haidar, Jasleen Kaur, Ana Maguitman, Predrag Radivojac, Andreas Rechtsteiner, Karin Verspoor, Zhiping Wang, Luis M Rocha

Journal article  |  2008  |  Genome Biology

Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

A Abi-Haidar, J Kaur, A Maguitman, P Radivojac, A Rechtsteiner, K Verspoor, Z Wang, LM Rocha

Journal article  |  2008  |  Genome Biology

Knowledge integration in open worlds: Utilizing the mathematics of hierarchical structure

Cliff A Joslyn, Karin M Verspoor, Damian DG Gessler

Conference Proceedings  |  2007  |  International Conference on Semantic Computing (ICSC 2007)

A categorization approach to automated ontological function annotation

Karin Verspoor, Judith Cohn, Susan Mniszewski, Cliff Joslyn

Journal article  |  2006  |  Protein Science

Introduction to BioNLP'06

K Verspoor, KB Cohen, B Goertzel, I Mani

Conference Proceedings  |  2006  |  HLT-NAACL 2006 - BioNLP 2006: Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis, Proceedings of the Workshop

Large-scale testing of bibliome informatics using Pfam protein families.

Ana G Maguitman, Andreas Rechtsteiner, Karin Verspoor, Charlie E Strauss, Luis M Rocha

Conference Proceedings  |  2006  |  Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006

Literature mining is expected to help not only with automatically sifting through huge biomedical literature and annotation databa..

Protein annotation as term categorization in the gene ontology using word proximity networks

K Verspoor, J Cohn, C Joslyn, S Mniszewski, A Rechtsteiner, LM Rocha, T Simas

Journal article  |  2005  |  BMC Bioinformatics

Towards a semantic lexicon for biological language processing

K Verspoor

Conference Proceedings  |  2005  |  Comparative and Functional Genomics

Dynamic document delivery: Generating natural language texts on demand

R Dale, SJ Green, M Milosavljevic, C Paris, C Verspoor, S Williams

Conference Proceedings  |  1998  |  Proceedings Ninth International Workshop on Database and Expert Systems Applications (Cat. No.98EX130)

Lexical limits on the influence of context

CM Verspoor

Conference Proceedings  |  1996  |  PROCEEDINGS OF THE EIGHTEENTH ANNUAL CONFERENCE OF THE COGNITIVE SCIENCE SOCIETY