Mining the pharmacogenomics literature--a survey of the state of the art

An overview of MetaMap: historical perspective and recent advances

(2014) Alan R Aronson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Building a biomedical ontology recommender web service

(2012) Clement Jonquet et al.   Journal of Biomedical Semantics

Discovering and visualizing indirect associations between biomedical concepts

(2011) Y. Tsuruoka et al.   BIOINFORMATICS

From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource

(2011) Ellen M McDonagh et al.   Biomarkers in Medicine

Semantic annotation of biological concepts interplaying microbial cellular responses

(2011) Rafael Carreira et al.   BMC BIOINFORMATICS

The BioLexicon: a large-scale terminological resource for biomedical text mining

(2011) Paul Thompson et al.   BMC BIOINFORMATICS

The biomedical discourse relation bank

(2011) Rashmi Prasad et al.   BMC BIOINFORMATICS

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

(2011) Yoshinobu Kano et al.   BMC BIOINFORMATICS

Mining the Gene Wiki for functional genomic knowledge

(2011) Benjamin M Good et al.   BMC GENOMICS

GenDrux: A biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer

(2011) Chiquito Crasto et al.   BMC Medical Informatics and Decision Making

Literature mining, ontologies and information visualization for drug repurposing

(2011) C. Andronis et al.   BRIEFINGS IN BIOINFORMATICS

Computational Polypharmacology with Text Mining and Ontologies

(2011) Conrad Plake et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Coreference resolution: A review of general methodologies and applications in the clinical domain

(2011) Jiaping Zheng et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Using a shallow linguistic kernel for drug–drug interaction extraction

(2011) Isabel Segura-Bedmar et al.   JOURNAL OF BIOMEDICAL INFORMATICS

A review of causal inference for biomedical informatics

(2011) Samantha Kleinberg et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Anaphoric relations in the clinical narrative: corpus creation

(2011) Guergana K Savova et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Automated concept-level information extraction to reduce the need for custom software and rules development

(2011) Leonard W D'Avolio et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin

(2011) Hua Xu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010

(2011) Berry de Bruijn et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions

(2011) Wendy W Chapman et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Natural language processing: an introduction

(2011) Prakash M Nadkarni et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text

(2011) Özlem Uzuner et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Normalized names for clinical drugs: RxNorm at 6 years

(2011) Stuart J Nelson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Drug repurposing and adverse event prediction using high-throughput literature analysis

(2011) Spyros N. Deftereos et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

OSCAR4: a flexible architecture for chemical text-mining

(2011) David M Jessop et al.   Journal of Cheminformatics

ChemicalTagger: A tool for semantic text-mining in chemistry

(2011) Lezan Hawizy et al.   Journal of Cheminformatics

Linked open drug data for pharmaceutical research and development

(2011) Matthias Samwald et al.   Journal of Cheminformatics

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

(2011) Dietrich Rebholz-Schuhmann et al.   Journal of Biomedical Semantics

Multi-way association extraction and visualization from biological text documents using hyper-graphs: Applications to genetic association studies for diseases

(2010) Snehasis Mukhopadhyay et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Discovering drug-drug interactions: a text-mining and reasoning approach based on properties of drug metabolism

(2010) L. Tari et al.   BIOINFORMATICS

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

(2010) K Bretonnel Cohen et al.   BMC BIOINFORMATICS

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

(2010) Bin Chen et al.   BMC BIOINFORMATICS

Algorithms and semantic infrastructure for mutation impact extraction and grounding

(2010) Jonas B Laurila et al.   BMC GENOMICS

Automatic de-identification of textual documents in the electronic health record: a review of recent research

(2010) Stephane M Meystre et al.   BMC Medical Research Methodology

Selecting information in electronic health records for knowledge acquisition

(2010) Xiaoyan Wang et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Using text to build semantic networks for pharmacogenomics

(2010) Adrien Coulet et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Mining connections between chemicals, proteins, and diseases extracted from Medline annotations

(2010) Nancy C. Baker et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Integrating existing natural language processing tools for medication extraction from discharge summaries

(2010) Son Doan et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Extracting medication information from clinical text

(2010) Özlem Uzuner et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

High accuracy information extraction of medication information from clinical notes: 2009 i2b2 medication extraction challenge

(2010) Jon Patrick et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

MedEx: a medication information extraction system for clinical narratives

(2010) H. Xu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease

(2010) Iftikhar J Kullo et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications

(2010) Guergana K Savova et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

Recent progress in automatically extracting information from the pharmacogenomic literature

(2010) Yael Garten et al.   PHARMACOGENOMICS

Pharmacogenomics and bioinformatics: PharmGKB

(2010) Caroline F Thorn et al.   PHARMACOGENOMICS

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases

(2010) Raoul Frijters et al.   PLoS Computational Biology

CALBC SILVER STANDARD CORPUS

(2010) DIETRICH REBHOLZ-SCHUHMANN et al.   Journal of Bioinformatics and Computational Biology

U-Compare: share and compare text mining tools with UIMA

(2009) Y. Kano et al.   BIOINFORMATICS

High-performance gene name normalization with GENO

(2009) J. Wermter et al.   BIOINFORMATICS

A dictionary to identify small molecules and drugs in free text

(2009) Kristina M. Hettne et al.   BIOINFORMATICS

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)

(2009) Thomas C Wiegers et al.   BMC BIOINFORMATICS

Construction of an annotated corpus to support biomedical information extraction

(2009) Paul Thompson et al.   BMC BIOINFORMATICS

Towards pharmacogenomics knowledge discovery with the semantic web

(2009) M. Dumontier et al.   BRIEFINGS IN BIOINFORMATICS

Generating Genome-Scale Candidate Gene Lists for Pharmacogenomics

(2009) N T Hansen et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

An Automated Approach to Mapping External Terminologies to the UMLS

(2009) M. Taboada et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Collaborative text-annotation resource for disease-centered relation extraction from biomedical text

(2009) C. Cano et al.   JOURNAL OF BIOMEDICAL INFORMATICS

What can natural language processing do for clinical decision support?

(2009) Dina Demner-Fushman et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Building a semantically annotated corpus of clinical texts

(2009) Angus Roberts et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Beyond genes, proteins, and abstracts: Identifying scientific claims from full-text biomedical articles

(2009) Catherine Blake   JOURNAL OF BIOMEDICAL INFORMATICS

Recognizing Obesity and Comorbidities in Sparse Data

(2009) O. Uzuner   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Active Computerized Pharmacovigilance Using Natural Language Processing, Statistics, and Electronic Health Records: A Feasibility Study

(2009) X. Wang et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Chemical Entities of Biological Interest: an update

(2009) Paula de Matos et al.   NUCLEIC ACIDS RESEARCH

Biomedical Discovery Acceleration, with Applications to Craniofacial Development

(2009) Sonia M. Leach et al.   PLoS Computational Biology

Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans

(2009) Ivan Iossifov et al.   PLoS Computational Biology

Biomedical Text Mining and Its Applications

(2009) Raul Rodriguez-Esteban   PLoS Computational Biology

Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts

(2009) Jiao Li et al.   PLoS Computational Biology

Detection of IUPAC and IUPAC-like chemical names

(2008) R. Klinger et al.   BIOINFORMATICS

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

(2008) Laura I Furlong et al.   BMC BIOINFORMATICS

Corpus annotation for mining biomedical events from literature

(2008) Jin-Dong Kim et al.   BMC BIOINFORMATICS

Extraction of semantic biomedical relations from text using conditional random fields

(2008) Markus Bundschus et al.   BMC BIOINFORMATICS

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

(2008) R. Winnenburg et al.   BRIEFINGS IN BIOINFORMATICS

Literature mining in support of drug discovery

(2008) P. Agarwal et al.   BRIEFINGS IN BIOINFORMATICS

Inter-Coder Agreement for Computational Linguistics

(2008) Ron Artstein et al.   COMPUTATIONAL LINGUISTICS

Drug name recognition and classification in biomedical texts

(2008) Isabel Segura-Bedmar et al.   DRUG DISCOVERY TODAY

Linking entries in protein interaction database to structured text: The FEBS Letters experiment

(2008) Arnaud Ceol et al.   FEBS LETTERS

Assessment of commercial NLP engines for medication information extraction from dictated clinical notes

(2008) V. Jagannathan et al.   INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS

Bio2RDF: Towards a mashup to build bioinformatics knowledge systems

(2008) François Belleau et al.   JOURNAL OF BIOMEDICAL INFORMATICS

A new evaluation methodology for literature-based discovery systems

(2008) Meliha Yetisgen-Yildiz et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Nominalization and Alternations in Biomedical Language

(2008) K. Bretonnel Cohen et al.   PLoS One

Gene mention normalization and interaction extraction with context models and sentence motifs

(2008) Jörg Hakenberg et al.   GENOME BIOLOGY

Identifying Smokers with a Medical Extraction System

(2007) C. Clark et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Automated Acquisition of Disease-Drug Knowledge from Biomedical and Clinical Documents: An Initial Study

(2007) E. S. Chen et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

The Evaluation of a Temporal Reasoning System in Processing Clinical Discharge Summaries

(2007) L. Zhou et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION