Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts

Analyzing a co-occurrence gene-interaction network to identify disease-gene association

(2019) Amira Al-Aamri et al.   BMC BIOINFORMATICS

PubTator central: automated concept annotation for biomedical full text articles

(2019) Chih-Hsuan Wei et al.   NUCLEIC ACIDS RESEARCH

CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision

(2019) Alexander Junge et al.   BIOINFORMATICS

Knowledge-guided convolutional networks for chemical-disease relation extraction

(2019) Huiwei Zhou et al.   BMC BIOINFORMATICS

Snorkel: rapid training data creation with weak supervision

(2019) Alexander Ratner et al.   VLDB JOURNAL

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

(2019) Jinhyuk Lee et al.   BIOINFORMATICS

A global network of biomedical relationships derived from text

(2018) Bethany Percha et al.   BIOINFORMATICS

The research on gene-disease association based on text-mining of PubMed

(2018) Jie Zhou et al.   BMC BIOINFORMATICS

Chemical–gene relation extraction using recursive neural network

(2018) Sangrak Lim et al.   Database-The Journal of Biological Databases and Curation

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

(2018) David Westergaard et al.   PLoS Computational Biology

Automatic extraction of gene-disease associations from literature using joint ensemble learning

(2018) Balu Bhasuran et al.   PLoS One

OUP accepted manuscript

(2018)   Database-The Journal of Biological Databases and Curation

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

(2017) Andres Cañada et al.   NUCLEIC ACIDS RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Systematic integration of biomedical knowledge prioritizes drugs for repurposing

(2017) Daniel Scott Himmelstein et al.   eLife

DTMiner: identification of potential disease targets through biomedical literature mining

(2016) Dong Xu et al.   BIOINFORMATICS

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

(2016) Robert Leaman et al.   BIOINFORMATICS

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

BioCreative V CDR task corpus: a resource for chemical disease relation extraction

(2016) Jiao Li et al.   Database-The Journal of Biological Databases and Curation

Large-scale extraction of gene interactions from full-text literature using DeepDive

(2015) Emily K. Mallory et al.   BIOINFORMATICS

Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research

(2015) Àlex Bravo et al.   BMC BIOINFORMATICS

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information

(2015) Manabu Torii et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

PKDE4J: Entity and relation extraction for public knowledge discovery

(2015) Min Song et al.   JOURNAL OF BIOMEDICAL INFORMATICS

DISEASES: Text mining and data integration of disease–gene associations

(2015) Sune Pletscher-Frankild et al.   METHODS

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

(2015) Yifeng Liu et al.   NUCLEIC ACIDS RESEARCH

GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains

(2015) Chih-Hsuan Wei et al.   Biomed Research International

Growth rates of modern science: A bibliometric analysis based on the number of publications and cited references

(2015) Lutz Bornmann et al.   Journal of the Association for Information Science and Technology

Comprehensive comparison of large-scale tissue expression datasets

(2015) Alberto Santos et al.   PeerJ

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Graph Theory Enables Drug Repurposing – How a Mathematical Model Can Drive the Discovery of Hidden Mechanisms of Action

(2014) Ruggero Gramatica et al.   PLoS One

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

(2014) J. X. Binder et al.   Database-The Journal of Biological Databases and Curation

Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

(2013) Rong Xu et al.   BMC BIOINFORMATICS

PPInterFinder—a mining tool for extracting causal relations on human proteins from literature

(2013) Kalpana Raja et al.   Database-The Journal of Biological Databases and Curation

The EU-ADR corpus: Annotated drugs, diseases, targets, and their relationships

(2012) Erik M. van Mulligen et al.   JOURNAL OF BIOMEDICAL INFORMATICS

SR4GN: A Species Recognition Software Tool for Gene Normalization

(2012) Chih-Hsuan Wei et al.   PLoS One

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

(2010) Raoul Frijters et al.   PLoS Computational Biology

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text

(2009) Yael Garten et al.   BMC BIOINFORMATICS

Comparative analysis of five protein-protein interaction corpora

(2008) Sampo Pyysalo 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