PEDL: extracting protein–protein associations using deep language models and distant supervision

PMC text mining subset in BioC: about three million full-text articles and growing

(2019) Donald C Comeau et al.   BIOINFORMATICS

PubTator central: automated concept annotation for biomedical full text articles

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

HUNER: Improving Biomedical NER with Pretraining

(2019) Leon Weber et al.   BIOINFORMATICS

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

(2019) Jinhyuk Lee et al.   BIOINFORMATICS

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

(2018) Ali Sinan Köksal et al.   Cell Reports

Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System

(2016) Beata Hat et al.   PLoS Computational Biology

The E3 Ubiquitin Ligase Siah2 Contributes to Castration-Resistant Prostate Cancer by Regulation of Androgen Receptor Transcriptional Activity

(2013) Jianfei Qi et al.   CANCER CELL

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

(2013) Sofie Van Landeghem et al.   PLoS One

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

EVENT EXTRACTION WITH COMPLEX EVENT CLASSIFICATION USING RICH FEATURES

(2010) MAKOTO MIWA et al.   Journal of Bioinformatics and Computational Biology

A Crohn's disease–associated NOD2 mutation suppresses transcription of human IL10 by inhibiting activity of the nuclear ribonucleoprotein hnRNP-A1

(2009) Eiichiro Noguchi et al.   NATURE IMMUNOLOGY

Comparative analysis of five protein-protein interaction corpora

(2008) Sampo Pyysalo et al.   BMC BIOINFORMATICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH