Author-sourced capture of pathway knowledge in computable form using Biofactoid

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

(2020) Marek Ostaszewski et al.   Scientific Data

Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible Succinylation

(2019) GuoXiao Wang et al.   MOLECULAR CELL

Towards reliable named entity recognition in the biomedical domain

(2019) John M Giorgi et al.   BIOINFORMATICS

SENP1-Sirt3 Signaling Controls Mitochondrial Protein Acetylation and Metabolism

(2019) Tianshi Wang et al.   MOLECULAR CELL

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

(2019) Igor Rodchenkov et al.   NUCLEIC ACIDS RESEARCH

The reactome pathway knowledgebase

(2019) Bijay Jassal et al.   NUCLEIC ACIDS RESEARCH

Transfer learning for biomedical named entity recognition with neural networks

(2018) John M Giorgi et al.   BIOINFORMATICS

Large-scale automated machine reading discovers new cancer-driving mechanisms

(2018) Marco A Valenzuela-Escárcega et al.   Database-The Journal of Biological Databases and Curation

From word models to executable models of signaling networks using automated assembly

(2017) Benjamin M Gyori et al.   Molecular Systems Biology

SourceData: a semantic platform for curating and searching figures

(2017) Robin Liechti et al.   NATURE METHODS

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

(2017) Denise N Slenter et al.   NUCLEIC ACIDS RESEARCH

An essential role for the IL-2 receptor in Treg cell function

(2016) Takatoshi Chinen et al.   NATURE IMMUNOLOGY

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Life Science’s Average Publishable Unit (APU) Has Increased over the Past Two Decades

(2016) Radames J. B. Cordero et al.   PLoS One

Cytoscape.js: a graph theory library for visualisation and analysis

(2015) Max Franz et al.   BIOINFORMATICS

ChEBI in 2016: Improved services and an expanding collection of metabolites

(2015) Janna Hastings et al.   NUCLEIC ACIDS RESEARCH

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

NDEx, the Network Data Exchange

(2015) Dexter Pratt et al.   Cell Systems

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

(2014) S. C. Mack et al.   NATURE

DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier

(2014) Margarida A. Santos et al.   NATURE

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Using Biological Pathway Data with Paxtools

(2013) Emek Demir et al.   PLoS Computational Biology

Software support for SBGN maps: SBGN-ML and LibSBGN

(2012) M. P. van Iersel et al.   BIOINFORMATICS

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

The FEBS Letters SDA corpus: A collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community

(2010) Florian Leitner et al.   FEBS LETTERS

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

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

(2008) Arnaud Ceol et al.   FEBS LETTERS