A natural language processing system for the efficient updating of highly curated pathophysiology mechanism knowledge graphs

Background: Biomedical knowledge graphs (KG) have become crucial for describing biological findings in a structured manner. To keep up with the constantly changing flow of knowledge, their embedded information must be regularly updated with the latest findings. Natural language processing (NLP) has...

Full description

Bibliographic Details
Published in:	Artificial Intelligence in the Life Sciences
Main Authors:	Negin Sadat Babaiha, Hassan Elsayed, Bide Zhang, Abish Kaladharan, Priya Sethumadhavan, Bruce Schultz, Jürgen Klein, Bruno Freudensprung, Vanessa Lage-Rupprecht, Alpha Tom Kodamullil, Marc Jacobs, Stefan Geissler, Sumit Madan, Martin Hofmann-Apitius
Format:	Article
Language:	English
Published:	Elsevier 2023-12-01
Subjects:	Knowledge graphs Relation extraction Natural language processing Biomedical text mining Biological expression language (BEL) Human brain pharmacome (HBP)
Online Access:	http://www.sciencedirect.com/science/article/pii/S2667318523000223

Similar Items

Rationalism in the face of GPT hypes: Benchmarking the output of large language models against human expert-curated biomedical knowledge graphs
by: Negin Sadat Babaiha, et al.
Published: (2024-06-01)

Three-layered semantic framework for public health intelligence
by: Sathvik Guru Rao, et al.
Published: (2025-09-01)

Unraveling the co-morbidity between COVID-19 and neurodegenerative diseases through multi-scale graph analysis: A systematic investigation of biological databases and text mining
by: Negin Sadat Babaiha, et al.
Published: (2025-12-01)

Heparin Binding Protein in Sepsis—A Comprehensive Overview of Pathophysiology, Clinical Usage and Utility as Biomarker
by: Foteini Tasouli, et al.
Published: (2025-09-01)

Is a unified blood pressure threshold feasible in the current scenario?
by: Saulat Siddique
Published: (2023-03-01)

Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk
by: Sepehr Golriz Khatami, et al.
Published: (2024-01-01)

Dining in the lions� den � Bel and the dragon, verses 28�42 (Old Greek/Theodotion)
by: Joseph J. de Bruyn
Published: (2015-03-01)

Daniel Dragonslayer – Bel and the dragon, Verses 23−27 (OG/Th)
by: Joseph J. de Bruyn
Published: (2015-04-01)

Meta-analysis of the accuracy of CD64, HBP, and PCT in differential diagnosis of sepsis patients
by: Bin Qiu, et al.
Published: (2025-05-01)

<i>Neisseria meningitidis</i> Factor H Binding Protein Surface Exposure on <i>Salmonella</i> Typhimurium GMMA Is Critical to Induce an Effective Immune Response against Both Diseases
by: Francesca Necchi, et al.
Published: (2021-06-01)

Teacher Competencies for Business English Purpose in the International Universities in Kurdistan
by: Korazon talib Abdullah
Published: (2020-10-01)

Vše, co jste chtěli vědět o feminismu…
by: Kateřina Machovcová
Published: (2014-08-01)

Heparin binding proteins in seminal plasma of breeding buffalo bulls and their relation with semen freezability and in vivo fertility
by: A K SINGH, et al.
Published: (2020-07-01)

IGF-I, leptina, insulina e proteínas associadas à qualidade do plasma seminal: ação local
by: Fernando Andrade Souza, et al.
Published: (2010-12-01)

Serological and genetic analysis of a Bel subtype caused by a novel 29insG mutation: a case report
by: ZHOU Renlong, et al.
Published: (2024-10-01)

Serum Crp Düzeylerinin Lomber Dejeneratif Hastalık Şiddetini Belirlemedeki Rolü
by: Yaşar Karataş
Published: (2020-03-01)

Primary Aldosteronism and Long‐Term Cardiovascular Complications: Comparison of Medical Versus Surgical Treatment
by: Sofia Benameur, et al.
Published: (2025-08-01)

Integrating experimental and numerical approaches to simulate viscous debris flows using an HBP-SPH framework
by: Nikhil Kumar Pandey, et al.
Published: (2025-05-01)

Heparin-Binding Protein (HBP), Neutrophil Gelatinase-Associated Lipocalin (NGAL) and S100 Calcium-Binding Protein B (S100B) Can Confirm Bacterial Meningitis and Inform Adequate Antibiotic Treatment
by: Maria Obreja, et al.
Published: (2022-06-01)

AZU1: a new promising marker for infection in orthopedic and trauma patients?
by: Philipp Hemmann, et al.
Published: (2024-01-01)

Protective Effect and Mechanism of Xbp1s Regulating HBP/O-GlcNAcylation through GFAT1 on Brain Injury after SAH
by: Kefan Wu, et al.
Published: (2023-04-01)

Hepatitis B virus P protein initiates glycolytic bypass in HBV-related hepatocellular carcinoma via a FOXO3/miRNA-30b-5p/MINPP1 axis
by: Wenbiao Chen, et al.
Published: (2021-01-01)

National and regional prevalence rates of hypertension in Saudi Arabia: A descriptive analysis using the national survey data
by: Aqeel M. Alenazi, et al.
Published: (2023-04-01)

Model-based estimation of the leaf area of ozone-indicator tobacco (Nicotiana tabacum L.) plants under ambient ozone conditions
by: Evgenios Agathokleous, et al.
Published: (2023-01-01)

Hasta Bakıcılarda Bel Ağrısı ve Yaşam Kalitesinin Değerlendirilmesi, Turgut Özal Tıp Merkezi Örneği
by: Ali Özer, et al.
Published: (2018-06-01)

A hónap eseményei az EU bel- és igazságügyi együttműködése terén (október)
by: Erika Asztalos, et al.
Published: (2010-11-01)

A hónap eseményei az EU bel- és igazságügyi együttműködése terén (szeptember)
by: Erika Asztalos, et al.
Published: (2010-10-01)

Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction
by: Yihao Wang, et al.
Published: (2023-11-01)

HBP1 inhibits chicken preadipocyte differentiation by activating the STAT3 signaling via directly enhancing JAK2 expression
by: Hong-yan CHEN, et al.
Published: (2022-06-01)

Targets and management of hypertension in heart failure: focusing on the stages of heart failure
by: Huanhuan Miao, et al.
Published: (2022-09-01)

The use of echocardiography compared to electrocardiogram when screening for left ventricular hypertrophy in hypertensive patients: A cross‐sectional study
by: Marijn Marc Bult, et al.
Published: (2024-08-01)

Çocukluk Çağı Sırt ve Bel Ağrıları.
by: Mehmet Bezer, et al.
Published: (2003-03-01)

Enhancement of red blood cell transfusion compatibility using CRISPR‐mediated erythroblast gene editing
by: Joseph Hawksworth, et al.
Published: (2018-04-01)

A hónap eseményei az EU bel- és igazságügyi együttműködés terén (november)
by: Erika Asztalos, et al.
Published: (2010-12-01)

‘Bellography’: Life and Contributions of Ross and Joyce Bell, two New England Naturalists
by: John Spence, et al.
Published: (2011-11-01)

Evaluating language model embeddings for Parkinson’s disease cohort harmonization using a novel manually curated variable mapping schema
by: Yasamin Salimi, et al.
Published: (2025-06-01)

O-GlcNAc of STING mediates antiviral innate immunity
by: Yujia Li, et al.
Published: (2024-03-01)

Nutlin-3a induces KRAS mutant/p53 wild type lung cancer specific methuosis-like cell death that is dependent on GFPT2
by: Dasom Kim, et al.
Published: (2023-12-01)

Motivation to move fast, motivation to wait and see: The association of prevention and promotion focus with clinicians’ implementation of the JNC‐7 hypertension treatment guidelines
by: Mechelle Sanders, et al.
Published: (2021-09-01)

Integrated transcriptomic and metabolomic analyses elucidate the regulatory role of SlBEL11 in tomato fruit ripening
by: Xiufen Dong, et al.
Published: (2025-09-01)