Talks

Software

EndoMineR

An R package for extracting structured data from free-text endoscopy and pathology reports, linking pathology to procedures and tracking Barrett’s surveillance timelines. View on GitHub

Gastrodatascience

An educational resource for gastroenterology data science, covering R, machine learning, and NLP applied to clinical data. Visit site

Gastroenterology Teaching Book

A free online resource for gastroenterology teaching aimed at medical students and junior doctors. Visit site

MiFlo

Research project exploring minimally invasive flow measurements in gastrointestinal physiology.

Physipop

Package to automate extraction of oesophageal physiology metrics https://github.com/sebastiz/Physipopv2.0.3

PhysiMiner & PhysiMinerpy

Libraries written in R and python to automate analysis of oesophageal physiology results (ph impedance, high resolution manometry and wireless pH capsules) (https://github.com/sebastiz/PhysiMineRpy & https://github.com/sebastiz/PhysiMineR)

pyEPIC & STH analytics

Python libraries for simplifying access to EPIC Clarity data and legacy data in the Enterprise Data Warehouse (EDW). (https://github.com/AgatheZ/pyEPIC & https://github.com/sebastiz/pySTH_Analytics)

EndoMiner

Zeki SS. EndoMineR for the extraction of endoscopic and associated pathology data from medical reports. Journal of Open Source Software. 2018;3(24):701. doi:10.21105/joss.00701.

Educational Role

I contribute across the KCL–GSTT academic pathway: undergraduate, postgraduate, and faculty development.

Undergraduate (KCL MBBS).

• Gastroenterology Small-Group Teaching Block (2016 to present),
• Delivering teaching bedside and through lectures ~25 students annually.
• Supervisor for scholarly project module 2025/6 Shan Lee “Is severe ineffective oesophageal motility at high resolution manometry related to gastro oesophageal reflux disease on impedance testing” Pierfrancesco Visaggi (June 2018 67(Suppl 1):A210.1-A210 DOI:10.1136/gutjnl-2018-BSGAbstracts.419 : “Oesophageal aperistalsis is under investigated in those without achalasia or reflux“ - oral presentation at British Society of Gastroenterology

Postgraduate:

• Created innovative single subject per page online learning materials (www.gastroenteroloybook.com) with interactive multiple choice questions to improve Specialty Certificate Examination performance.
• Publication of MRCP book (Zeki S. The Illustrated MRCP PACES Primer. Abingdon: Radcliffe Publishing; 2009. doi:10.1201/9780429091254) to help OSCE preparation for exams
• Development of gastroenterology data science online teaching materials including full code examples to help manipulate large data sets using R (https://sebastiz.github.io/gastrodatascience//index.html)
• Endoscopy trainer
• Educational Supervisor Guy’s and St Thomas’ NHS Trust.

Supervision & mentoring.

• Primary/secondary supervisor for 2 PhD candidates (topics: NLP for endoscopy):
• One PhD completion to date: Zhang X. Automating Surveillance Timing for Barrett’s Oesophagus: An Information Extraction Approach Using Natural Language Processing [Doctoral thesis]. London: King’s College London; 2026.
• Current primary PhD Supervisor for a second PhD : PhD supervision via the DRIVE Health programme (Agathe Zecevic “Development and deployment of a single unified natural language model for the supervised and automated prediction of follow up for precancerous GI conditions.”) (DRIVE- Health Programme)- Topol Digital Fellow

Educational innovation.

• Designed an “Introduction to Clinical NLP for Gastroenterologists” workshop (hands-on notebooks using de-identified endoscopy text).
• Website for NLP in gastroenterology

Training & standards.

• JAG trainer and DOPS assessor;
• Performance optimisation done with EndoMineR.
• Contribution to Nocgca submission as national audit.
• Development of automated adenoma detection rates for colonoscopy with demonstration (Regular feedback to individual endoscopists is associated with improved adenoma detection rate and other key performance indicators for colonoscopy.Lim S, Tritto G, Zeki S, DeMartino S.Frontline Gastroenterol. 2022 May 6;13(6):509-516. doi: 10.1136/flgastro-2022-102091. eCollection 2022)

Endoscopy Videos

Endoscopic procedures and techniques from my practice.