kgsteward: a tool for building, reproducing and maintaining distributed knowledge graphs

📅 2026-09-18
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🤖 AI Summary
为了解决生命科学研究中数据整合的问题，本文介绍了一种名为kgsteward的工具，它通过从单一版本控制配置文件构建和维护RDF存储中的知识图谱。
📝 Abstract
Collaborative research projects in life sciences increasingly need to integrate private, embargoed consortium data with public reference databases in order to reach statistically meaningful interpretations. The Resource Description Framework (RDF) is well suited to this task: it facilitates the integration of heterogeneous data sources, and allows researchers to keep data and their documentation as metadata in the same place, provided the knowledge graph itself remains private during the time course of the project. Nevertheless, the development and long-term maintenance of a scientific knowledge graph remains a challenging, labour-intensive endeavour owing to the state of constant flux of most public resources. To tackle this challenge, we present kgsteward, a Python command-line tool that builds and maintains knowledge graphs inside RDF stores from a single, version-controlled configuration file. kgsteward supports multiple triplestores, keeps the local graph up-to-date with its external sources possibly already in RDF, or transformed into it on the fly, and uses SPARQL 1.1 UPDATE commands to amend further imported RDF on the fly. It can also validate the resulting graph with SPARQL queries that double as usage examples for both human users and AI agents. kgsteward has already been used in several collaborative projects at the SIB Swiss Institute of Bioinformatics, and we demonstrate its applicability in two real-world international research projects: one that builds a library of plant extracts with chemical analyses and associated bio-activities, and a second that reconciles public reference resources for human metabolic-network reconstruction.
Problem

Research questions and friction points this paper is trying to address.

collaborative research
life sciences
knowledge graph
data integration
RDF
Innovation

Methods, ideas, or system contributions that make the work stand out.

knowledge graph
RDF
triplestores
SPARQL 1.1 UPDATE
version-controlled configuration
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Affiliations4
National University of Ireland, Galway
Université Côte d’Azur
University of Fribourg
University of Geneva
Authors to Follow
Marco Pagni
Marco Pagni
VitaI-IT group, SIB Swiss Institute of Bioinformatics
BioinformaticsMicrobiologyComputational Biology
R
Robin Engler
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
F
Frederic Burdet
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
S
Sebastien Moretti
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
L
Loic Le Gregam
Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
L
Luis Quiros-Guerrero
Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
J
Jahn Nitschke
Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
P
Pierre-Marie Allard
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Biology, University of Fribourg, Fribourg, Switzerland
L
Louis-Felix Nothias
Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland; Université Côte d’Azur, Institut de Chimie de Nice, Campus Valrose, Nice, France
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Jack McGoldrick
School of Medicine, University of Galway, Galway, Ireland
R
Ronan M. T. Fleming
School of Medicine, University of Galway, Galway, Ireland
A
Alan Bridge
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
Vincent Emonet
Vincent Emonet
Data science developer, Swiss Institute of Bioinformatics
Web sémantiqueontologieslinked open data
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Tarcisio Mendes de Farias
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
A
Ana-Claudia Sima
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
M
Mark Ibberson
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
J
Jean-Luc Wolfender
Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
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Florence Mehl
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland