arXiv subjects

Ana-Claudia Sima

Publications and source records attributed to Ana-Claudia Sima.

5 recordsLinked to original sources

arXiv2026

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

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.

cs.DB↗

arXiv2025

SPARQL-LLM: Real-Time SPARQL Query Generation from Natural Language Questions

The advent of large language models is contributing to the emergence of novel approaches that promise to better tackle the challenge of generating structured queries, such as SPARQL queries, from natural language. However, these new approaches mostly focus on response accuracy over a single source while ignoring other evaluation criteria, such as federated query capability over distributed data stores, as well as runtime and cost to generate SPARQL queries. Consequently, they are often not production-ready or easy to deploy over (potentially federated) knowledge graphs with good accuracy. To mitigate these issues, in this paper, we extend our previous work and describe and systematically evaluate SPARQL-LLM, an open-source and triplestore-agnostic approach, powered by lightweight metadata, that generates SPARQL queries from natural language text. First, we describe its architecture, which consists of dedicated components for metadata indexing, prompt building, and query generation and execution. Then, we evaluate it based on a state-of-the-art challenge with multilingual questions, and a collection of questions from three of the most prevalent knowledge graphs within the field of bioinformatics. Our results demonstrate a substantial increase of 24% in the F1 Score on the state-of-the-art challenge, adaptability to high-resource languages such as English and Spanish, as well as ability to form complex and federated bioinformatics queries. Furthermore, we show that SPARQL-LLM is up to 36x faster than other systems participating in the challenge, while costing a maximum of $0.01 per question, making it suitable for real-time, low-cost text-to-SPARQL applications. One such application deployed over real-world decentralized knowledge graphs can be found at https://www.expasy.org/chat.

cs.IR↗

arXiv2025

A user-friendly SPARQL query editor powered by lightweight metadata

SPARQL query editors often lack intuitive interfaces to aid SPARQL-savvy users to write queries. To address this issue, we propose an easy-to-deploy, triple store-agnostic and open-source query editor that offers three main features: (i) automatic query example rendering, (ii) precise autocomplete based on existing triple patterns including within SERVICE clauses, and (iii) a data-aware schema visualization. It can be easily set up with a custom HTML element. The tool has been successfully tested on various public endpoints, and is deployed online at https://sib-swiss.github.io/sparql-editor with open-source code available at https://github.com/sib-swiss/sparql-editor.

cs.DB↗

arXiv2023

On the Potential of Artificial Intelligence Chatbots for Data Exploration of Federated Bioinformatics Knowledge Graphs

In this paper, we present work in progress on the role of artificial intelligence (AI) chatbots, such as ChatGPT, in facilitating data access to federated knowledge graphs. In particular, we provide examples from the field of bioinformatics, to illustrate the potential use of Conversational AI to describe datasets, as well as generate and explain (federated) queries across datasets for the benefit of domain experts.

cs.AI↗

arXiv2022

Federating and querying heterogeneous and distributed Web APIs and triple stores

Today's international corporations such as BASF, a leading company in the crop protection industry, produce and consume more and more data that are often fragmented and accessible through Web APIs. In addition, part of the proprietary and public data of BASF's interest are stored in triple stores and accessible with the SPARQL query language. Homogenizing the data access modes and the underlying semantics of the data without modifying or replicating the original data sources become important requirements to achieve data integration and interoperability. In this work, we propose a federated data integration architecture within an industrial setup, that relies on an ontology-based data access method. Our performance evaluation in terms of query response time showed that most queries can be answered in under 1 second.

cs.DB↗