Tootfinder

Retrieval-Augmented Generation of Ontologies from Relational Databases
Mojtaba Nayyeri, Athish A Yogi, Nadeen Fathallah, Ratan Bahadur Thapa, Hans-Michael Tautenhahn, Anton Schnurpel, Steffen Staab
https://arxiv.org/abs/2506.01232

Retrieval-Augmented Generation of Ontologies from Relational Databases
Transforming relational databases into knowledge graphs with enriched ontologies enhances semantic interoperability and unlocks advanced graph-based learning and reasoning over data. However, previous approaches either demand significant manual effort to derive an ontology from a database schema or produce only a basic ontology. We present RIGOR, Retrieval-augmented Iterative Generation of RDB Ontologies, an LLM-driven approach that turns relational schemas into rich OWL ontologies with minimal…

AnnoDPO: Protein Functional Annotation Learning with Direct Preference Optimization
Zixuan Jiang, Renjing Xu
https://arxiv.org/abs/2506.07035 https://

AnnoDPO: Protein Functional Annotation Learning with Direct Preference Optimization
Deciphering protein function remains a fundamental challenge in protein representation learning. The task presents significant difficulties for protein language models (PLMs) due to the sheer volume of functional annotation categories and the highly imbalanced distribution of annotated instances across biological ontologies. Inspired by the remarkable success of reinforcement learning from human feedback (RLHF) in large language model (LLM) alignment, we propose AnnoDPO, a novel multi-modal fra…

OntoRAG: Enhancing Question-Answering through Automated Ontology Derivation from Unstructured Knowledge Bases
Yash Tiwari, Owais Ahmad Lone, Mayukha Pal
https://arxiv.org/abs/2506.00664

OntoRAG: Enhancing Question-Answering through Automated Ontology Derivation from Unstructured Knowledge Bases
Ontologies are pivotal for structuring knowledge bases to enhance question answering (QA) systems powered by Large Language Models (LLMs). However, traditional ontology creation relies on manual efforts by domain experts, a process that is time intensive, error prone, and impractical for large, dynamic knowledge domains. This paper introduces OntoRAG, an automated pipeline designed to derive ontologies from unstructured knowledge bases, with a focus on electrical relay documents. OntoRAG integr…

Our colleague Ebrahim Norouzi is presenting ConExion: Concept Extraction with Large Language Models, yoint work with Sven Hertling. Comprehensive Prompt Engineering Study of LLM-based concept extraction for domain coverage evaluation of ontologies.
arxive version: https://arxiv.org/abs/2504.12915…

ConExion: Concept Extraction with Large Language Models
In this paper, an approach for concept extraction from documents using pre-trained large language models (LLMs) is presented. Compared with conventional methods that extract keyphrases summarizing the important information discussed in a document, our approach tackles a more challenging task of extracting all present concepts related to the specific domain, not just the important ones. Through comprehensive evaluations of two widely used benchmark datasets, we demonstrate that our method improv…

Excellent keynote in the #SemDH2025 workshop by Laura Hollink on Cultural Bias in Linked Open Data. Laura is addressing all bias related aspects in cultural heritage items itself, in the data representing it, the data schemata, vocabularies, and ontologies on which the data are based, as well as in the knowledge representation languages used to create the schemata.

OxO2 -- A SSSOM mapping browser for logically sound crosswalks
Henriette Harmse, Haider Iqbal, Helen Parkinson, James McLaughlin
https://arxiv.org/abs/2506.04286

OxO2 -- A SSSOM mapping browser for logically sound crosswalks
EMBL-EBI created OxO to enable users to map between datasets that are annotated with different ontologies. Mappings identified by the first version of OxO were not necessarily logically sound, missed important provenance information such as author and reviewer, and could timeout or crash for certain requests. In this paper we introduce OxO2 to address these concerns. Provenance is addressed by implementing SSSOM, a mapping standard that defines provenance for mappings. SSSOM defines the conditi…