Pages

Other

Thematic series on biomedical ontologies in JBMS: challenges and new directions

Year: 2014 Venue: Journal of Biomedical Semantics Authors: Robert Hoehndorf, Melissa Haendel, Robert Stevens, Dietrich Rebholz-Schuhmann Abstract Over the past 15 years, the biomedical research community has increased its efforts to produce ontologies encoding biomedical knowledge, and to provide the corresponding infrastructure to maintain them. As ontologies are becoming a central part of biological and biomedical research, a communication channel to publish frequent updates and latest developments on them would be an advantage.Here, we introduce the JBMS thematic series on Biomedical

Theses

Theses produced by BORG members at KAUST. Author names link to their BORG profile. PhD theses Yang Liu (2026, Bioengineering) — Reference Bias and Variant Interpretation in Human Disease Genomics — defended 2026-04-27 Fernando Zhapa-Camacho (2026, Computer Science) — Neuro-symbolic methods for embedding ontologies, and applications in life sciences — defended 2026-04-26 Sumyyah Toonsi (2025, Computer Science) — Data Driven Mining of Causal Disease Relations to Enhance Disease Centric Predictions — defended 2025-05-15 Rund Tawfiq (2025, Bioengineering) — Computational Methods for Functional

To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO)

Year: 2016 Venue: International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016) Authors: Luke Slater, Georgios V. Gkoutos, Paul N Schofield, Robert Hoehndorf Abstract MIREOT is a mechanism for the selective re-use of individual ontology classes in other ontologies. Designed to minimise effort and to support orthogonality, it is now in widespread use. The consequences for ontology integrity and automated reasoning of using the MIREOT mechanism have so far not been fully assessed. In this paper, we perform an analysis of the Experimental Factor Ontology (EFO), an

Topics

Research topics the Bio-Ontology Research Group works on. Open a topic for the full overview, related projects, software, and publications. Neuro-symbolic AI We work on methods that integrate symbolic knowledge with statistical learning. This includes mapping entities in formal ontologies into vector spaces while preserving their semantic relations. We develop embedding frameworks for Description Logics (e.g., EL++ and ALC) that provide mathematical guarantees for logical soundness and approximate the interpretation of formalized theories. ontology embeddings description logic geometric

Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies

Year: 2020 Venue: BMC Medical Informatics and Decision Making Authors: Luke T. Slater, Georgios V. Gkoutos, Robert Hoehndorf DOI: 10.1186/s12911-020-01336-2 Abstract Abstract Background Ontologies are widely used throughout the biomedical domain. These ontologies formally represent the classes and relations assumed to exist within a domain. As scientific domains are deeply interlinked, so too are their representations. While individual ontologies can be tested for consistency and coherency using automated reasoning methods, systematically combining ontologies of multiple domains together may

Towards similarity-based differential diagnostics for common diseases

Year: 2021 Venue: Computers in Biology and Medicine Authors: Luke T. Slater, Andreas Karwath, John A. Williams, Sophie Russell, Silver Makepeace, Alexander Carberry, Robert Hoehndorf, Georgios V. Gkoutos DOI: 10.1016/j.compbiomed.2021.104360 Abstract Ontology-based phenotype profiles have been utilised for the purpose of differential diagnosis of rare genetic diseases, and for decision support in specific disease domains. Particularly, semantic similarity facilitates diagnostic hypothesis generation through comparison with disease phenotype profiles. However, the approach has not been applied

Updating the CEMO ontology for future epidemiological challenges

Year: 2023 Venue: 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Basel, Switzerland, February 13-16, 2023 Authors: N\'uria Queralt-Rosinach, Paul N. Schofield, Marco Roos, Robert Hoehndorf Abstract The COVID-19 epidemiology and monitoring ontology (CEMO) is an OWL ontology built during the COVID-19 pandemic for better exchange, integration and reuse of epidemiological information. Here, we present an update of the development of the ontology and future directions in order to make it usable under different scenarios and

Usage of cell nomenclature in biomedical literature

Year: 2017 Venue: BMC Bioinformatics Authors: \cSenay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf DOI: 10.1186/s12859-017-1978-0 Abstract Cell lines and cell types are extensively studied in biomedical research yielding to a significant amount of publications each year. Identifying cell lines and cell types precisely in publications is crucial for science reproducibility and knowledge integration. There are efforts for standardisation of the cell nomenclature based on ontology development to support FAIR principles of the cell knowledge. However, it is important to analyse the usage of cell

Using Aber-OWL for fast and scalable reasoning over BioPortal ontologies

Year: 2015 Venue: Proceedings of International Conference on Biomedical Ontologies (ICBO) Authors: Luke Slater, Georgios Gkoutos, Paul N. Schofield, Robert Hoehndorf Abstract Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repositories, as well as most other tools utilizing ontologies, either provide access to ontologies without use of automated reasoning, or limit the number of ontologies for which automated reasoning-based access is

Using AberOWL for fast and scalable reasoning over BioPortal ontologies

Year: 2016 Venue: Journal of Biomedical Semantics Authors: Luke Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf DOI: 10.1186/s13326-016-0090-0 Abstract Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repositories, as well as most other tools utilizing ontologies, either provide access to ontologies without use of automated reasoning, or limit the number of ontologies for which automated reasoning-based access is provided

Using SPARQL to Unify Queries over Data, Ontologies, and Machine Learning Models in the PhenomeBrowser Knowledgebase

Year: 2022 Venue: Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022 Authors: Ali Syed, Senay Kafkas, Maxat Kulmanov, Robert Hoehndorf Topics Ontology engineering · Applied Ontology Acknowledged projects ccf-microbial-cell-factories crg-complex-variant-prioritization crg-ibnsina-qi

VarLand: A pipeline to map the structural landscape of missense variants at the proteome scale

Year: 2026 Venue: Journal of Biological Chemistry Authors: Francisco J. Guzman-Vega, Kelly J. Cardona-Londono, Ana C. Gonzalez-Alvarez, Karla A. Pena-Guerra, Azza Althagafi, Tanisha Khan, Robert Hoehndorf, Stefan T. Arold DOI: 10.1016/j.jbc.2025.111071 Abstract Missense variant pathogenicity often arises from disruptions to protein structural features. The integration of large-scale genetic sequencing into clinical workflows, and the availability of accurate artificial intelligence-based protein structure predictions present an opportunity to assess the structure-function relationship of

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings

Year: 2018 Venue: Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2018, Antwerp, Belgium, December 3-6, 2018. Authors: Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V. Gkoutos, Michel Dumontier, Robert Hoehndorf Topics Neuro-symbolic AI · Ontology engineering Acknowledged projects ccf-microbial-cell-factories crg-bio2vec

What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations

Year: 2020 Venue: BMC Medical Genomics Authors: Ahmed Alfares, Lamia Alsubaie, Taghrid Aloraini, Aljoharah Alaskar, Azza Althagafi, Ahmed Alahmad, Mamoon Rashid, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid, Faroug Ababneh, Mohammed Albalwi, Raniah Alotaibi, Mashael Almutairi, Nouf Altharawi, Alhanouf Alsamer, Marwa Abdelhakim, Senay Kafkas, Katsuhiko Mineta, Nicole Cheung, Abdallah M. Abdallah, Stine B\"uchmann-M\oller, Yoshinori Fukasawa, Xiang Zhao, Issaac Rajan, Robert Hoehndorf, Fuad Al Mutairi, Takashi Gojobori, Majid Alfadhel DOI: 10.1186/s12920-020-00743-8 Abstract There was no

Whole genome transcriptomic profiling reveals distinct sex-specific responses to heat stroke

Year: 2025 Venue: Journal of Applied Physiology Authors: Abderrezak Bouchama, Maria Gomez, Mashan L. Abdullah, Saeed Al Mahri, Shuja Shafi Malik, Saber Yezli, Sameer Mohammad, Cynthia Lehe, Bisher Abuyassin, Robert Hoehndorf DOI: 10.1152/japplphysiol.00001.2025 Abstract Heat-related mortality remains health challenges exacerbated by climate change, with sex-based differences in outcomes, yet underlying mechanisms remain poorly understood. This study examined transcriptomic responses to heat exposure in peripheral blood mononuclear cells from 19 patients with heat stroke (HS; 8 males, mean age