A Rule Based System for Semantical Enrichment of Building Information Exchange. - Tarcisio M. Farias; Ana Roxin; Christophe Nicolle (Challenge+DC@RuleML, 2014)

COBieOWL, an OWL Ontology Based on COBie Standard. - Tarcisio M. Farias; Ana Roxin; Christophe Nicolle (OTM Conferences, 2015)

FOWLA, A Federated Architecture for Ontologies. - Tarcisio M. Farias; Ana Roxin; Christophe Nicolle (RuleML, 2015)

IfcWoD, Semantically Adapting IFC Model Relations into OWL Properties. - Tarcisio Mendes de Farias; Ana Roxin; Christophe Nicolle (CoRR, 2015)

Querying and reasoning over large scale building data sets: an outline of a performance benchmark. - Pieter Pauwels; Tarcisio Mendes de Farias; Chi Zhang; Ana Roxin; Jakob Beetz; Jos De Roo (SBD@SIGMOD, 2016)

SWRL rule-selection methodology for ontology interoperability. - Tarcisio Mendes de Farias; Ana Roxin; Christophe Nicolle (Data Knowl. Eng., 2016)

Leveraging Logical Rules for Efficacious Representation of Large Orthology Datasets. - Tarcisio M. Farias; Hirokazu Chiba; Jesualdo Tomás Fernández-Breis (SWAT4LS, 2017)

A performance benchmark over semantic rule checking approaches in construction industry. - Pieter Pauwels; Tarcisio Mendes de Farias; Chi Zhang; Ana Roxin; Jakob Beetz; Jos De Roo; Christophe Nicolle (Adv. Eng. Informatics, 2017)

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. - Adrian M. Altenhoff; Natasha M. Glover; Clément-Marie Train; Klara Kaleb; Alex Warwick Vesztrocy; David Dylus; Tarcisio M. Farias; Karina Zile; Charles Stevenson; Jiao Long; Henning Redestig; Gaston H. Gonnet; et al. (Nucleic Acids Res., 2018)

VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links. - Tarcisio Mendes de Farias; Kurt Stockinger; Christophe Dessimoz (OTM Conferences, 2019)

Enabling semantic queries across federated bioinformatics databases. - Ana Claudia Sima; Tarcisio Mendes de Farias; Erich Zbinden; Maria Anisimova; Manuel Gil; Heinz Stockinger; Kurt Stockinger; Marc Robinson-Rechavi; Christophe Dessimoz (Database J. Biol. Databases Curation, 2019)

Enhancing interoperable datasets with virtual links. - Tarcisio Mendes de Farias; Christophe Dessimoz (CoRR, 2019)

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL. - Ana Claudia Sima; Christophe Dessimoz; Kurt Stockinger; Monique Zahn-Zabal; Tarcisio Mendes de Farias (F1000Research, 2019)

Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. - Ana Claudia Sima; Tarcisio Mendes de Farias; Maria Anisimova; Christophe Dessimoz; Marc Robinson-Rechavi; Erich Zbinden; Kurt Stockinger (SSDBM, 2021)

INODE: Building an End-to-End Data Exploration System in Practice [Extended Vision]. - Sihem Amer-Yahia; Georgia Koutrika; Frederic B. Bastian; Theofilos Belmpas; Martin Braschler; Ursin Brunner; Diego Calvanese; Maximilian Fabricius; Orest Gkini; Catherine Kosten; Davide Lanti; Antonis Litke; et al. (CoRR, 2021)

Querying knowledge graphs in natural language. - Shiqi Liang; Kurt Stockinger; Tarcisio Mendes de Farias; Maria Anisimova; Manuel Gil (J. Big Data, 2021)

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. - Adrian M. Altenhoff; Clément-Marie Train; Kimberly J. Gilbert; Ishita Mediratta; Tarcisio Mendes de Farias; David Moi; Yannis Nevers; Hale-Seda Radoykova; Victor Rossier; Alex Warwick Vesztrocy; Natasha M. Glover; Christophe Dessimoz (Nucleic Acids Res., 2021)

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. - Frederic B. Bastian; Julien Roux; Anne Niknejad; Aurélie Comte; Sara S. Fonseca Costa; Tarcisio Mendes de Farias; Sébastien Moretti; Gilles Parmentier; Valentine Rech de Laval; Marta Rosikiewicz; Julien Wollbrett; Amina Echchiki; et al. (Nucleic Acids Res., 2021)

Accessing scientific data through knowledge graphs with Ontop. - Diego Calvanese; Davide Lanti; Tarcisio Mendes de Farias; Alessandro Mosca 001; Guohui Xiao 001 (Patterns, 2021)

INODE: Building an End-to-End Data Exploration System in Practice. - Sihem Amer-Yahia; Georgia Koutrika; Martin Braschler; Diego Calvanese; Davide Lanti; Hendrik Lücke-Tieke; Alessandro Mosca 001; Tarcisio Mendes de Farias; Dimitris Papadopoulos; Yogendra Patil; Guillem Rull; Ellery Smith; et al. (SIGMOD Rec., 2021)

Federating and querying heterogeneous and distributed Web APIs and triple stores. - Tarcisio Mendes de Farias; Christophe Dessimoz; Aarón Ayllón-Benítez; Chen Yang; Jiao Long; Ana Claudia Sima (CoRR, 2022)

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation. - Ana Claudia Sima; Tarcisio Mendes de Farias; Maria Anisimova; Christophe Dessimoz; Marc Robinson-Rechavi; Erich Zbinden; Kurt Stockinger (Distributed Parallel Databases, 2022)

On the Potential of Artificial Intelligence Chatbots for Data Exploration of Federated Bioinformatics Knowledge Graphs. - Ana Claudia Sima; Tarcisio Mendes de Farias (SeWeBMeDA@ESWC, 2023)

Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets. - Tarcisio Mendes de Farias; Tatsuya Kushida; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frédéric B. Bastian; Hiroshi Masuya (SWAT4HCLS, 2023)

Towards predicting essential proteins via federated SPARQL queries. - Petros Liakopoulous; Borbala Banfalvi; Xinyi Wang; Sina Majidian; Tarcisio Mendes de Farias; Christophe Dessimoz; Ana Claudia Sima (SWAT4HCLS, 2023)

Boosting interoperability: towards an increasingly reusable bioinformatics knowledge base. - Tarcisio Mendes de Farias; Julien Wollbrett; Marc Robinson-Rechavi; Frederic B. Bastian (CoRR, 2023)

LLM-based SPARQL Query Generation from Natural Language over Federated Knowledge Graphs. - Vincent Emonet; Jerven T. Bolleman; Severine Duvaud; Tarcisio Mendes de Farias; Ana Claudia Sima (HGAIS@ISWC, 2024)

CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods. - Jerven T. Bolleman; Elias Crum; Iulian Dragan; Jakub Galgonek; Mark Ibberson; Tarcisio Mendes de Farias; Marek Moos; Marco Pagni; Ruben Taelman; Jirí Vondrásek; Ana Claudia Sima (SWAT4HCLS, 2024)

SPARQL generation: an analysis on fine-tuning OpenLLaMA for Question Answering over a Life Science Knowledge Graph. - Julio Cesar Rangel Reyes; Tarcisio Mendes de Farias; Ana Claudia Sima; Norio Kobayashi (SWAT4HCLS, 2024)

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications. - Jerven T. Bolleman; Vincent Emonet; Adrian M. Altenhoff; Amos Bairoch; Marie-Claude Blatter; Alan J. Bridge; Severine Duvaud; Elisabeth Gasteiger; Dmitry Kuznetsov; Sébastien Moretti; Pierre-André Michel; Anne Morgat; et al. (CoRR, 2024)

A user-friendly SPARQL query editor powered by lightweight metadata. - Vincent Emonet; Ana Claudia Sima; Tarcisio Mendes de Farias (CoRR, 2025)

Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs. - Tatsuya Kushida; Tarcisio Mendes de Farias; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frederic B. Bastian; Hiroshi Masuya (BMC Medical Informatics Decis. Mak., 2025)