Tarcisio Mendes de Farias

Publications | Mémoires et thèses

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22 publications

2025 | 2024 | 2023 | 2022 | 2021 | 2019 | 2018 | 2017 |
2025
 
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.
Bastian F.B., Cammarata A.B., Carsanaro S., Detering H., Huang W.T., Joye S., Niknejad A., Nyamari M., Mendes de Farias T., Moretti S. et al., 2025/01/06. Nucleic acids research, 53 (D1) pp. D878-D885. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3F567BF2FDA6]
2024
 
The SIB Swiss Institute of Bioinformatics Semantic Web of data.
SIB Swiss Institute of Bioinformatics RDF Group Members, Mendes de Farias T., 2024/01/05. Nucleic acids research, 52 (D1) pp. D44-D51. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A29FECE3B301]
2023
On the Potential of Artificial Intelligence Chatbots for Data Exploration of Federated Bioinformatics Knowledge Graphs
Sima Ana-Claudia, Mendes de Farias Tarcisio, 2023/08/29. dans SeWebMeDa’23: 6th Workshop on Semantic Web solutions for large-scale biomedical data analytics, CEUR Workshop Proceedings (CEUR-WS.org).
[URN][serval:BIB_85E3858D9118]
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience.
Mendes de Farias T., Wollbrett J., Robinson-Rechavi M., Bastian F., 2023/08/17. GigaScience, 12 pp. giad058. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_D4A608774943]
Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets
Mendes de Farias Tarcisio, Kushida Tatsuya, Sima Ana-Claudia, Dessimoz Christophe, Chiba Hirokazu, Bastian Frédéric, Masuya Hiroshi, 2023/06/22. dans SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.
[URN][serval:BIB_818CA7FA57C2]
 
Towards predicting essential proteins via federated SPARQL queries
Liakopoulos Petros, Banfalvi Borbala, Wang Xinyi, Majidian Sina, Mendes de Farias Tarcisio, Dessimoz Christophe, Sima Ana Claudia, 2023/06/22. dans SWAT4HCLS 2023: The 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences.
[serval:BIB_5DBECBB5FD4F]
2022
Federating and querying heterogeneous and distributed Web APIs and triple stores
Mendes de Farias Tarcisio, Dessimoz Christophe, Ayllon Benitez Aaron, Yang Chen, Long Jiao, Sima Ana-Claudia, 2022/08/02. dans 2022 ISMB Bio-Ontologies Community of Special Interest. Peer-reviewed.
[URN][DOI][serval:BIB_6A2C0BEAD983]
 
INODE : Building an End-to-End Data Exploration System in Practice
Amer-Yahia Sihem, Koutrika Georgia, Braschler Martin, Calvanese Diego, Lanti Davide, Lücke-Tieke Hendrik, Mosca Alessandro, Mendes de Farias Tarcisio, Papadopoulos Dimitris, Patil Yogendra et al., 2022/01/31. ACM SIGMOD Record, 50 (4) pp. 23-29.
[DOI][serval:BIB_E16BD277810E]
Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation.
Sima A.C., Mendes de Farias T., Anisimova M., Dessimoz C., Robinson-Rechavi M., Zbinden E., Stockinger K., 2022. Distributed and parallel databases, 40 (2-3) pp. 409-440. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EE90AD3795B0]
2021
Accessing scientific data through knowledge graphs with Ontop.
Calvanese D., Lanti D., Mendes De Farias T., Mosca A., Xiao G., 2021/10/08. Patterns, 2 (10) p. 100346. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_962C4367A194]
Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data
Sima Ana Claudia, Mendes de Farias Tarcisio, Anisimova Maria, Dessimoz Christophe, Robinson-Rechavi Marc, Zbinden Erich, Stockinger Kurt, 2021/07/06. 33rd International Conference on Scientific and Statistical Database Management. Peer-reviewed.
[URN][DOI][serval:BIB_A6616600154D]
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.
Altenhoff A.M., Train C.M., Gilbert K.J., Mediratta I., Mendes de Farias T., Moi D., Nevers Y., Radoykova H.S., Rossier V., Warwick Vesztrocy A. et al., 2021/01/08. Nucleic acids research, 49 (D1) pp. D373-D379. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A827EF929B38]
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.
Bastian F.B., Roux J., Niknejad A., Comte A., Fonseca Costa S.S., de Farias T.M., Moretti S., Parmentier G., Rech de Laval V., Rosikiewicz M. et al., 2021/01/08. Nucleic acids research, 49 (D1) pp. D831-D847. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_FD0CF4F734E7]
Querying knowledge graphs in natural language.
Liang S., Stockinger K., de Farias T.M., Anisimova M., Gil M., 2021. Journal of big data, 8 (3) pp. 1-23. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_673D6C6C570E]
2019
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL
Sima Ana Claudia, Dessimoz Christophe, Stockinger Kurt, Zahn-Zabal Monique, Mendes de Farias Tarcisio, 2019/10/29. F1000Research, 8 p. 1822. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_EF5C14AC5C45]
Enabling semantic queries across federated bioinformatics databases.
Sima A.C., Mendes de Farias T., Zbinden E., Anisimova M., Gil M., Stockinger H., Stockinger K., Robinson-Rechavi M., Dessimoz C., 2019/01/01. Database, 2019. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_ED991CD0F569]
 
Semantic Integration and Enrichment of Heterogeneous Biological Databases
Sima Ana Claudia, Stockinger Kurt, de Farias Tarcisio Mendes, Gil Manuel, 2019. pp. 655-690 dans Methods in Molecular Biology, Springer New York.
[DOI][WoS][Pmid][serval:BIB_3D396F44C44D]
 
VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links
Mendes de Farias Tarcisio, Stockinger Kurt, Dessimoz Christophe, 2019. Lecture Notes in Computer Science pp. 607-625. Peer-reviewed.
[DOI][serval:BIB_B5FCAC161AA9]
2018
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
Altenhoff A.M., Glover N.M., Train C.M., Kaleb K., Warwick Vesztrocy A., Dylus D., de Farias T.M., Zile K., Stevenson C., Long J. et al., 2018/01/04. Nucleic acids research, 46 (D1) pp. D477-D485. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FC0F04688D1D]
 
A rule-based methodology to extract building model views
de Farias T.M., Roxin A., Nicolle C., 2018. Automation in Construction, 92 pp. 214-229. Peer-reviewed.
[DOI][WoS][serval:BIB_8B3224E4448D]
2017
Leveraging logical rules for efficacious representation of large orthology datasets
Mendes de Farias Tarcisio, Chiba Hirokazu, Fernández-Breis Jesualdo T. (eds.), 2017/12/01..
[URN][serval:BIB_8D8E82340A71]
 
A performance benchmark over semantic rule checking approaches in construction industry
Pauwels P., de Farias T.M., Zhang C., Roxin A., Beetz J., De Roo J., Nicolle C., 2017/08. Advanced Engineering Informatics, 33 pp. 68-88. Peer-reviewed.
[DOI][WoS][serval:BIB_97A6B1A2B677]
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