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Semantic Search, Knowledge Graphs

Activities

Employment (1)

Swiss Institute of Bioinformatics Geneva: Geneva, Geneva, CH

(Knowledge Representation Unit)
Employment
Source: Self-asserted source
Ana Claudia Sima

Education and qualifications (2)

University of Lausanne: Lausanne, CH

2016-11-01 to 2020-11-01 | Ph.D. (Computational Biology)
Education
Source: Self-asserted source
Ana Claudia Sima

École Polytechnique FĂ©dĂ©rale de Lausanne: Lausanne, CH

2012-09-01 to 2015-03-01 | Master (Computer Science)
Education
Source: Self-asserted source
Ana Claudia Sima

Works (21)

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications

2024 | Preprint
Contributors: Jerven Bolleman; Vincent Emonet; Adrian Altenhoff; Amos Bairoch; Marie-Claude Blatter; Alan Bridge; Severine Duvaud; Elisabeth Gasteiger; Dmitry Kuznetsov; Sebastien Moretti et al.
Source: Self-asserted source
Ana Claudia Sima

LLM-based SPARQL Query Generation from Natural Language over Federated Knowledge Graphs

The 23rd International Semantic Web Conference (ISWC)
2024 | Conference paper
Contributors: Vincent Emonet; Jerven Bolleman; Severine Duvaud; Tarcisio Mendes de Farias; Ana Claudia Sima
Source: Self-asserted source
Ana Claudia Sima

SPARQL Generation: an analysis on fine-tuning OpenLLaMA for Question Answering over a Life Science Knowledge Graph

Proceedings of SWAT4HCLS 2024
2024 | Journal article
Contributors: Rangel, Julio C; de Farias, Tarcisio Mendes; Sima, Ana Claudia; Kobayashi, Norio
Source: Self-asserted source
Ana Claudia Sima

Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets

2023 | Journal article
Contributors: de Farias, Tarcisio Mendes; Kushida, Tatsuya; Sima, Ana C; Dessimoz, Christophe; Chiba, Hirokazu; Bastian, Frédéric; Masuya, Hiroshi
Source: Self-asserted source
Ana Claudia Sima

Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets

bioRxiv
2023 | Journal article
Contributors: Kushida, Tatsuya; Mendes de Farias, Tarcisio; Sima, Ana-Claudia; Dessimoz, Christophe; Chiba, Hirokazu; Bastian, Frederic; Masuya, Hiroshi
Source: Self-asserted source
Ana Claudia Sima

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

arXiv preprint arXiv:2304.10427
2023 | Journal article
Contributors: Sima, Ana-Claudia; de Farias, Tarcisio Mendes
Source: Self-asserted source
Ana Claudia Sima

The SIB Swiss Institute of Bioinformatics Semantic Web of data

Nucleic Acids Research
2023 | Journal article
Contributors: SIB Swiss Institute of Bioinformatics RDF Group Members
Source: Self-asserted source
Ana Claudia Sima

Towards predicting essential proteins via federated SPARQL queries

2023 | Journal article
Contributors: Liakopoulos, Petros; Banfalvi, Borbala; Wang, Xinyi; Majidian, Sina; de Farias, Tarcisio Mendes; Dessimoz, Christophe; Sima, Ana Claudia
Source: Self-asserted source
Ana Claudia Sima

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation

Distributed and Parallel Databases
2022 | Journal article
Contributors: Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt
Source: Self-asserted source
Ana Claudia Sima

Federating and querying heterogeneous and distributed Web APIs and triple stores

arXiv e-prints
2022 | Journal article
Contributors: Mendes de Farias, Tarcisio; Dessimoz, Christophe; Ayllon Benitez, Aaron; Yang, Chen; Long, Jiao; Sima, Ana-Claudia
Source: Self-asserted source
Ana Claudia Sima

Bio-SODA: Enabling natural language question answering over knowledge graphs without training data

33rd International Conference on Scientific and Statistical Database Management
2021 | Conference paper
Contributors: Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt
Source: Self-asserted source
Ana Claudia Sima

INODE: Building an End-to-End Data Exploration System in Practice [Extended Vision]

arXiv preprint arXiv:2104.04194
2021 | Journal article
Contributors: Amer-Yahia, Sihem; Koutrika, Georgia; Bastian, Frederic; Belmpas, Theofilos; Braschler, Martin; Brunner, Ursin; Calvanese, Diego; Fabricius, Maximilian; Gkini, Orest; Kosten, Catherine et al.
Source: Self-asserted source
Ana Claudia Sima

INODE: Building an End-to-End Data Exploration System in Practice Authors' Copy

2021 | Journal article
Contributors: Amer-Yahia, Sihem; Koutrika, Georgia; Bastian, Frederic; Belmpas, Theofilos; Braschler, Martin; Brunner, Ursin; Calvanese, Diego; Fabricius, Maximilian; Gkini, Orest; Kosten, Catherine et al.
Source: Self-asserted source
Ana Claudia Sima

Big Data architecture for intelligent maintenance: a focus on query processing and machine learning algorithms

Journal of Big Data
2020 | Journal article
Contributors: Lehmann, Claude; Huber, Lilach Goren; Horisberger, Thomas; Scheiba, Georg; Sima, Ana Claudia; Stockinger, Kurt
Source: Self-asserted source
Ana Claudia Sima

Enabling Complex Semantic Queries to Bioinformatics Databases Through Intuitive Search Over Data

2020 | Dissertation or Thesis
Contributors: Sima, Ana Claudia; Dessimoz, Christophe; Stockinger, Kurt; Robinson-Rechavi, Marc; Kossman, Donald; Xenarios, Ioannis
Source: Self-asserted source
Ana Claudia Sima

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

F1000Research
2019 | Journal article
Contributors: Sima, Ana Claudia; Dessimoz, Christophe; Stockinger, Kurt; Zahn-Zabal, Monique; de Farias, Tarcisio Mendes
Source: Self-asserted source
Ana Claudia Sima

Enabling semantic queries across federated bioinformatics databases

Database
2019 | Journal article
Contributors: Sima, Ana Claudia; Mendes de Farias, Tarcisio; Zbinden, Erich; Anisimova, Maria; Gil, Manuel; Stockinger, Heinz; Stockinger, Kurt; Robinson-Rechavi, Marc; Dessimoz, Christophe
Source: Self-asserted source
Ana Claudia Sima

Semantic integration and enrichment of heterogeneous biological databases

Evolutionary genomics: Statistical and computational methods
2019 | Journal article
Contributors: Sima, Ana Claudia; Stockinger, Kurt; de Farias, Tarcisio Mendes; Gil, Manuel
Source: Self-asserted source
Ana Claudia Sima

A hybrid approach for alarm verification using stream processing, machine learning and text analytics

EDBT 2018, Vienna, Austria, 26-29 March 2018
2018 | Conference paper
Contributors: Sima, Ana-Claudia; Stockinger, Kurt; Affolter, Katrin; Braschler, Martin; Monte, Peter; Kaiser, Lukas
Source: Self-asserted source
Ana Claudia Sima

Cyclone: Unified stream and batch processing

2016 45th International Conference on Parallel Processing Workshops (ICPPW)
2016 | Conference paper
Contributors: Harvan, MatĂș; Locher, Thomas; Sima, Ana Claudia
Source: Self-asserted source
Ana Claudia Sima

Optimizing Parallel CFD Simulations of 2D Compressible Flows

2012 14th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing
2012 | Conference paper
Contributors: Sima, Ana Claudia; Slusanschi, Emil
Source: Self-asserted source
Ana Claudia Sima