@article{DBLP:journals/semweb/ChenJHCM23,author={Chen, Jiaoyan and Jim{\'{e}}nez{-}Ruiz, Ernesto and Horrocks, Ian and Chen, Xi and Myklebust, Erik Bryhn},title={An assertion and alignment correction framework for large scale knowledge
bases},journal={Semantic Web},volume={14},number={1},pages={29--53},year={2023},url={https://doi.org/10.3233/SW-210448},doi={10.3233/SW-210448},}
AI Assistants
AI Assistants: A Framework for Semi-Automated Data Wrangling
Tomas Petricek, Gerrit J. J. Burg, Alfredo Nazábal, Taha Ceritli, Ernesto Jiménez-Ruiz, and Christopher K. I. Williams
@article{DBLP:journals/tkde/PetricekBNCJW23,author={Petricek, Tomas and van den Burg, Gerrit J. J. and Naz{\'{a}}bal, Alfredo and Ceritli, Taha and Jim{\'{e}}nez{-}Ruiz, Ernesto and Williams, Christopher K. I.},title={{AI} Assistants: {A} Framework for Semi-Automated Data Wrangling},journal={{IEEE} Trans. Knowl. Data Eng.},volume={35},number={9},pages={9295--9306},year={2023},url={https://doi.org/10.1109/TKDE.2022.3222538},doi={10.1109/TKDE.2022.3222538},}
BERTSubs
Contextual semantic embeddings for ontology subsumption prediction
Jiaoyan Chen, Yuan He, Yuxia Geng, Ernesto Jiménez-Ruiz, Hang Dong, and Ian Horrocks
@article{DBLP:journals/www/ChenHGJDH23,author={Chen, Jiaoyan and He, Yuan and Geng, Yuxia and Jim{\'{e}}nez{-}Ruiz, Ernesto and Dong, Hang and Horrocks, Ian},title={Contextual semantic embeddings for ontology subsumption prediction},journal={World Wide Web {(WWW)}},volume={26},number={5},pages={2569--2591},year={2023},url={https://doi.org/10.1007/s11280-023-01169-9},doi={10.1007/S11280-023-01169-9},}
OntoLAMA
Language Model Analysis for Ontology Subsumption Inference
Yuan He, Jiaoyan Chen, Ernesto Jiménez-Ruiz, Hang Dong, and Ian Horrocks
In Findings of the Association for Computational Linguistics: ACL 2023, Toronto, Canada, July 9-14, 2023, 2023
@inproceedings{DBLP:conf/acl/0008CJ0023,author={He, Yuan and Chen, Jiaoyan and Jim{\'{e}}nez{-}Ruiz, Ernesto and Dong, Hang and Horrocks, Ian},editor={Rogers, Anna and Boyd{-}Graber, Jordan L. and Okazaki, Naoaki},title={Language Model Analysis for Ontology Subsumption Inference},booktitle={Findings of the Association for Computational Linguistics: {ACL} 2023,
Toronto, Canada, July 9-14, 2023},pages={3439--3453},publisher={Association for Computational Linguistics},year={2023},url={https://doi.org/10.18653/v1/2023.findings-acl.213},doi={10.18653/V1/2023.FINDINGS-ACL.213},}
2022
KG Ecotox.
Prediction of adverse biological effects of chemicals using knowledge graph embeddings
Erik B. Myklebust, Ernesto Jiménez-Ruiz, Jiaoyan Chen, Raoul Wolf, and Knut Erik Tollefsen
@article{DBLP:journals/semweb/MyklebustJCWT22,author={Myklebust, Erik B. and Jim{\'{e}}nez{-}Ruiz, Ernesto and Chen, Jiaoyan and Wolf, Raoul and Tollefsen, Knut Erik},title={Prediction of adverse biological effects of chemicals using knowledge
graph embeddings},journal={Semantic Web},volume={13},number={3},pages={299--338},year={2022},url={https://doi.org/10.3233/SW-222804},doi={10.3233/SW-222804},}
OAEI Bio-ML
Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching
Yuan He, Jiaoyan Chen, Hang Dong, Ernesto Jiménez-Ruiz, Ali Hadian, and Ian Horrocks
In The Semantic Web - ISWC 2022 - 21st International Semantic Web Conference, Virtual Event, October 23-27, 2022, Proceedings, 2022
@inproceedings{DBLP:conf/semweb/HeCDJHH22,author={He, Yuan and Chen, Jiaoyan and Dong, Hang and Jim{\'{e}}nez{-}Ruiz, Ernesto and Hadian, Ali and Horrocks, Ian},editor={Sattler, Ulrike and Hogan, Aidan and Keet, C. Maria and Presutti, Valentina and Almeida, Jo{\~{a}}o Paulo A. and Takeda, Hideaki and Monnin, Pierre and Pirr{\`{o}}, Giuseppe and d'Amato, Claudia},title={Machine Learning-Friendly Biomedical Datasets for Equivalence and
Subsumption Ontology Matching},booktitle={The Semantic Web - {ISWC} 2022 - 21st International Semantic Web Conference,
Virtual Event, October 23-27, 2022, Proceedings},series={Lecture Notes in Computer Science},volume={13489},pages={575--591},publisher={Springer},year={2022},url={https://doi.org/10.1007/978-3-031-19433-7\_33},doi={10.1007/978-3-031-19433-7\_33},}
SSSOM
A Simple Standard for Sharing Ontological Mappings (SSSOM)
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, and Christopher J. Mungall
@article{DBLP:journals/biodb/MatentzogluBBBB22,author={Matentzoglu, Nicolas and Balhoff, James P. and Bello, Susan M. and Bizon, Chris and Brush, Matthew H. and Callahan, Tiffany J. and Chute, Christopher G. and Duncan, William D. and Evelo, Chris T. A. and Gabriel, Davera and Graybeal, John and Gray, Alasdair J. G. and Gyori, Benjamin M. and Haendel, Melissa A. and Harmse, Henriette and Harris, Nomi L. and Harrow, Ian and Hegde, Harshad and Hoyt, Amelia L. and Hoyt, Charles Tapley and Jiao, Dazhi and Jim{\'{e}}nez{-}Ruiz, Ernesto and Jupp, Simon and Kim, Hyeongsik and K{\"{o}}hler, Sebastian and Liener, Thomas and Long, Qinqin and Malone, James and McLaughlin, James A. and McMurry, Julie A. and Moxon, Sierra A. T. and Munoz{-}Torres, Monica C. and Osumi{-}Sutherland, David and Overton, James A. and Peters, Bjoern and Putman, Tim E. and Queralt{-}Rosinach, N{\'{u}}ria and Shefchek, Kent A. and Solbrig, Harold and Thessen, Anne E. and Tudorache, Tania and Vasilevsky, Nicole A. and Wagner, Alex H. and Mungall, Christopher J.},title={A Simple Standard for Sharing Ontological Mappings {(SSSOM)}},journal={Database J. Biol. Databases Curation},volume={2022},number={2022},year={2022},url={https://doi.org/10.1093/database/baac035},doi={10.1093/DATABASE/BAAC035},}
2021
OWL2Vec*
OWL2Vec*: embedding of OWL ontologies
Jiaoyan Chen, Pan Hu, Ernesto Jiménez-Ruiz, Ole Magnus Holter, Denvar Antonyrajah, and Ian Horrocks
@article{DBLP:journals/ml/ChenHJHAH21,author={Chen, Jiaoyan and Hu, Pan and Jim{\'{e}}nez{-}Ruiz, Ernesto and Holter, Ole Magnus and Antonyrajah, Denvar and Horrocks, Ian},title={OWL2Vec*: embedding of {OWL} ontologies},journal={Mach. Learn.},volume={110},number={7},pages={1813--1845},year={2021},url={https://doi.org/10.1007/s10994-021-05997-6},doi={10.1007/S10994-021-05997-6},}
LogMap-ML
Augmenting Ontology Alignment by Semantic Embedding and Distant Supervision
Jiaoyan Chen, Ernesto Jiménez-Ruiz, Ian Horrocks, Denvar Antonyrajah, Ali Hadian, and Jaehun Lee
In The Semantic Web - 18th International Conference, ESWC 2021, Virtual Event, June 6-10, 2021, Proceedings, 2021
@inproceedings{DBLP:conf/esws/ChenJHAHL21,author={Chen, Jiaoyan and Jim{\'{e}}nez{-}Ruiz, Ernesto and Horrocks, Ian and Antonyrajah, Denvar and Hadian, Ali and Lee, Jaehun},editor={Verborgh, Ruben and Hose, Katja and Paulheim, Heiko and Champin, Pierre{-}Antoine and Maleshkova, Maria and {\'{O}}scar Corcho and Ristoski, Petar and Alam, Mehwish},title={Augmenting Ontology Alignment by Semantic Embedding and Distant Supervision},booktitle={The Semantic Web - 18th International Conference, {ESWC} 2021, Virtual
Event, June 6-10, 2021, Proceedings},series={Lecture Notes in Computer Science},volume={12731},pages={392--408},publisher={Springer},year={2021},url={https://doi.org/10.1007/978-3-030-77385-4\_23},doi={10.1007/978-3-030-77385-4\_23},}
STILTool
A Framework for Quality Assessment of Semantic Annotations of Tabular Data
Roberto Avogadro, Marco Cremaschi, Ernesto Jiménez-Ruiz, and Anisa Rula
In The Semantic Web - ISWC 2021 - 20th International Semantic Web Conference, ISWC 2021, Virtual Event, October 24-28, 2021, Proceedings, 2021
@inproceedings{DBLP:conf/semweb/AvogadroCJR21,author={Avogadro, Roberto and Cremaschi, Marco and Jim{\'{e}}nez{-}Ruiz, Ernesto and Rula, Anisa},editor={Hotho, Andreas and Blomqvist, Eva and Dietze, Stefan and Fokoue, Achille and Ding, Ying and Barnaghi, Payam M. and Haller, Armin and Dragoni, Mauro and Alani, Harith},title={A Framework for Quality Assessment of Semantic Annotations of Tabular
Data},booktitle={The Semantic Web - {ISWC} 2021 - 20th International Semantic Web Conference,
{ISWC} 2021, Virtual Event, October 24-28, 2021, Proceedings},series={Lecture Notes in Computer Science},volume={12922},pages={528--545},publisher={Springer},year={2021},url={https://doi.org/10.1007/978-3-030-88361-4\_31},doi={10.1007/978-3-030-88361-4\_31},}
2020
OA Division
Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-Based Modules
Ernesto Jiménez-Ruiz, Asan Agibetov, Jiaoyan Chen, Matthias Samwald, and Valerie Cross
In ECAI 2020 - 24th European Conference on Artificial Intelligence, 29 August-8 September 2020, Santiago de Compostela, Spain, 2020
@inproceedings{DBLP:conf/ecai/Jimenez-RuizACS20,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Agibetov, Asan and Chen, Jiaoyan and Samwald, Matthias and Cross, Valerie},editor={Giacomo, Giuseppe De and Catal{\'{a}}, Alejandro and Dilkina, Bistra and Milano, Michela and Barro, Sen{\'{e}}n and Bugar{\'{\i}}n, Alberto and Lang, J{\'{e}}r{\^{o}}me},title={Dividing the Ontology Alignment Task with Semantic Embeddings and
Logic-Based Modules},booktitle={{ECAI} 2020 - 24th European Conference on Artificial Intelligence,
29 August-8 September 2020, Santiago de Compostela, Spain},series={Frontiers in Artificial Intelligence and Applications},volume={325},pages={784--791},publisher={{IOS} Press},year={2020},url={https://doi.org/10.3233/FAIA200167},doi={10.3233/FAIA200167},}
SemTab
SemTab 2019: Resources to Benchmark Tabular Data to Knowledge Graph Matching Systems
@inproceedings{DBLP:conf/esws/Jimenez-RuizHEC20,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Hassanzadeh, Oktie and Efthymiou, Vasilis and Chen, Jiaoyan and Srinivas, Kavitha},editor={Harth, Andreas and Kirrane, Sabrina and Ngomo, Axel{-}Cyrille Ngonga and Paulheim, Heiko and Rula, Anisa and Gentile, Anna Lisa and Haase, Peter and Cochez, Michael},title={SemTab 2019: Resources to Benchmark Tabular Data to Knowledge Graph
Matching Systems},booktitle={The Semantic Web - 17th International Conference, {ESWC} 2020, Heraklion,
Crete, Greece, May 31-June 4, 2020, Proceedings},series={Lecture Notes in Computer Science},volume={12123},pages={514--530},publisher={Springer},year={2020},url={https://doi.org/10.1007/978-3-030-49461-2\_30},doi={10.1007/978-3-030-49461-2\_30},}
Tough Tables
Tough Tables: Carefully Evaluating Entity Linking for Tabular Data
Vincenzo Cutrona, Federico Bianchi, Ernesto Jiménez-Ruiz, and Matteo Palmonari
In The Semantic Web - ISWC 2020 - 19th International Semantic Web Conference, Athens, Greece, November 2-6, 2020, Proceedings, Part II, 2020
@inproceedings{DBLP:conf/semweb/CutronaBJP20,author={Cutrona, Vincenzo and Bianchi, Federico and Jim{\'{e}}nez{-}Ruiz, Ernesto and Palmonari, Matteo},editor={Pan, Jeff Z. and Tamma, Valentina A. M. and d'Amato, Claudia and Janowicz, Krzysztof and Fu, Bo and Polleres, Axel and Seneviratne, Oshani and Kagal, Lalana},title={Tough Tables: Carefully Evaluating Entity Linking for Tabular Data},booktitle={The Semantic Web - {ISWC} 2020 - 19th International Semantic Web Conference,
Athens, Greece, November 2-6, 2020, Proceedings, Part {II}},series={Lecture Notes in Computer Science},volume={12507},pages={328--343},publisher={Springer},year={2020},url={https://doi.org/10.1007/978-3-030-62466-8\_21},doi={10.1007/978-3-030-62466-8\_21},}
2019
OA User Valid.
User validation in ontology alignment: functional assessment and impact
Huanyu Li, Zlatan Dragisic, Daniel Faria, Valentina Ivanova, Ernesto Jiménez-Ruiz, Patrick Lambrix, and Catia Pesquita
@article{DBLP:journals/ker/LiDFIJLP19,author={Li, Huanyu and Dragisic, Zlatan and Faria, Daniel and Ivanova, Valentina and Jim{\'{e}}nez{-}Ruiz, Ernesto and Lambrix, Patrick and Pesquita, Catia},title={User validation in ontology alignment: functional assessment and impact},journal={Knowl. Eng. Rev.},volume={34},pages={e15},year={2019},url={https://doi.org/10.1017/S0269888919000080},doi={10.1017/S0269888919000080},}
ColNet
ColNet: Embedding the Semantics of Web Tables for Column Type Prediction
Jiaoyan Chen, Ernesto Jiménez-Ruiz, Ian Horrocks, and Charles Sutton
In The Thirty-Third AAAI Conference on Artificial Intelligence, AAAI 2019, Honolulu, Hawaii, USA, January 27 - February 1, 2019, 2019
@inproceedings{DBLP:conf/aaai/ChenJHS19,author={Chen, Jiaoyan and Jim{\'{e}}nez{-}Ruiz, Ernesto and Horrocks, Ian and Sutton, Charles},title={ColNet: Embedding the Semantics of Web Tables for Column Type Prediction},booktitle={The Thirty-Third {AAAI} Conference on Artificial Intelligence, {AAAI}
2019, Honolulu, Hawaii,
USA, January 27 - February 1, 2019},pages={29--36},publisher={{AAAI} Press},year={2019},url={https://doi.org/10.1609/aaai.v33i01.330129},doi={10.1609/AAAI.V33I01.330129},}
Christoph Pinkel, Carsten Binnig, Ernesto Jiménez-Ruiz, Evgeny Kharlamov, Wolfgang May, Andriy Nikolov, Ana Sasa Bastinos, Martin G. Skjæveland, Alessandro Solimando, Mohsen Taheriyan, Christian Heupel, and Ian Horrocks
@article{DBLP:journals/semweb/PinkelBJKMNBSST18,author={Pinkel, Christoph and Binnig, Carsten and Jim{\'{e}}nez{-}Ruiz, Ernesto and Kharlamov, Evgeny and May, Wolfgang and Nikolov, Andriy and Bastinos, Ana Sasa and Skj{\ae}veland, Martin G. and Solimando, Alessandro and Taheriyan, Mohsen and Heupel, Christian and Horrocks, Ian},title={{RODI:} Benchmarking relational-to-ontology mapping generation quality},journal={Semantic Web},volume={9},number={1},pages={25--52},year={2018},url={https://doi.org/10.3233/SW-170268},doi={10.3233/SW-170268},}
OptiqueVQS
OptiqueVQS: A visual query system over ontologies for industry
Ahmet Soylu, Evgeny Kharlamov, Dmitriy Zheleznyakov, Ernesto Jiménez-Ruiz, Martin Giese, Martin G. Skjæveland, Dag Hovland, Rudolf Schlatte, Sebastian Brandt, Hallstein Lie, and Ian Horrocks
@article{DBLP:journals/semweb/SoyluKZJGSHSBLH18,author={Soylu, Ahmet and Kharlamov, Evgeny and Zheleznyakov, Dmitriy and Jim{\'{e}}nez{-}Ruiz, Ernesto and Giese, Martin and Skj{\ae}veland, Martin G. and Hovland, Dag and Schlatte, Rudolf and Brandt, Sebastian and Lie, Hallstein and Horrocks, Ian},title={OptiqueVQS: {A} visual query system over ontologies for industry},journal={Semantic Web},volume={9},number={5},pages={627--660},year={2018},url={https://doi.org/10.3233/SW-180293},doi={10.3233/SW-180293},}
Causality Bio
Supporting shared hypothesis testing in the biomedical domain
Asan Agibetov, Ernesto Jiménez-Ruiz, Marta Ondresik, Alessandro Solimando, Imon Banerjee, Giovanna Guerrini, Chiara Eva Catalano, Joaquim Miguel Oliveira, Giuseppe Patanè, Rui Luı́s Reis, and Michela Spagnuolo
@article{DBLP:journals/biomedsem/AgibetovJOSBGCO18,author={Agibetov, Asan and Jim{\'{e}}nez{-}Ruiz, Ernesto and Ondresik, Marta and Solimando, Alessandro and Banerjee, Imon and Guerrini, Giovanna and Catalano, Chiara Eva and Oliveira, Joaquim Miguel and Patan{\`{e}}, Giuseppe and Reis, Rui Lu{\'{\i}}s and Spagnuolo, Michela},title={Supporting shared hypothesis testing in the biomedical domain},journal={J. Biomed. Semant.},volume={9},number={1},pages={9:1--9:22},year={2018},url={https://doi.org/10.1186/s13326-018-0177-x},doi={10.1186/S13326-018-0177-X},}
2017
LogMap Repair
Minimizing conservativity violations in ontology alignments: algorithms and evaluation
Alessandro Solimando, Ernesto Jiménez-Ruiz, and Giovanna Guerrini
@article{DBLP:journals/kais/SolimandoJG17,author={Solimando, Alessandro and Jim{\'{e}}nez{-}Ruiz, Ernesto and Guerrini, Giovanna},title={Minimizing conservativity violations in ontology alignments: algorithms
and evaluation},journal={Knowl. Inf. Syst.},volume={51},number={3},pages={775--819},year={2017},url={https://doi.org/10.1007/s10115-016-0983-3},doi={10.1007/S10115-016-0983-3},}
OAEI Phenotype
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative
Ian Harrow, Ernesto Jiménez-Ruiz, Andrea Splendiani, Martin Romacker, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, James Malone, and Arild Waaler
@article{DBLP:journals/biomedsem/HarrowJSRWMAKMW17,author={Harrow, Ian and Jim{\'{e}}nez{-}Ruiz, Ernesto and Splendiani, Andrea and Romacker, Martin and Woollard, Peter and Markel, Scott and Alam{-}Faruque, Yasmin and Koch, Martin and Malone, James and Waaler, Arild},title={Matching disease and phenotype ontologies in the ontology alignment
evaluation initiative},journal={J. Biomed. Semant.},volume={8},number={1},pages={55:1--55:13},year={2017},url={https://doi.org/10.1186/s13326-017-0162-9},doi={10.1186/S13326-017-0162-9},}
OBDA Optique
Ontology Based Data Access in Statoil
Evgeny Kharlamov, Dag Hovland, Martin G. Skjæveland, Dimitris Bilidas, Ernesto Jiménez-Ruiz, Guohui Xiao, Ahmet Soylu, Davide Lanti, Martin Rezk, Dmitriy Zheleznyakov, Martin Giese, Hallstein Lie, Yannis E. Ioannidis, Yannis Kotidis, Manolis Koubarakis, and Arild Waaler
@article{DBLP:journals/ws/KharlamovHSBJXS17,author={Kharlamov, Evgeny and Hovland, Dag and Skj{\ae}veland, Martin G. and Bilidas, Dimitris and Jim{\'{e}}nez{-}Ruiz, Ernesto and Xiao, Guohui and Soylu, Ahmet and Lanti, Davide and Rezk, Martin and Zheleznyakov, Dmitriy and Giese, Martin and Lie, Hallstein and Ioannidis, Yannis E. and Kotidis, Yannis and Koubarakis, Manolis and Waaler, Arild},title={Ontology Based Data Access in Statoil},journal={J. Web Semant.},volume={44},pages={3--36},year={2017},url={https://doi.org/10.1016/j.websem.2017.05.005},doi={10.1016/J.WEBSEM.2017.05.005},}
2016
OA Reasoners
Pushing the limits of OWL 2 reasoners in ontology alignment repair problems
Alessandro Solimando, Ernesto Jiménez-Ruiz, and Giovanna Guerrini
@article{DBLP:journals/ia/SolimandoJG16,author={Solimando, Alessandro and Jim{\'{e}}nez{-}Ruiz, Ernesto and Guerrini, Giovanna},title={Pushing the limits of {OWL} 2 reasoners in ontology alignment repair
problems},journal={Intelligenza Artificiale},volume={10},number={1},pages={1--18},year={2016},url={https://doi.org/10.3233/IA-160091},doi={10.3233/IA-160091},}
OA Negotiation
Limiting Logical Violations in Ontology Alignnment Through Negotiation
Ernesto Jiménez-Ruiz, Terry R. Payne, Alessandro Solimando, and Valentina A. M. Tamma
In Principles of Knowledge Representation and Reasoning: Proceedings of the Fifteenth International Conference, KR 2016, Cape Town, South Africa, April 25-29, 2016, 2016
@inproceedings{DBLP:conf/kr/Jimenez-RuizPST16,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Payne, Terry R. and Solimando, Alessandro and Tamma, Valentina A. M.},editor={Baral, Chitta and Delgrande, James P. and Wolter, Frank},title={Limiting Logical Violations in Ontology Alignnment Through Negotiation},booktitle={Principles of Knowledge Representation and Reasoning: Proceedings
of the Fifteenth International Conference, {KR} 2016, Cape Town, South
Africa, April 25-29, 2016},pages={217--226},publisher={{AAAI} Press},year={2016},url={http://www.aaai.org/ocs/index.php/KR/KR16/paper/view/12893},}
CMR-QA Onto.
Towards the Semantic Enrichment of Free-Text Annotation of Image Quality Assessment for UK Biobank Cardiac Cine MRI Scans
Valentina Carapella, Ernesto Jiménez-Ruiz, Elena Lukaschuk, Nay Aung, Kenneth Fung, José Miguel Paiva, Mihir Sanghvi, Stefan Neubauer, Steffen E. Petersen, Ian Horrocks, and Stefan K. Piechnik
In Deep Learning and Data Labeling for Medical Applications - First International Workshop, LABELS 2016, and Second International Workshop, DLMIA 2016, Held in Conjunction with MICCAI 2016, Athens, Greece, October 21, 2016, Proceedings, 2016
@inproceedings{DBLP:conf/miccai/CarapellaJLAFPS16,author={Carapella, Valentina and Jim{\'{e}}nez{-}Ruiz, Ernesto and Lukaschuk, Elena and Aung, Nay and Fung, Kenneth and Paiva, Jos{\'{e}} Miguel and Sanghvi, Mihir and Neubauer, Stefan and Petersen, Steffen E. and Horrocks, Ian and Piechnik, Stefan K.},editor={Carneiro, Gustavo and Mateus, Diana and Peter, Lo{\"{\i}}c and Bradley, Andrew P. and Tavares, Jo{\~{a}}o Manuel R. S. and Belagiannis, Vasileios and Papa, Jo{\~{a}}o Paulo and Nascimento, Jacinto C. and Loog, Marco and Lu, Zhi and Cardoso, Jaime S. and Cornebise, Julien},title={Towards the Semantic Enrichment of Free-Text Annotation of Image Quality
Assessment for {UK} Biobank Cardiac Cine {MRI} Scans},booktitle={Deep Learning and Data Labeling for Medical Applications - First International
Workshop, {LABELS} 2016, and Second International Workshop, {DLMIA}
2016, Held in Conjunction with {MICCAI} 2016, Athens, Greece, October
21, 2016, Proceedings},series={Lecture Notes in Computer Science},volume={10008},pages={238--248},year={2016},url={https://doi.org/10.1007/978-3-319-46976-8\_25},doi={10.1007/978-3-319-46976-8\_25},}
OWL Constraints
Capturing Industrial Information Models with Ontologies and Constraints
Evgeny Kharlamov, Bernardo Cuenca Grau, Ernesto Jiménez-Ruiz, Steffen Lamparter, Gulnar Mehdi, Martin Ringsquandl, Yavor Nenov, Stephan Grimm, Mikhail Roshchin, and Ian Horrocks
In The Semantic Web - ISWC 2016 - 15th International Semantic Web Conference, Kobe, Japan, October 17-21, 2016, Proceedings, Part II, 2016
@inproceedings{DBLP:conf/semweb/KharlamovGJLMRN16a,author={Kharlamov, Evgeny and Grau, Bernardo Cuenca and Jim{\'{e}}nez{-}Ruiz, Ernesto and Lamparter, Steffen and Mehdi, Gulnar and Ringsquandl, Martin and Nenov, Yavor and Grimm, Stephan and Roshchin, Mikhail and Horrocks, Ian},editor={Groth, Paul and Simperl, Elena and Gray, Alasdair J. G. and Sabou, Marta and Kr{\"{o}}tzsch, Markus and L{\'{e}}cu{\'{e}}, Freddy and Fl{\"{o}}ck, Fabian and Gil, Yolanda},title={Capturing Industrial Information Models with Ontologies and Constraints},booktitle={The Semantic Web - {ISWC} 2016 - 15th International Semantic Web Conference,
Kobe, Japan, October 17-21, 2016, Proceedings, Part {II}},series={Lecture Notes in Computer Science},volume={9982},pages={325--343},year={2016},url={https://doi.org/10.1007/978-3-319-46547-0\_30},doi={10.1007/978-3-319-46547-0\_30},}
2015
BootOX
BootOX: Practical Mapping of RDBs to OWL 2
Ernesto Jiménez-Ruiz, Evgeny Kharlamov, Dmitriy Zheleznyakov, Ian Horrocks, Christoph Pinkel, Martin G. Skjæveland, Evgenij Thorstensen, and Jose Mora
In The Semantic Web - ISWC 2015 - 14th International Semantic Web Conference, Bethlehem, PA, USA, October 11-15, 2015, Proceedings, Part II, 2015
@inproceedings{DBLP:conf/semweb/Jimenez-RuizKZH15,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Kharlamov, Evgeny and Zheleznyakov, Dmitriy and Horrocks, Ian and Pinkel, Christoph and Skj{\ae}veland, Martin G. and Thorstensen, Evgenij and Mora, Jose},editor={Arenas, Marcelo and {\'{O}}scar Corcho and Simperl, Elena and Strohmaier, Markus and d'Aquin, Mathieu and Srinivas, Kavitha and Groth, Paul and Dumontier, Michel and Heflin, Jeff and Thirunarayan, Krishnaprasad and Staab, Steffen},title={BootOX: Practical Mapping of RDBs to {OWL} 2},booktitle={The Semantic Web - {ISWC} 2015 - 14th International Semantic Web Conference,
Bethlehem, PA, USA, October 11-15, 2015, Proceedings, Part {II}},series={Lecture Notes in Computer Science},volume={9367},pages={113--132},publisher={Springer},year={2015},url={https://doi.org/10.1007/978-3-319-25010-6\_7},doi={10.1007/978-3-319-25010-6\_7},}
2014
BioPortal Repair
Towards Annotating Potential Incoherences in BioPortal Mappings
Daniel Faria, Ernesto Jiménez-Ruiz, Catia Pesquita, Emanuel Santos, and Francisco M. Couto
In The Semantic Web - ISWC 2014 - 13th International Semantic Web Conference, Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part II, 2014
@inproceedings{DBLP:conf/semweb/FariaJPSC14,author={Faria, Daniel and Jim{\'{e}}nez{-}Ruiz, Ernesto and Pesquita, Catia and Santos, Emanuel and Couto, Francisco M.},editor={Mika, Peter and Tudorache, Tania and Bernstein, Abraham and Welty, Chris and Knoblock, Craig A. and Vrandecic, Denny and Groth, Paul and Noy, Natasha F. and Janowicz, Krzysztof and Goble, Carole A.},title={Towards Annotating Potential Incoherences in BioPortal Mappings},booktitle={The Semantic Web - {ISWC} 2014 - 13th International Semantic Web Conference,
Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part {II}},series={Lecture Notes in Computer Science},volume={8797},pages={17--32},publisher={Springer},year={2014},url={https://doi.org/10.1007/978-3-319-11915-1\_2},doi={10.1007/978-3-319-11915-1\_2},}
2013
OA Repair
Evaluating Mapping Repair Systems with Large Biomedical Ontologies
Ernesto Jiménez-Ruiz, Christian Meilicke, Bernardo Cuenca Grau, and Ian Horrocks
In Informal Proceedings of the 26th International Workshop on Description Logics, Ulm, Germany, July 23 - 26, 2013, 2013
@inproceedings{DBLP:conf/dlog/Jimenez-RuizMGH13,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Meilicke, Christian and Grau, Bernardo Cuenca and Horrocks, Ian},editor={Eiter, Thomas and Glimm, Birte and Kazakov, Yevgeny and Kr{\"{o}}tzsch, Markus},title={Evaluating Mapping Repair Systems with Large Biomedical Ontologies},booktitle={Informal Proceedings of the 26th International Workshop on Description
Logics, Ulm, Germany, July 23 - 26, 2013},series={{CEUR} Workshop Proceedings},volume={1014},pages={246--257},publisher={CEUR-WS.org},year={2013},url={https://ceur-ws.org/Vol-1014/paper\_63.pdf},}
ORE Eval.
OWL Reasoner Evaluation (ORE) Workshop 2013 Results: Short Report
Rafael S. Gonçalves, Samantha Bail, Ernesto Jiménez-Ruiz, Nicolas Matentzoglu, Bijan Parsia, Birte Glimm, and Yevgeny Kazakov
In Informal Proceedings of the 2nd International Workshop on OWL Reasoner Evaluation (ORE-2013), Ulm, Germany, July 22, 2013, 2013
@inproceedings{DBLP:conf/ore/GoncalvesBJMPGK13,author={Gon{\c{c}}alves, Rafael S. and Bail, Samantha and Jim{\'{e}}nez{-}Ruiz, Ernesto and Matentzoglu, Nicolas and Parsia, Bijan and Glimm, Birte and Kazakov, Yevgeny},editor={Bail, Samantha and Glimm, Birte and Gon{\c{c}}alves, Rafael S. and Jim{\'{e}}nez{-}Ruiz, Ernesto and Kazakov, Yevgeny and Matentzoglu, Nicolas and Parsia, Bijan},title={{OWL} Reasoner Evaluation {(ORE)} Workshop 2013 Results: Short Report},booktitle={Informal Proceedings of the 2nd International Workshop on {OWL} Reasoner
Evaluation (ORE-2013), Ulm, Germany, July 22, 2013},series={{CEUR} Workshop Proceedings},volume={1015},pages={1--18},publisher={CEUR-WS.org},year={2013},url={https://ceur-ws.org/Vol-1015/ore2013\_report.pdf},}
2012
3D-Browser
Exploring and linking biomedical resources through multidimensional semantic spaces
Rafael Berlanga Llavori, Ernesto Jiménez-Ruiz, and Victoria Nebot
@article{DBLP:journals/bmcbi/LlavoriJN12,author={Llavori, Rafael Berlanga and Jim{\'{e}}nez{-}Ruiz, Ernesto and Nebot, Victoria},title={Exploring and linking biomedical resources through multidimensional
semantic spaces},journal={{BMC} Bioinform.},volume={13},number={{S-1}},pages={S6},year={2012},url={https://doi.org/10.1186/1471-2105-13-S1-S6},doi={10.1186/1471-2105-13-S1-S6},}
LogMap 2
Large-scale Interactive Ontology Matching: Algorithms and Implementation
Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Yujiao Zhou, and Ian Horrocks
In ECAI 2012 - 20th European Conference on Artificial Intelligence, Montpellier, France, August 27-31 , 2012, 2012
@inproceedings{DBLP:conf/ecai/Jimenez-RuizGZH12,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Grau, Bernardo Cuenca and Zhou, Yujiao and Horrocks, Ian},editor={Raedt, Luc De and Bessiere, Christian and Dubois, Didier and Doherty, Patrick and Frasconi, Paolo and Heintz, Fredrik and Lucas, Peter J. F.},title={Large-scale Interactive Ontology Matching: Algorithms and Implementation},booktitle={{ECAI} 2012 - 20th European Conference on Artificial Intelligence,
Montpellier, France, August 27-31 , 2012},series={Frontiers in Artificial Intelligence and Applications},volume={242},pages={444--449},publisher={{IOS} Press},year={2012},url={https://doi.org/10.3233/978-1-61499-098-7-444},doi={10.3233/978-1-61499-098-7-444},}
Onto. Evol.
Ontology Evolution Under Semantic Constraints
Bernardo Cuenca Grau, Ernesto Jiménez-Ruiz, Evgeny Kharlamov, and Dmitriy Zheleznyakov
In Principles of Knowledge Representation and Reasoning: Proceedings of the Thirteenth International Conference, KR 2012, Rome, Italy, June 10-14, 2012, 2012
@inproceedings{DBLP:conf/kr/GrauJKZ12,author={Grau, Bernardo Cuenca and Jim{\'{e}}nez{-}Ruiz, Ernesto and Kharlamov, Evgeny and Zheleznyakov, Dmitriy},editor={Brewka, Gerhard and Eiter, Thomas and McIlraith, Sheila A.},title={Ontology Evolution Under Semantic Constraints},booktitle={Principles of Knowledge Representation and Reasoning: Proceedings
of the Thirteenth International Conference, {KR} 2012, Rome, Italy,
June 10-14, 2012},publisher={{AAAI} Press},year={2012},url={http://www.aaai.org/ocs/index.php/KR/KR12/paper/view/4480},}
2011
UMLS Repair
Logic-based assessment of the compatibility of UMLS ontology sources
Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Ian Horrocks, and Rafael Berlanga Llavori
@article{DBLP:journals/biomedsem/Jimenez-RuizGHL11,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Grau, Bernardo Cuenca and Horrocks, Ian and Llavori, Rafael Berlanga},title={Logic-based assessment of the compatibility of {UMLS} ontology sources},journal={J. Biomed. Semant.},volume={2},number={{S-1}},pages={S2},year={2011},url={http://www.jbiomedsem.com/content/2/S1/S2},}
Onto. CVS
Supporting concurrent ontology development: Framework, algorithms and tool
Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Ian Horrocks, and Rafael Berlanga Llavori
@article{DBLP:journals/dke/Jimenez-RuizGHL11,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Grau, Bernardo Cuenca and Horrocks, Ian and Llavori, Rafael Berlanga},title={Supporting concurrent ontology development: Framework, algorithms
and tool},journal={Data Knowl. Eng.},volume={70},number={1},pages={146--164},year={2011},url={https://doi.org/10.1016/j.datak.2010.10.001},doi={10.1016/J.DATAK.2010.10.001},}
DL Images
Describing Images Using Qualitative Models and Description Logics
Zoe Falomir, Ernesto Jiménez-Ruiz, M. Teresa Escrig, and Lledó Museros Cabedo
@article{DBLP:journals/scc/FalomirJEC11,author={Falomir, Zoe and Jim{\'{e}}nez{-}Ruiz, Ernesto and Escrig, M. Teresa and Cabedo, Lled{\'{o}} Museros},title={Describing Images Using Qualitative Models and Description Logics},journal={Spatial Cogn. Comput.},volume={11},number={1},pages={45--74},year={2011},url={https://doi.org/10.1080/13875868.2010.545611},doi={10.1080/13875868.2010.545611},}
LogMap
LogMap: Logic-Based and Scalable Ontology Matching
Ernesto Jiménez-Ruiz, and Bernardo Cuenca Grau
In The Semantic Web - ISWC 2011 - 10th International Semantic Web Conference, Bonn, Germany, October 23-27, 2011, Proceedings, Part I, 2011
@inproceedings{DBLP:conf/semweb/Jimenez-RuizG11,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Grau, Bernardo Cuenca},editor={Aroyo, Lora and Welty, Chris and Alani, Harith and Taylor, Jamie and Bernstein, Abraham and Kagal, Lalana and Noy, Natasha Fridman and Blomqvist, Eva},title={LogMap: Logic-Based and Scalable Ontology Matching},booktitle={The Semantic Web - {ISWC} 2011 - 10th International Semantic Web Conference,
Bonn, Germany, October 23-27, 2011, Proceedings, Part {I}},series={Lecture Notes in Computer Science},volume={7031},pages={273--288},publisher={Springer},year={2011},url={https://doi.org/10.1007/978-3-642-25073-6\_18},doi={10.1007/978-3-642-25073-6\_18},}
2010
PhD Thesis
Logic-based support for Ontology Development in Open Environments
@phdthesis{DBLP:phd/es/Ruiz10,author={Jim{\'{e}}nez{-}Ruiz, Ernesto},title={Logic-based support for Ontology Development in Open Environments},school={Jaume {I} University, Spain},year={2010},url={http://hdl.handle.net/10803/10493},}
2009
Reuse Lex.
Reuse of terminological resources for efficient ontological engineering in Life Sciences
Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga Llavori, and Dietrich Rebholz-Schuhmann
@article{DBLP:journals/bmcbi/Jimeno-YepesJLR09,author={Jimeno{-}Yepes, Antonio and Jim{\'{e}}nez{-}Ruiz, Ernesto and Llavori, Rafael Berlanga and Rebholz{-}Schuhmann, Dietrich},title={Reuse of terminological resources for efficient ontological engineering
in Life Sciences},journal={{BMC} Bioinform.},volume={10},number={{S-10}},pages={4},year={2009},url={https://doi.org/10.1186/1471-2105-10-S10-S4},doi={10.1186/1471-2105-10-S10-S4},}
XML Bio.
XML-based approaches for the integration of heterogeneous bio-molecular data
Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga Llavori, Paolo Perlasca, Giorgio Valentini, and David Manset
@article{DBLP:journals/bmcbi/MesitiJSLPVM09,author={Mesiti, Marco and Jim{\'{e}}nez{-}Ruiz, Ernesto and Sanz, Ismael and Llavori, Rafael Berlanga and Perlasca, Paolo and Valentini, Giorgio and Manset, David},title={XML-based approaches for the integration of heterogeneous bio-molecular
data},journal={{BMC} Bioinform.},volume={10},number={{S-12}},pages={7},year={2009},url={https://doi.org/10.1186/1471-2105-10-S12-S7},doi={10.1186/1471-2105-10-S12-S7},}
ContentMap
Ontology Integration Using Mappings: Towards Getting the Right Logical Consequences
Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Ian Horrocks, and Rafael Berlanga Llavori
In The Semantic Web: Research and Applications, 6th European Semantic Web Conference, ESWC 2009, Heraklion, Crete, Greece, May 31-June 4, 2009, Proceedings, 2009
@inproceedings{DBLP:conf/esws/Jimenez-RuizGHL09,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Grau, Bernardo Cuenca and Horrocks, Ian and Llavori, Rafael Berlanga},editor={Aroyo, Lora and Traverso, Paolo and Ciravegna, Fabio and Cimiano, Philipp and Heath, Tom and Hyv{\"{o}}nen, Eero and Mizoguchi, Riichiro and Oren, Eyal and Sabou, Marta and Simperl, Elena},title={Ontology Integration Using Mappings: Towards Getting the Right Logical
Consequences},booktitle={The Semantic Web: Research and Applications, 6th European Semantic
Web Conference, {ESWC} 2009, Heraklion, Crete, Greece, May 31-June
4, 2009, Proceedings},series={Lecture Notes in Computer Science},volume={5554},pages={173--187},publisher={Springer},year={2009},url={https://doi.org/10.1007/978-3-642-02121-3\_16},doi={10.1007/978-3-642-02121-3\_16},}
2008
NER Disease
Assessment of disease named entity recognition on a corpus of annotated sentences
Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga Llavori, and Dietrich Rebholz-Schuhmann
@article{DBLP:journals/bmcbi/JimenoJLGLR08,author={Jimeno{-}Yepes, Antonio and Jim{\'{e}}nez{-}Ruiz, Ernesto and Lee, Vivian and Gaudan, Sylvain and Llavori, Rafael Berlanga and Rebholz{-}Schuhmann, Dietrich},title={Assessment of disease named entity recognition on a corpus of annotated
sentences},journal={{BMC} Bioinform.},volume={9},number={{S-3}},year={2008},url={https://doi.org/10.1186/1471-2105-9-S3-S3},}
Onto. Modules
Safe and Economic Re-Use of Ontologies: A Logic-Based Methodology and Tool Support
Ernesto Jiménez-Ruiz, Bernardo Cuenca Grau, Ulrike Sattler, Thomas Schneider, and Rafael Berlanga Llavori
In The Semantic Web: Research and Applications, 5th European Semantic Web Conference, ESWC 2008, Tenerife, Canary Islands, Spain, June 1-5, 2008, Proceedings, 2008
@inproceedings{DBLP:conf/esws/Jimenez-RuizGSSL08,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Grau, Bernardo Cuenca and Sattler, Ulrike and Schneider, Thomas and Llavori, Rafael Berlanga},editor={Bechhofer, Sean and Hauswirth, Manfred and Hoffmann, J{\"{o}}rg and Koubarakis, Manolis},title={Safe and Economic Re-Use of Ontologies: {A} Logic-Based Methodology
and Tool Support},booktitle={The Semantic Web: Research and Applications, 5th European Semantic
Web Conference, {ESWC} 2008, Tenerife, Canary Islands, Spain, June
1-5, 2008, Proceedings},series={Lecture Notes in Computer Science},volume={5021},pages={185--199},publisher={Springer},year={2008},url={https://doi.org/10.1007/978-3-540-68234-9\_16},doi={10.1007/978-3-540-68234-9\_16},}
2007
OntoPath
OntoPath: A Language for Retrieving Ontology Fragments
Ernesto Jiménez-Ruiz, Rafael Berlanga Llavori, Victoria Nebot, and Ismael Sanz
In On the Move to Meaningful Internet Systems 2007: ODBASE Conferences, Vilamoura, Portugal, November 25-30, 2007, Proceedings, Part I, 2007
@inproceedings{DBLP:conf/otm/Jimenez-RuizBNS07,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Llavori, Rafael Berlanga and Nebot, Victoria and Sanz, Ismael},editor={Meersman, Robert and Tari, Zahir},title={OntoPath: {A} Language for Retrieving Ontology Fragments},booktitle={On the Move to Meaningful Internet Systems 2007: ODBASE Conferences,
Vilamoura, Portugal, November 25-30, 2007, Proceedings, Part {I}},series={Lecture Notes in Computer Science},volume={4803},pages={897--914},publisher={Springer},year={2007},url={https://doi.org/10.1007/978-3-540-76848-7\_60},doi={10.1007/978-3-540-76848-7\_60},}
2006
Health-e-Child
The Management and Integration of Biomedical Knowledge: Application in the Health-e-Child Project (Position Paper)
Ernesto Jiménez-Ruiz, Rafael Berlanga Llavori, Ismael Sanz, Richard McClatchey, Roxana Dánger, David Manset, Jordi Paraire, and Alfonso Rios
In On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops, Montpellier, France, October 29 - November 3, 2006. Proceedings, Part II, 2006
@inproceedings{DBLP:conf/otm/Jimenez-RuizBSMDMPR06,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Llavori, Rafael Berlanga and Sanz, Ismael and McClatchey, Richard and D{\'{a}}nger, Roxana and Manset, David and Paraire, Jordi and Rios, Alfonso},editor={Meersman, Robert and Tari, Zahir and Herrero, Pilar},title={The Management and Integration of Biomedical Knowledge: Application
in the Health-e-Child Project (Position Paper)},booktitle={On the Move to Meaningful Internet Systems 2006: {OTM} 2006 Workshops,
Montpellier, France, October 29 - November 3, 2006. Proceedings, Part {II}},series={Lecture Notes in Computer Science},volume={4278},pages={1062--1067},publisher={Springer},year={2006},url={https://doi.org/10.1007/11915072\_8},doi={10.1007/11915072\_8},}
VIMethCOE
A View-Based Methodology for Collaborative Ontology Engineering: An Approach for Complex Applications (VIMethCOE)
Ernesto Jiménez-Ruiz, and Rafael Berlanga Llavori
In 15th IEEE International Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprises (WETICE 2006), 26-28 June 2006, Manchester, United Kingdom, 2006
@inproceedings{DBLP:conf/wetice/Jimenez-RuizB06,author={Jim{\'{e}}nez{-}Ruiz, Ernesto and Llavori, Rafael Berlanga},title={A View-Based Methodology for Collaborative Ontology Engineering: An
Approach for Complex Applications (VIMethCOE)},booktitle={15th {IEEE} International Workshops on Enabling Technologies: Infrastructures
for Collaborative Enterprises (WETICE 2006), 26-28 June 2006, Manchester,
United Kingdom},pages={376--381},publisher={{IEEE} Computer Society},year={2006},url={https://doi.org/10.1109/WETICE.2006.13},doi={10.1109/WETICE.2006.13},}