Ernesto Jimenez-Ruiz

Researcher - Centre for Scalable Data Access

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Email ernestoj@ifi.uio.no

Room 8165

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Visiting address Ole Johan Dahls hus Gaustadalleen 23 B 0373 OSLO

Postal address Postboks 1080 Blindern 0316 OSLO

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Academic interests

My research has covered several areas, including bio-medical information processing and integration, ontology reuse, ontology versioning and evolution, ontology alignment, and text mining. I have also designed novel algorithmic techniques and developed java-based tools to serve as a proof of concept of the conducted theoretical research. My current research interest focuses on the application of Semantic Web technologies to Data Analytics.

PhD Students

Erik Bryhn Myklebust. Topic: Ecotoxicological Effect Prediction using Knowledge Graphs and Deep Learning. More information.

Teaching (2017-2018)

Semantic Technologies: INF3580 and INF4580

Short bio

Since April 2018 I am also a Senior Research Associate at The Alan Turing Institute in London (UK) working in the Artificial Intelligence for Data Analytics (AIDA) project. I will be physically working in UK from July 2018.

In September 2016 I moved to Oslo to work as a researcher in the Centre for Scalable Data Access (SIRIUS) and the Logic and Intelligent Data (LogID) group led by Prof. Arild Waaler and Prof. Martin Giese, respectively.

In May 2015 Alessandro Solimando, a PhD student from the University of Genoa I was co-supervising together with Prof. Giovana Guerrini, defended his thesis on "Change Management in the Traditional and Semantic Web"

In January 2011, I joined the Information Systems group (University of Oxford, UK) led by Prof. Georg Gottlob and Prof. Ian Horrocks as a Research Assistant to work in the EPSRC project LogMap. Later in 2012 I worked as a researcher in the FP7 IP project Optique.

I got the doctor degree with honors in Computer Science from the University Jaume I of Castellon (Spain) under the supervision of Dr. Rafael Berlanga Llavori (University Jaume I) and Dr. Bernardo Cuenca Grau (University of Oxford). The Jaume I University awarded a Premio extraordinario de doctorado (roughly translated as a Extraordinary Doctoral Award) to my doctoral thesis (Engineering category 2010-2011). During my PhD I visited several leading institutions in the UK, including the Text Mining Group at the European Bio-informatics Institute in Cambridge; the Information Management Group at University of Manchester; and the Oxford University Computing Laboratory (now Department of Computer Science).

Tags: semantic web, semantic technologies, ontologies, ontology alignment

My complete list of publications can be found here. The PDF of most of the articles are available online.

Algergawy, Alsayed; Faria, Daniel; Ferrara, Alfio; Fundulaki, Irini; Harrow, Ian; Hertling, Sven; Jimenez-Ruiz, Ernesto; Karam, Naouel; Khiat, Abderrahmane; Lambrix, Patrick; Li, Huanyu; Montanelli, Stefano; Paulheim, Heiko; Pesquita, Catia; Saveta, Tzanina; Shvaiko, Pavel; Splendiani, Andrea; Thiéblin, Elodie; Trojahn, Cassia; Vataščinová, Jana; Zamazal, Ondrej & Zhou, Lu (2019). Results of the ontology alignment evaluation initiative 2019. CEUR Workshop Proceedings. ISSN 1613-0073. 2536, s 46- 85
Chen, Jiaoyan; Jimenez-Ruiz, Ernesto & Horrocks, Ian (2019). Canonicalizing Knowledge Base Literals. Lecture Notes in Computer Science (LNCS). ISSN 0302-9743. 11778 LNCS, s 110- 127 . doi: 10.1007/978-3-030-30793-6_7 Full text in Research Archive.
Chen, Jiaoyan; Jimenez-Ruiz, Ernesto; Horrocks, Ian & Sutton, Charles (2019). ColNet: Embedding the Semantics of Web Tables for Column Type Prediction. PROCEEDINGS OF THE THIRTIETH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE AND THE TWENTY-EIGHTH INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE. ISSN 2159-5399. 30, s 29- 36 . doi: 10.1609/aaai.v33i01.330129 Show summary
Automatically annotating column types with knowledge base (KB) concepts is a critical task to gain a basic understanding of web tables. Current methods rely on either table metadata like column name or entity correspondences of cells in the KB, and may fail to deal with growing web tables with incomplete meta information. In this paper we propose a neural network based column type annotation framework named ColNet which is able to integrate KB reasoning and lookup with machine learning and can automatically train Convolutional Neural Networks for prediction. The prediction model not only considers the contextual semantics within a cell using word representation, but also embeds the semantics of a column by learning locality features from multiple cells. The method is evaluated with DBPedia and two different web table datasets, T2Dv2 from the general Web and Limaye from Wikipedia pages, and achieves higher performance than the state-of-the-art approaches.
Chen, Jiaoyan; Jimenez-Ruiz, Ernesto; Horrocks, Ian & Sutton, Charles (2019). Learning semantic annotations for tabular data. IJCAI International Joint Conference on Artificial Intelligence. ISSN 1045-0823. 2019-August, s 2088- 2094 Full text in Research Archive.
Chen, Jiaoyan; Jimenez-Ruiz, Ernesto; Horrocks, Ian & Sutton, Charles A (2019). Learning Semantic Annotations for Tabular Data, In Sarit Kraus (ed.), Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence, {IJCAI} 2019, Macao, China, August 10-16, 2019. International Joint Conferences on Artificial Intelligence. ISBN 978-0-9992411-4-1. Conference paper. s 2088 - 2094
Harrow, Ian; Balakrishnan, Rama; Jimenez-Ruiz, Ernesto; Jupp, Simon; Lomax, Jane; Reed, Jane; Romacker, Martin; Senger, Christian; Splendiani, Andrea; Wilson, Jabe & Woollard, Peter (2019). Ontology mapping for semantically enabled applications. Drug Discovery Today. ISSN 1359-6446. 24(10), s 2068- 2075 . doi: 10.1016/j.drudis.2019.05.020
Holter, Ole Magnus; Myklebust, Erik B; Chen, Jiaoyan & Jimenez-Ruiz, Ernesto (2019). Embedding OWL ontologies with OWL2Vec. CEUR Workshop Proceedings. ISSN 1613-0073. 2456, s 33- 36 Full text in Research Archive. Show summary
In this paper, we present a preliminary study to compute embeddings for OWL 2 ontologies by projecting the ontology axioms into a graph and performing (random) walks over the ontology graph to create a corpus of sentences. This corpus is then given to a neural language model to create concept embeddings. The conducted preliminary evaluation shows promising results.
Huanyu, Li; Dragisic, Zlatan; Faria, Daniel; Ivanova, Valentina; Jimenez-Ruiz, Ernesto; Lambrix, Patrick & Pesquita, Catia (2019). User validation in ontology alignment: functional assessment and impact. Knowledge engineering review (Print). ISSN 0269-8889. 34 . doi: 10.1017/S0269888919000080 Full text in Research Archive.
Jimenez-Ruiz, Ernesto (2019). LogMap Family Participation in the OAEI 2019, In Pavel Shvaiko; Jérôme Euzenat; Ernesto Jimenez-Ruiz; Oktie Hassanzadeh & Cassia Trojahn (ed.), Proceedings of the 14th International Workshop on Ontology Matching. CEUR-WS.org. Challenge paper. Full text in Research Archive.
Klungre, Vidar Norstein; Soylu, Ahmet; Jimenez-Ruiz, Ernesto; Kharlamov, Evgeny & Giese, Martin (2019). Query Extension Suggestions for Visual Query Systems Through Ontology Projection and Indexing. New generation computing. ISSN 0288-3635. 37(4), s 361- 392 . doi: 10.1007/s00354-019-00071-1 Full text in Research Archive.
Myklebust, Erik Bryhn; Jimenez-Ruiz, Ernesto; Chen, Jiaoyan; Wolf, Raoul & Tollefsen, Knut-Erik (2019). Knowledge Graph Embedding for Ecotoxicological Effect Prediction, In Chiara Ghidini; Olaf Hartig; Maria Maleshkova; Vojtěch Svátek; Isabel Cruz; Aidan Hogan; Jie Song; Maxime Lefrançois & Fabien Gandon (ed.), The Semantic Web – ISWC 2019. Springer. ISBN 978-3-030-30795-0. 30. s 490 - 506 Show summary
Exploring the effects a chemical compound has on a species takes a considerable experimental effort. Appropriate methods for estimating and suggesting new effects can dramatically reduce the work needed to be done by a laboratory. In this paper we explore the suitability of using a knowledge graph embedding approach for ecotoxicological effect prediction. A knowledge graph has been constructed from publicly available data sets, including a species taxonomy and chemical classification and similarity. The publicly available effect data is integrated to the knowledge graph using ontology alignment techniques. Our experimental results show that the knowledge graph based approach improves the selected baselines.
Agibetov, Asan; Jimenez-Ruiz, Ernesto; Ondrésik, Marta; Solimando, Alessandro; Banerjee, Imon; Guerrini, Giovanna; Catalano, Chiara E; Oliveira, Joaquim M.; Patanè, Giuseppe; Reis, Rui L. & Spagnuolo, Michela (2018). Supporting shared hypothesis testing in the biomedical domain. Journal of Biomedical Semantics. ISSN 2041-1480. 9:9, s 1- 22 . doi: 10.1186/s13326-018-0177-x Full text in Research Archive.
Algergawy, Alsayed; Cheatham, Michelle; Faria, Daniel; Ferrara, Alfio; Fundulaki, Irini; Harrow, Ian; Hertling, Sven; Jimenez-Ruiz, Ernesto; Karam, Naouel; Khiat, Abderrahmane; Lambrix, Patrick; Li, Huanyu; Montanelli, Stefano; Paulheim, Heiko; Pesquita, Catia; Saveta, Tzanina; Schmidt, Daniela; Shvaiko, Pavel; Splendiani, Andrea; Thiéblin, Elodie; Trojahn, Cassia; Vataščinová, Jana; Zamazal, Ondrej & Zhou, Lu (2018). Results of the ontology alignment evaluation initiative 2018. CEUR Workshop Proceedings. ISSN 1613-0073. 2288, s 76- 116
Jimenez-Ruiz, Ernesto; Agibetov, Asan; Samwald, Matthias & Cross, Valerie (2018). We divide, you conquer: From large-scale ontology alignment to manageable subtasks with a lexical index and neural embeddings. CEUR Workshop Proceedings. ISSN 1613-0073. 2180, s 1- 12 Full text in Research Archive.
Jimenez-Ruiz, Ernesto; Saveta, Tzanina; Zamazal, Ondrej; Hertling, Sven; Roder, Michael; Fundulaki, Irini; Ngomo, Axel-Cyrille Ngonga; Sherif, Mostafa Hashem; Annane, Amina; Bellahsene, Zohra; Ben Yahia, Sadok; Diallo, Gayo; Faria, Daniel; Kachroudi, Marouen; Khiat, Abderrahmane; Lambrix, Patrick; Li, Huanyu; Mackeprang, Maximilian; Mohammadi, Majid; Rybinski, Maciej; Balasubramani, Booma Sowkarthiga & Trojahn, Cassia (2018). Introducing the HOBBIT platform into the Ontology Alignment Evaluation campaign. CEUR Workshop Proceedings. ISSN 1613-0073. 2288, s 49- 60
Kharlamov, Evgeny; Skjæveland, Martin G; Hovland, Dag; Mailis, Theofilos; Jimenez-Ruiz, Ernesto; Xiao, Guohui; Soylu, Ahmet; Horrocks, Ian & Waaler, Arild (2018). Finding Data Should be Easier than Finding Oil, In Naoki Abe; Huan Liu; Xiaohua Hu; Nesreen Ahmed; Mu Qiao; Yang Song; Donald Kossmann; Bing Liu; Kisung Lee; Jiliang Tang; Jingrui He & Jeffrey Saltz (ed.), 2018 IEEE International Conference on Big Data (Big Data), Seattle, 10-13 Dec. 2018. IEEE. ISBN 978-1-5386-5035-6. artikkel. Full text in Research Archive. Show summary
The competitiveness of modern enterprises heavily depends on their ability to make the right business decisions by relying on efficient and timely analysis of the right business critical data. In large and data intensive companies such as Equinor, a Norwegian multinational oil and gas company with more than 20,000 employees, gathering such data is not a trivial task due to the growing size and complexity of corporate information sources. As a result, the data gathering task is often the most time-consuming part of the decision making process, in particular when it comes to the work processes of Equinor’s Exploration geologists that should find in a timely manner New exploitable accumulations of oil or gas in given areas by analysing data about these areas. In this work we present our experience in addressing this data challenge tast at Equinor. We have developed and deployed at Equinor a semantic data access system that relies on the Ontology Based Data Access (OBDA) approach. Our system is based on our solid theoretical contributions and has been extensively evaluated at Equinor
Pinkel, Christoph; Binning, Carsten; Jimenez-Ruiz, Ernesto; Kharlamov, Evgeny; May, Wolfgang; Nikolov, Andriy; Bastinos, Ana Sasa; Skjæveland, Martin G; Solimando, Alessandro; Taheriyan, Mohsen; Heupel, Christian & Horrocks, Ian (2018). RODI: Benchmarking Relational-to-Ontology Mapping Generation Quality. Semantic Web Journal. ISSN 1570-0844. 9(1), s 25- 52 . doi: 10.3233/SW-170268 Full text in Research Archive.
Achichi, Manel; Cheatham, Michelle; Dragisic, Zlatan; Euzenat, Jerome; Faria, Daniel; Ferrara, Alfio; Flouris, Giorgos; Fundulaki, Irini; Harrow, Ian; Ivanova, Valentina; Jimenez-Ruiz, Ernesto; Kuss, Elena; Lambrix, Patrick; Leopold, Henrik; Li, Huanyu; Meilicke, Christian; Montanelli, Stefano; Pesquita, Catia; Saveta, Tzanina; Shvaiko, Pavel; Splendiani, Andrea; Stuckenschmidt, Heiner; Todorov, Konstantin; Trojahn, Cassia & Zamazal, Ondrej (2017). Results of the ontology alignment evaluation initiative 2016. CEUR Workshop Proceedings. ISSN 1613-0073. 1766, s 73- 129
Harrow, Ian; Jimenez-Ruiz, Ernesto; Splendiani, Andrea; Romacker, Martin; Woollard, Peter; Markel, Scott; Alam-Faruque, Yasmin; Koch, Martin; Malone, James & Waaler, Arild Torolv Søetorp (2017). Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. Journal of Biomedical Semantics. ISSN 2041-1480. 8(1), s 1- 13 . doi: 10.1186/s13326-017-0162-9 Full text in Research Archive.
Jimenez-Ruiz, Ernesto; Carapella, Valentina; Lukaschuk, Elena; Aung, Nay; Fung, Kenneth; Paiva, Jose; Sanghvi, Mihir; Neubauer, Stefan; Petersen, Steffen; Horrocks, Ian & Piechnik, Stefan (2017). Towards the creation of the cardiovascular magnetic resonance quality assessment ontology (CMR-QA). CEUR Workshop Proceedings. ISSN 1613-0073. 1795
Jimenez-Ruiz, Ernesto; Grau, B Cuenca & Cross, V (2017). LogMap family participation in the OAEI 2017. CEUR Workshop Proceedings. ISSN 1613-0073. 2032, s 153- 157
Kharlamov, Evgeny; Hovland, Dag; Skjæveland, Martin G; Bilidas, Dimitris; Jimenez-Ruiz, Ernesto; Xiao, Guohui; Soylu, Ahmet; Lanti, Davide; Rezk, Martin; Zheleznyakov, Dmitriy; Giese, Martin; Lie, Hallstein; Ioannidis, Yannis; Kotidis, Yannis; Koubarakis, Manolis & Waaler, Arild Torolv Søetorp (2017). Ontology Based Data Access in Statoil. Journal of Web Semantics. ISSN 1570-8268. 44, s 3- 36 . doi: 10.1016/j.websem.2017.05.005 Full text in Research Archive.
Kudama, Shahad; Berlanga, Rafael & Jimenez-Ruiz, Ernesto (2017). Enriching the Human Phenotype Ontology with inferred axioms from textual descriptions. CEUR Workshop Proceedings. ISSN 1613-0073. 2042, s 1- 5
Solimando, Alessandro; Jimenez-Ruiz, Ernesto & Guerrini, Giovanna (2017). Minimizing Conservativity Violations in Ontology Alignments: Algorithms and Evaluation. Knowledge and Information Systems. ISSN 0219-1377. 51(3) . doi: 10.1007/s10115-016-0983-3
Soylu, Ahmet; Giese, Martin; Schlatte, Rudolf; Jimenez-Ruiz, Ernesto; Kharlamov, Evgeny; Özçep, Özgür; Neuenstadt, Christian & Brandt, Sebastian (2017). Querying industrial stream-temporal data: An ontology-based visual approach. Journal of Ambient Intelligence and Smart Environments. ISSN 1876-1364. 9(1), s 77- 95 . doi: 10.3233/AIS-160415 Full text in Research Archive.
Soylu, Ahmet; Kharlamov, Evgeny; Zheleznyakov, Dmitriy; Jimenez-Ruiz, Ernesto; Giese, Martin; Skjæveland, Martin G; Hovland, Dag; Schlatte, Rudolf; Brandt, Sebastian; Lie, Hallstein & Horrocks, Ian (2017). OptiqueVQS: a Visual Query System over Ontologies for Industry. Semantic Web Journal. ISSN 1570-0844. s 1- 28 Full text in Research Archive.
Achichi, Manel; Cheatham, Michelle; Dragisic, Zlatan; Euzenat, Jerome; Faria, Daniel; Ferrara, Alfio; Flouris, Giorgos; Fundulaki, Irini; Harrow, Ian; Ivanova, Valentina; Jimenez-Ruiz, Ernesto; Kuss, Elena; Lambrix, Patrick; Leopold, Henrik; Li, Huanyu; Meilicke, Christian; Montanelli, Stefano; Pesquita, Catia; Saveta, Tzanina; Shvaiko, Pavel; Splendiani, Andrea; Stuckenschmidt, Heiner; Todorov, Konstantin; Trojahn, Cassia & Zamazal, Ondrej (2016). Results of the Ontology Alignment Evaluation Initiative 2016. CEUR Workshop Proceedings. ISSN 1613-0073. 1766, s 73- 129
Jimenez-Ruiz, Ernesto; Cuenca Grau, Bernardo Cuenca & Cross, Valerie V. (2016). LogMap family participation in the OAEI 2016. CEUR Workshop Proceedings. ISSN 1613-0073. 1766, s 185- 189
Kharlamov, Evgeny; Brandt, Sebastian; Giese, Martin; Jimenez-Ruiz, Ernesto; Kotidis, Yannis; Lamparter, Steffen; Mailis, Theofilis P.; Neuenstadt, Christian; Özcep, Özgür; Pinkel, Christoph; Soylu, Ahmet; Svingos, Christoforos; Zheleznyakov, Dmitriy; Horrocks, Ian; Ioannidis, Yannis; Möller, Ralf & Waaler, Arild (2016). Enabling semantic access to static and streaming distributed data with optique: demo, In Avigdor Gal; Matthias Weidlich; Vana Kalogeraki & Nalini Venkasubramanian (ed.), Proceedings of the 10th ACM International Conference on Distributed and Event-based Systems, DEBS '16, Irvine, CA,USA, June 20 -24. ACM Publications. ISBN 978-1-4503-4021-2. Chapter. s 350 - 353
Kharlamov, Evgeny; Mailis, Theofilis P.; Bereta, Konstantina; Bilidas, Dimitris; Brandt, Sebastian; Jimenez-Ruiz, Ernesto; Lamparter, Steffen; Neuenstadt, Christian; Özcep, Özgür; Soylu, Ahmet; Svingos, Christoforos; Xiao, Guohui; Zheleznyakov, Dmitriy; Calvanese, Diego; Horrocks, Ian; Giese, Martin; Ioannidis, Yannis; Kotidis, Yannis; Möller, Ralf & Waaler, Arild (2016). A Semantic Approach to Polystores, In James Joshi (ed.), Proceedings 2016 IEEE International Conference on Big Data. IEEE. ISBN 978-1-4673-9005-7. KAPITTEL. s 2565 - 2573
Soylu, Ahmet; Giese, Martin; Jimenez-Ruiz, Ernesto; Kharlamov, Evgeny; Schlatte, Rudolf; Neuenstadt, Christian; Ozcep, Ozgur; Lie, Hallstein; Klungre, Vidar Norstein; Brandt, Sebastian & Horrocks, Ian (2016). Ontology-based visual querying with OptiqueVQS: Statoil and Siemens cases. CEUR Workshop Proceedings. ISSN 1613-0073. 1818, s 34- 39

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Shvaiko, Pavel; Euzenat, Jérôme; Jimenez-Ruiz, Ernesto; Hassanzadeh, Oktie & Trojahn, Cassia (ed.) (2019). Proceedings of the 14th International Workshop on Ontology Matching. CEUR-WS.org. 202 s.
Shvaiko, Pavel; Euzenat, Jérôme; Jimenez-Ruiz, Ernesto; Cheatham, Michelle & Hassanzadeh, Oktie (ed.) (2018). Proceedings of the 13th International Workshop on Ontology Matching. CEUR-WS.org. 227 s.
Dragoni, Mauro; Poveda-Villalon, Maria & Jimenez-Ruiz, Ernesto (ed.) (2017). OWL: Experiences and Directions - Reasoner Evaluation. Springer. ISBN 978-3-319-54626-1. 153 s.

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Myklebust, Erik Bryhn; Jimenez-Ruiz, Ernesto; Chen, Jiaoyan; Wolf, Raoul & Tollefsen, Knut-Erik (2019). Ecotoxicological Effect Prediction Using Knowledge Graph Embedding.
Myklebust, Erik Bryhn; Jimenez-Ruiz, Ernesto; Chen, Jiaoyan; Wolf, Raoul & Tollefsen, Knut-Erik (2019). Knowledge Graph Embedding for Ecotoxicological Effect Prediction.
Myklebust, Erik Bryhn; Jimenez-Ruiz, Ernesto; Wolf, Raoul; Rudjord, Zofia Czyczula & Tollefsen, Knut-Erik (2019). Integrating semantic technologies in environmental risk assessment: A vision..
Dragoni, Mauro; Poveda-Villalon, Maria & Jimenez-Ruiz, Ernesto (2017). Preface. Lecture Notes in Computer Science (LNCS). ISSN 0302-9743. 10161 LNCS, s I- IX
Jimenez-Ruiz, Ernesto; Hovland, Dag; Slaughter, Laura; Håndstad, Tony & Waaler, Arild (2017). On adopting ontology alignment techniques within the phenotype acquisition process. CEUR Workshop Proceedings. ISSN 1613-0073. 2042, s 1- 2
Pereira, Sunny; Cross, Valerie & Jimenez-Ruiz, Ernesto (2017). On partitioning for ontology alignment. CEUR Workshop Proceedings. ISSN 1613-0073. 2032, s 219- 220
Pereira, Sunny; Cross, Valerie & Jimenez-Ruiz, Ernesto (2017). On partitioning for ontology alignment. CEUR Workshop Proceedings. ISSN 1613-0073. 1963, s 1- 4
Soylu, Ahmet; Giese, Martin; Jimenez-Ruiz, Ernesto; Kharlamov, Evgeny; Schlatte, Rudolf; Neuenstadt, Christian; Özcep, Özgür; Lie, Hallstein; Klungre, Vidar Norstein; Brandt, Sebastian & Horrocks, Ian (2016). Ontology-based Visual Querying with OptiqueVQS: Statoil and Siemens Cases. CEUR Workshop Proceedings. ISSN 1613-0073. 1818

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Published Oct. 3, 2016 1:08 PM - Last modified Sep. 11, 2019 3:39 PM

Ernesto Jimenez-Ruiz

Academic interests

PhD Students

Teaching (2017-2018)

Short bio

Publications

Projects

Research groups

Visiting address

Mail address

Phone, fax, e-mail

Ernesto Jimenez-Ruiz

Academic interests

PhD Students

Teaching (2017-2018)

Short bio

Publications

Projects

Research groups

Systems

Evaluation