Ernesto Jiménez-Ruiz

• PhD in Computer Science
• Lecturer at City, University of London

Knowledge graphs (KGs) feature ever more frequently as symbolic components in neurosymbolic research and systems. But even though a central concern of neurosymbolic artificial intelligence is to combine neural learning with symbolic reasoning, relatively little neurosymbolic research focuses on leveraging the logical representation and reasoning ca...

Tabular data plays a pivotal role in various fields, making it a popular format for data manipulation and exchange, particularly on the web. The interpretation, extraction, and processing of tabular information are invaluable for knowledge-intensive applications. Notably, significant efforts have been invested in annotating tabular data with ontolo...

This poster paper describes the ongoing research project for the creation of a use-case-driven Knowledge Graph resource tailored to the needs of teaching education in Knowledge Graphs (KGs). We gather resources related to KG courses from lectures offered by the Semantic Web community, with the help of the COST Action Distributed Knowledge Graphs an...

Ontology alignment is integral to achieving semantic interoperability as the number of available ontologies covering intersecting domains is increasing. This paper proposes OWL2Vec4OA, an extension of the ontology embedding system OWL2Vec*. While OWL2Vec* has emerged as a powerful technique for ontology embedding, it currently lacks a mechanism to...

The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and gra...

NeSy4VRD is a multifaceted resource designed to support the development of neurosymbolic AI (NeSy) research. NeSy4VRD re-establishes public access to the images of the VRD dataset and couples them with an extensively revised, quality-improved version of the VRD visual relationship annotations. Crucially, NeSy4VRD provides a well-aligned, companion...

Automating ontology construction and curation is an important but challenging task in knowledge engineering and artificial intelligence. Prediction by machine learning techniques such as contextual semantic embedding is a promising direction, but the relevant research is still preliminary especially for expressive ontologies in Web Ontology Languag...

Pre-trained language models (LMs) have made significant advances in various Natural Language Processing (NLP) domains, but it is unclear to what extent they can infer formal semantics in ontologies, which are often used to represent conceptual knowledge and serve as the schema of data graphs. To investigate an LM's knowledge of ontologies, we propo...

The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity and use different evaluation modalities. The OAEI 2023 campaign offered 15 tracks and was attended by 16 participants. This paper is an overall...

Data wrangling tasks such as obtaining and linking data from various sources, transforming data formats, and correcting erroneous records, can constitute up to 80% of typical data engineering work. Despite the rise of machine learning and artificial intelligence, data wrangling remains a tedious and manual task. We introduce AI assistants, a class...

Extrapolation of adverse biological (toxic) effects of chemicals is an important contribution to expand available hazard data in (eco)toxicology without the use of animals in laboratory experiments. In this work, we extrapolate effects based on a knowledge graph (KG) consisting of the most relevant effect data as domain-specific background knowledg...

Automatic knowledge graph (KG) construction is widely used in industry for data integration and access, and there are several approaches to enable (semi-)automatic construction of knowledge graphs. One important approach is to map the raw data to a given knowledge graph schema, often a domain ontology, and construct the entities and properties acco...

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation...

The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity and use different evaluation modalities. The OAEI 2022 campaign offered 14 tracks and was attended by 18 participants. This paper is an overall...

Industrial analytics that includes among others equipment diagnosis and anomaly detection heavily relies on integration of heterogeneous production data. Knowledge Graphs (KGs) as the data format and ontologies as the unified data schemata are a prominent solution that offers high quality data integration and a convenient and standardised way to ex...

In the context of Industry 4.0 [1] and Internet of Things (IoT) [2], modern manufacturing and production [3, 4] lines are equipped with software systems and sensors that constantly collect and send a high volume of data.

Industrial analytics that includes among others equipment diagnosis and anomaly detection heavily relies on integration of heterogeneous production data. Knowledge Graphs (KGs) as the data format and ontologies as the unified data schemata are a prominent solution that offers high quality data integration and a convenient and standardised way to ex...

Introduction. Modern industry witnesses a fast growth in volume and complexity of heterogeneous manufacturing (big) data [1, 2] thanks to the technological advances of Industry 4.0 [1, 3], including development in perception, communication, processing, and actuation.

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be...

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation...

We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment. We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction. We have evaluated nine knowledge graph embedding models from a selection of geometric, decomposition, and convolutional models on thi...

SemTab 2021 was the third edition of the Semantic Web Challenge on Tabular Data to Knowledge Graph Matching, successfully collocated with the 20th International Semantic Web Conference (ISWC) and the 16th Ontology Matching (OM) Workshop. SemTab provides a common framework to conduct a systematic evaluation of state-of-the-art systems.

Automating ontology curation is a crucial task in knowledge engineering. Prediction by machine learning techniques such as semantic embedding is a promising direction, but the relevant research is still preliminary. In this paper, we present a class subsumption prediction method named BERTSubs, which uses the pre-trained language model BERT to comp...

Data wrangling tasks such as obtaining and linking data from various sources, transforming data formats, and correcting erroneous records, can constitute up to 80% of typical data engineering work. Despite the rise of machine learning and artificial intelligence, data wrangling remains a tedious and manual task. We introduce AI assistants , a cla...

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be...

We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment. We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction. We have evaluated nine knowledge graph embedding models from a selection of geometric, decomposition, and convolutional models on thi...

Various knowledge bases (KBs) have been constructed via information extraction from encyclopedias, text and tables, as well as alignment of multiple sources. Their usefulness and usability is often limited by quality issues. One common issue is the presence of erroneous assertions and alignments, often caused by lexical or semantic confusion. We st...

The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2021 campaign offered 13 tracks and w...

Much information is conveyed within tables, which can be semantically annotated by humans or (semi)automatic approaches. Nevertheless, many applications cannot take full advantage of semantic annotations because of the low quality. A few methodologies exist for the quality assessment of semantic annotation of tabular data, but they do not automatic...

Semantic embedding of knowledge graphs has been widely studied and used for prediction and statistical analysis tasks across various domains such as Natural Language Processing and the Semantic Web. However, less attention has been paid to developing robust methods for embedding OWL (Web Ontology Language) ontologies, which contain richer semantic...

Ontology alignment plays a critical role in knowledge integration and has been widely investigated in the past decades. State of the art systems, however, still have considerable room for performance improvement especially in dealing with new (industrial) alignment tasks. In this paper we present a machine learning based extension to traditional on...

This paper describes STILTool, an open-source tool for the automatic evaluation of the quality of semantic annotations computed by semantic table interpretation approaches. STILTool provides a graphical interface allowing users to analyse the correctness of the annotations of tabular data. The tool also provides a set of statistics in order to iden...

In this paper, we present a novel unsupervised and automatic approach for Semantic Table Interpretation. The technique presented is performed against DBpedia and Wikidata, and it can be easily adapted to any other Knowledge Graph (KG). Moreover, we provide a tool (LamAPI) that allows to efficiently fetch data needed for Semantic Table Interpretatio...

Table annotation is a key task to improve querying the Web and support the Knowledge Graph population from legacy sources (tables). Last year, the SemTab challenge was introduced to unify different efforts to evaluate table annotation algorithms by providing a common interface and several general-purpose datasets as a ground truth. The SemTab datas...

Semantic embedding of knowledge graphs has been widely studied and used for prediction and statistical analysis tasks across various domains such as Natural Language Processing and the Semantic Web. However, less attention has been paid to developing robust methods for embedding OWL (Web Ontology Language) ontologies. In this paper, we propose a la...

The quality of a dataset used for evaluating data linking methods, techniques, and tools depends on the availability of a set of mappings, called reference alignment , that is known to be correct. In particular, it is crucial that mappings effectively represent relations between pairs of entities that are indeed similar due to the fact that they de...

Tabular data to Knowledge Graph matching is the process of assigning semantic tags from knowledge graphs (e.g., Wikidata or DB-pedia) to the elements of a table. This task is a challenging problem for various reasons, including the lack of metadata (e.g., table and column names), the noisiness, heterogeneity, incompleteness and ambiguity in the dat...

Tabular data to Knowledge Graph matching is the process of assigning semantic tags from knowledge graphs (e.g., Wikidata or DBpedia) to the elements of a table. This task is a challenging problem for various reasons, including the lack of metadata (e.g., table and column names), the noisiness, heterogeneity, incompleteness and ambiguity in the data...

Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In this paper we present an approach that combines a neural embedding model and logic-based modules to accurately divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation usin...

Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In this paper we present an approach that combines a neural embedding model and logic-based modules to accurately divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation usin...

The usefulness and usability of knowledge bases (KBs) is often limited by quality issues. One common issue is the presence of erroneous assertions, often caused by lexical or semantic confusion. We study the problem of correcting such assertions, and present a general correction framework which combines lexical matching, semantic embedding, soft co...

15th International Workshop on Ontology Matching co-located with the 19th International Semantic Web Conference (ISWC 2020)

User validation is one of the challenges facing the ontology alignment community, as there are limits to the quality of the alignments produced by automated alignment algorithms. In this paper we present a broad study on user validation of ontology alignments that encompasses three distinct but interrelated aspects: the profile of the user, the ser...

The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consen...

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 pred...

Ontology-based knowledge bases (KBs) like DBpedia are very valuable resources, but their usefulness and usability are limited by various quality issues. One such issue is the use of string literals instead of semantically typed entities. In this paper we study the automated canonicalization of such literals, i.e., replacing the literal with an exis...

Experimental effort and animal welfare are concerns when exploring the effects a compound has on an organism. Appropriate methods for extrapolating chemical effects can further mitigate these challenges. In this paper we present the efforts to (i) (pre)process and gather data from public and private sources, varying from tabular files to SPARQL end...

Ontology-based visual query formulation is a viable alternative to tex-tual query editors in the Semantic Web domain for extracting data from structured data sources in terms of the skills and knowledge required. A visual query system is at any moment responsible for providing the user with query extension suggestions ; however, suggestions leading...

The usefulness of tabular data such as web tables critically depends on understanding their semantics. This study focuses on column type prediction for tables without any meta data. Unlike traditional lexical matching-based methods, we propose a deep prediction model that can fully exploit a table’s contextual semantics, including table locality fe...

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...

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 pred...

Ontology-based knowledge bases (KBs) like DBpedia are very valuable resources, but their usefulness and usability is limited by various quality issues. One such issue is the use of string literals instead of semantically typed entities. In this paper we study the automated canonicalization of such literals, i.e., replacing the literal with an exist...

The usefulness of tabular data such as web tables critically depends on understanding their semantics. This study focuses on column type prediction for tables without any meta data. Unlike traditional lexical matching-based methods, we propose a deep prediction model that can fully exploit a table's contextual semantics, including table locality fe...

In this review, we provide a summary of recent progress in ontology mapping at a crucial time when biomedical research is under a deluge of an increasing amount and variety of data. This is particularly important for realising the full potential of semantically enabled or enriched applications and for meaningful insights, such as drug discovery, us...

Transfer learning which aims at utilizing knowledge learned from one problem (source domain) to solve another different but related problem (target domain) has attracted wide research attentions. However, the current transfer learning methods are mostly uninterpretable, especially to people without ML expertise. In this extended abstract, we brief...

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...

This paper describes the Ontology Alignment Evaluation Initiative 2017.5 pre-campaign. Like in 2012, when we transitioned the evaluation to the SEALS platform, we have also conducted a pre-campaign to assess the feasibility of moving to the HOBBIT platform. We report the experiences of this pre-campaign and discuss the future steps for the OAEI.

The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consen...

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...

Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In the paper we present an approach that combines a lexical index, a neural embedding model and locality modules to effectively divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive e...

Background: Pathogenesis of inflammatory diseases can be tracked by studying the causality relationships among the factors contributing to its development. We could, for instance, hypothesize on the connections of the pathogenesis outcomes to the observed conditions. And to prove such causal hypotheses we would need to have the full understanding...

Background The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery...

An important application of semantic technologies in industry has been the formalisation of information models using OWL 2 ontologies and the use of RDF for storing and exchanging application data. Moreover, legacy data can be virtualised as RDF using ontologies following the ontology-based data access (OBDA) approach. In all these applications, it...

Value creation in an organisation is a time-sensitive and data-intensive process, yet it is often delayed and bounded by the reliance on IT experts extracting data for domain experts. Hence, there is a need for providing people who are not professional developers with the flexibility to pose relatively complex and ad hoc queries in an easy and intu...

In order to enable interoperability between ontology-based systems, ontology matching techniques have been proposed. However, when the generated mappings lead to undesired logical consequences, their usefulness may be diminished. In this paper, we present an approach to detect and minimize the violations of the so-called conservativity principle wh...

Ontology Based Data Access (OBDA) is a prominent approach to query databases which uses an ontology to expose data in a conceptually clear manner by abstracting away from the technical schema-level details of the underlying data. The ontology is ‘connected’ to the data via mappings that allow to automatically translate queries posed over the ontolo...

s. This approach crucially relies on useful mappings to relate the ontology and the data, the latter being typically stored in relational databases. A number of systems to support the construction of such mappings have recently been developed. A generic and effective benchmark for reliable and comparable evaluation of the practical utility of such...

An increasing number of sensors are being deployed in business-critical environments, systems, and equipment; and stream a vast amount of data. The operational efficiency and effectiveness of business processes rely on domain experts' agility in interpreting data into actionable business information. A domain expert has extensive domain knowledge b...

This book constitutes the thoroughly refereed conference proceedings of the 13International Workshop on OWL: Experiences and Directions, OWLED 2016, and the 5th International Workshop on OWL: Reasoner Evaluation, ORE 2016, held in Bologna, Italy in November 20, 2016. The Workshops were co-located with the 20th International Conference on Knowledge...