Jesualdo Tomas Fernandez-Breis

• PhD in Computer Science
• Professor at University of Murcia

Ontologies play a vital role in organizing and constructing knowledge across various domains, enabling effective knowledge management and sharing. The development of domain-specific ontologies, such as the ONTO-TDM ontology for teaching domain modeling, is essential for providing a comprehensive and standardized representation of knowledge within a...

Knowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases but also has a determinative genome location aspect. Here, we exploit these location and functional aspects together to develop n...

Particulate matter monitoring and climate change mitigation actions have been promoted due to the Paris Agreement because of their impact on health and high mortality rate. High-resolution networks based on hyperlocal IoT sensors can play a fundamental role in improving data quality. In this context, hyperlocal refers to air quality IoT systems tha...

According to the Air Quality Directive 2008/50/EC, air quality zoning divides a territory into air quality zones where pollution and citizen exposure are similar and can be monitored using similar strategies. However, there is no standardized computational methodology to solve this problem, and only a few experiences in the Comunidad of Madrid base...

Repetitive sequences represent about 45% of the human genome. Some are transposable elements (TEs) with the ability to change their position in the genome, creating genetic variability both as insertions or deletions, with potential pathogenic consequences. We used long-read nanopore sequencing to identify TE variants in the genomes of 24 patients...

The World Health Organization has estimated that air pollution will be one of the most significant challenges related to the environment in the following years, and air quality monitoring and climate change mitigation actions have been promoted due to the Paris Agreement because of their impact on mortality risk. Thus, generating a methodology that...

In the field of Medicine, Process Mining (PM) can be used to analyse healthcare-related data to infer the underlying diagnostic, treatment, and management processes. The PM paradigm provides techniques and tools to obtain information about the processes carried out by analysing the trace of healthcare events in the Electronic Health Records. In PM,...

Short term experiments have identified heat shock and cold response elements in many biological systems. However, the effect of long-term low or high temperatures is not well documented. To address this gap, we grew Antirrhinum majus plants from two-weeks old until maturity under control (normal) (22/16°C), cold (15/5°C), and hot (30/23°C) conditio...

The increasing use of ontologies requires their quality assurance. Ontology quality assurance consists of a set of activities that allow analyzing the ontology, identifying strengths and weaknesses, and proposing improvement actions. Human readability is a quality aspect that improves the use and reuse of ontologies. The human readable content refe...

Surveys in mobile learning developed so far have analysed in a global way the effects on the usage of mobile devices by means of general apps or apps already developed. However, more and more teachers are developing their own apps to address issues not covered by existing m-learning apps. In this article, by means of a systematic literature review...

Introduction Whole-genome sequencing using nanopore technologies can uncover structural variants, which are DNA rearrangements larger than 50 base pairs. Nanopore technologies can also characterize their boundaries with single-base accuracy, owing to the kilobase-long reads that encompass either full variants or their junctions. Other methods, such...

The effect of mutations has been traditionally predicted by studying what may happen due to the substitution of one amino acid for another one. This approach may be effective for mutations with impact in the function of the protein, but ineffective for mutations in the translation initiation codon. Such mutation might avoid the generation of the pr...

Background: Immune signatures at birth could be associated with clinical outcomes and will improve our understanding of immunity prenatal programming. Methods: Data come from 235 newborns from the cohort study NELA. Production of cytokines was determined using Luminex technology. Associations between cytokine concentrations with sex and season o...

Background: Ontology matching should contribute to the interoperability aspect of FAIR data (Findable, Accessible, Interoperable, and Reusable). Multiple data sources can use different ontologies for annotating their data and, thus, creating the need for dynamic ontology matching services. In this experimental study, we assessed the performance of...

Endocrine disrupting chemicals (EDCs) set a public health risk through disruption of normal physiological processes. The toxicoepigenetic mechanisms of developmental exposure to common EDCs, such as bisphenol A (BPA), are poorly known. The present study aimed to evaluate associations between perinatal maternal urinary concentrations of BPA, bisphen...

The process of gene regulation extends as a network in which both genetic se- quences and proteins are involved. The levels of regulation and the mechanisms involved are multiple. Transcription is the main control mechanism for most genes, being the downstream steps responsible for refining the transcription patterns. In turn, gene transcription is...

Background and objective: Metrics are commonly used by biomedical researchers and practitioners to measure and evaluate properties of individuals, instruments, models, methods, or datasets. Due to the lack of a standardized validation procedure for a metric, it is assumed that if a metric is appropriate for analyzing a dataset in a certain domain,...

Computational genomics aim at supporting the discovery of how the functionality of the genome of the organism under study is affected both by its own sequence and structure, and by the network of interaction between this genome and different biological or physical factors. In this work, we focus on the analysis of ChIP-seq data, for which many meth...

Gene regulation computational research requires handling and integrating large amounts of heterogeneous data. The Gene Ontology has demonstrated that ontologies play a fundamental role in biological data interoperability and integration. Ontologies help to express data and knowledge in a machine processable way, which enables complex querying and a...

The COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC, CA15205, www.greekc.org) organized nine workshops in a four-year period, starting September 2016. The workshops brought together a wide range of experts from all over the world working on various parts of the knowledge cycle that is central to understanding gene regu...

The prevalence of asthma is considerably high among women of childbearing age. Most asthmatic women also often have other atopic disorders. Therefore, the differentiation between patients with atopic diseases without asthma and asthmatics with coexisting diseases is essential to avoid underdiagnosis of asthma and to design strategies to reduce symp...

TheWeb of Data aims at linking Internet data repositories. SemanticWeb technologies make data easily readable by computer agents, enabling the automation of complex tasks and facilitating data integration. They facilitate the achievement of the Web of Data in which users can query the connected datasets in the search engine style, i.e. by using key...

Background The increasing adoption of ontologies in biomedical research and the growing number of ontologies available have made it necessary to assure the quality of these resources. Most of the well-established ontologies, such as the Gene Ontology or SNOMED CT, have their own quality assurance processes. These have demonstrated their usefulness...

Quantitative metrics are generally applied by scientists to measure and assess the properties of data and knowledge resources. In ontology engineering, a number of metrics have been developed to analyse different features of ontologies in the last few years. However, this community has not generated any standard framework for studying the propertie...

Background and Objective Effective sharing and reuse of Electronic Health Records (EHR) requires technological solutions which deal with different representations and different models of data. This includes information models, domain models and, ideally, inference models, which enable clinical decision support based on a knowledge base and facts. O...

Chromatin immunoprecipitation experiments and the subsequent sequencing of these fragments (ChIP-Seq) are subject to great uncertainty, due to execution errors, technical and calculation limitations and the inherent complexity of the biological systems to be studied. Therefore, one of the challenges that researchers face when analyzing the results...

The development and application of biological ontologies have increased significantly in recent years. These ontologies can be retrieved from different repositories, which do not provide much information about quality aspects of the ontologies. In the past years, some ontology structural metrics have been proposed, but their validity as measurement...

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data...

During the last decades, there has been significant changes in science that have provoked a big increase in the number of articles published every year. This increment implies a new difficulty for scientists, who have to do an extra effort for selecting literature relevant for their activity. In this work, we present a pipeline for the generation o...

Colorectal cancer (CRC) is the third leading cause of cancer mortality worldwide. Different pathological pathways and molecular drivers have been described and some of the associated markers are used to select effective anti-neoplastic therapy. More recent evidence points to a causal role of microbiota and altered microRNA expression in CRC carcino...

The Internet of Things (IoT) is becoming a buzz word due to the extensive application of it. It can be found anywhere nowadays, Healthcare, Smart cities, Smart energy, smart buildings and so on. The internet of thing has been a subject of improvement in terms of the price, size and persistence, but one of the main challenges in understanding IoT is...

Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major section...

[This corrects the article DOI: 10.1371/journal.pgen.1008192.].

Hospital Information Systems (H.I.S) use Electronic Health Record to store heterogeneous data from the patients. One important goal in this kind of systems is that the information must be, normalized and codify with a clinical terminology to represent exactly the healthcare meaning. Usually this process need human experts to identify and map the co...

Quorum sensing (QS), a mechanism of microbial communication dependent on cell density, governs developmental decisions in many bacteria and in some pathogenic and non-pathogenic fungi including yeasts. In these simple eukaryotes this response is mediated by the release into the growth medium of quorum-sensing molecules (QSMs) whose concentration in...

The digital age is making more datasets available through the Internet, but their interoperability is still limited. The Semantic Web should play a fundamental role in achieving interoperable datasets. The semantic exploitation of data requires its efficient transformation into semantic formats and the integration of heterogeneous sources. Either t...

Clinical Practice Guidelines (CPGs) contain recommendations intended to optimize patient care, produced based on a systematic review of evidence. In turn, Computer-Interpretable Guidelines (CIGs) are formalized versions of CPGs for use as decision-support systems. We consider the enrichment of the CIG by means of an OWL ontology that describes the...

Motivation: Translation is a key biological process controlled in eukaryotes by the initiation AUG codon. Variations affecting this codon may have pathological consequences by disturbing the correct initiation of translation. Unfortunately, there is no systematic study describing these variations in the human genome. Moreover, we aimed to develop...

Ontologies and terminologies have been identified as key resources for the achievement of semantic interoperability in biomedical domains. The development of ontologies is performed as a joint work by domain experts and knowledge engineers. The maintenance and auditing of these resources is also the responsibility of such experts, and this is usual...

The growth of the Life Science Semantic Web is illustrated by the increasing number of resources available in the Linked Open Data Cloud. Our SWIT tool supports the generation of semantic repositories, and it has been successfully applied in the field of orthology resources, helping to achieve objectives of the Quest for Orthologs consortium. Howev...

Las Tecnologías de la Información y las Comunicaciones (TIC) han demostrado que pueden ser útiles prácticamente en cualquier aspecto de la atención sanitaria, incluyendo la provisión de información y comunicación entre organizaciones, dando soporte a procesos diagnósticos y terapéuticos, permitiendo la atención sanitaria remota, etc. En este libro...

Background Regional and epidemiological cancer registries are important for cancer research and the quality management of cancer treatment. Many technological solutions are available to collect and analyse data for cancer registries nowadays. However, the lack of a well-defined common semantic model is a problem when user-defined analyses and data...

We present OntoEnrich, an online platform for the automatic detection and guided analysis of lexical regularities in ontology labels. An analysis guided by these regularities permits users to explore different lexical and semantic aspects as the application of the OBO Foundry principles in biomedical ontologies. The goal of this demonstration is to...

The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have esta...

The biomedical community has developed many ontologies in the last years, which may follow a set of community accepted principles for ontology development such as the ones proposed by the OBO Foundry. One of such principles is the orthogonality of biomedical ontologies, which should be based on the reuse of existing content. Previous works have stu...

Nowadays, one of the main challenges in biology is to make use of several sources of data to improve our understanding of life. When analyzing experimental data, researchers aim at clustering genes that show a similar behavior through specific external conditions. Thus, the functional interpretation of genes is crucial and involves making use of th...

The interoperability of Electronic Health Records (EHR) and Clinical Decision Support (CDS) systems is a major challenge in the medical informatics field. International initiatives propose the use of ontologies for bridging both types of systems. The next-generation of EHR and CDS systems are supposed to use ontologies, or at least ontologies shoul...

The heterogeneity of clinical data is a key problem in the sharing and reuse of Electronic Health Record (EHR) data. We approach this problem through the combined use of EHR standards and semantic web technologies, concretely by means of clinical data transformation applications that convert EHR data in proprietary format, first into clinical infor...

ArchMS is a framework that represents clinical information and knowledge using ontologies in OWL, which facilitates semantic interoperability and thereby the exploitation and secondary use of clinical data. However, it does not yet support the automated assessment of quality of care. CLIF is a stepwise method to formalize quality indicators. The me...

The biomedical community has now developed a significant number of ontologies. The curation of biomedical ontologies is a complex task as they evolve rapidly, being new versions regularly published. Therefore, methods to support ontology developers in analysing and tracking the evolution of their ontologies are needed. OQuaRE is an ontology evaluat...

This volume contains papers from the Doctoral Symposium of the 33rdInternational Conference of the Spanish Society for Natural Language Processing, held on September 19, 2017, in Murcia, Spain.This scientific event convened PhD researchers with an interest in the latest research work and developments in the field of Natural Language Processing (NLP...

The heterogeneity of clinical data is a key problem in the sharing and reuse of Electronic Health Record (EHR) data. We approach this problem through the combined use of EHR standards and semantic web technologies, concretely by means of clinical data transformation applications that convert EHR data in proprietary format, first into clinical infor...

Background The biomedical community has now developed a significant number of ontologies. The curation of biomedical ontologies is a complex task and biomedical ontologies evolve rapidly, so new versions are regularly and frequently published in ontology repositories. This has the implication of there being a high number of ontology versions over a...

Background: Computational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology analysis can play a central role in comparative genomics; it guides establishing evolutionary relations among genes of organisms and allows functional inference of gene products. However, the wide vari...

Background Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natural technological space for data integration and exploitation by generating content readable by machines. Linked Open Data is a Se...

The advent of electronic healthcare records (EHR) systems has triggered the need for their semantic interoperability, which is reinforced by the opportunities for the secondary use of EHR data. The joint use of EHR standards and semantic resources has been identified as key for semantic interoperability. To date, existing tools focused on EHR stand...

Genomic medicine pursues to develop methods for improving early diagnosis processes, the efficiency of treatments and facilitating the discovery of new therapies, and mainly searches for associations between the genotype of individuals and their phenotypical features. The huge genomic variability is a major difficulty for developing effective compu...

The construction and publication of predications form scientific literature databases like MEDLINE is necessary due to the large amount of resources available. The main goal is to infer meaningful predicates between relevant co-occurring MeSH concepts manually annotated from MEDLINE records. The resulting predications are formed as subject-predicat...

The number of biomedical ontologies has increased significantly in recent years. Many of such ontologies are the result of efforts of communities of domain experts and ontology engineers. The development and application of quality assurance (QA) methods should help these communities to develop useful ontologies for both humans and machines. Accordi...

The amount of resources and data about orthology, together with the increasing interest in orthologs in biomedical research has triggered the need for the shareability of the content generated by the different tools and stored in the different databases. In recent years OrthoXML permitted to advance in the standardization of the content for exchang...

Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources. Such heterogeneity makes difficult not only the generation of research-oriented dataset but also its exploitation. In recent years, the Open Data paradigm has proposed new ways for making data available in ways that sharing and integration are...

Hundreds of biomedical ontologies have been produced, with many of the significant, widely used ones being developed in collaborative efforts and following a set of construction principles, which include using a systematic naming convention for their labels. Despite their success, many of these ontologies have lacked a foundation of axioms that wou...

The content of the labels in ontologies is usually considered hidden semantics, because the domain knowledge of such labels is not available as logical axioms in the ontology. The use of systematic naming conventions as best practice for the design of the content of the labels generates labels with structural regularities, namely, lexical regularit...

The semantic interoperability of electronic healthcare records (EHRs) systems is a major challenge in the medical informatics area. International initiatives pursue the use of semantically interoperable clinical models, and ontologies have frequently been used in semantic interoperability efforts. The objective of this paper is to propose a generic...

Syntactic regularities or syntactic patterns are sets of axioms in an OWL ontology with a regular structure. Detecting these patterns and reporting them in human readable form should help the understanding the authoring style of an ontology and is therefore useful in itself. However, pattern detection is sensitive to syntactic variations in the ass...

The main goal of this work is to measure how lexical regularities in biomedical ontology labels can be used for the automatic creation of formal relationships between classes, and to evaluate the results of applying our approach to the Gene Ontology (GO). In recent years, we have developed a method for the lexical analysis of regularities in biomed...

The semantic interoperability of clinical information requires methods able to transform heterogeneous data sources from both technological and structural perspectives, into representations that facilitate the sharing of meaning. The SemanticHealthNet (SHN) project proposes using semantic content patterns for representing clinical information based...

Objective: To (1) evaluate the GoodOD guideline for ontology development by applying the OQuaRE evaluation method and metrics to the ontology artefacts that were produced by students in a randomized controlled trial, and (2) informally compare the OQuaRE evaluation method with gold standard and competency questions based evaluation methods, respec...

Introduction: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". Objectives: In previous work, we have defined methods for the extraction of lexical patterns from labels as an initial step towards semi-automatic ontology enrichment methods. Our previous f...

Semantic interoperability of clinical information requires their unambiguous interpretation by clinical systems. Formal ontologies provide clinical information with a formal and principles-based representation. We describe a semantic infrastructure, which consists of an OWL DL ontological framework and a set of ontology content patterns. It aims at...

OGOLOD is a Linked Open Data dataset derived from different biomedical resources by an automated pipeline, using a tailored ontology as a scaffold. The key contribution of OGOLOD is that it links, in new RDF triples, genetic human diseases and orthologous genes, paving the way for a more efficient translational biomedical research exploiting the Li...

The implementation of shared health information platforms based on social networks can produce interesting applications to consider. Web 2.0 tools can promote the empowerment of patients by making them more informed and, at the same time, may be used to identify subjects for recruitment in clinical trials, overcoming the frequent obstacle of achiev...

The secondary use of electronic healthcare records (EHRs) often requires the identification of patient cohorts. In this context, an important problem is the heterogeneity of clinical data sources, which can be overcome with the combined use of standardized information models, virtual health records, and semantic technologies, since each of them con...

The generation of a semantic clinical infostructure requires linking ontologies, clinical models and terminologies [1]. Here we describe an approach that would permit data coming from different sources and represented in different standards to be queried in a homogeneous and integrated way. Our assumption is that data providers should be able to ag...

No cuestionamos ya el importante papel que tienen las Tecnologías de la Información y la Comunicación (TIC) en nuestra realidad universitaria actual. El rápido devenir de estas herramientas ha supuesto la configuración de nuevos espacios de enseñanza-aprendizaje dentro de las distintas modalidades de enseñanza universitaria actuales. En este artícu...

The increasing importance of ontologies has resulted in the development of a large number of ontologies in both coordinated and non-coordinated efforts. The number and complexity of such ontologies make hard to ontology and tool developers to select which ontologies to use and reuse. So far, there are no mechanism for making such decisions in an in...

The increasing interest of the biomedical community in ontologies can be exemplified by the availability of hundreds of biomedical ontologies and controlled vocabularies, and by the international recommendations and efforts that suggest ontologies should play a critical role in the achievement of semantic interoperability in healthcare. However, ma...

The time spent by users are almost two or more hours looking for papers that generates the possibility to make a search engine to optimize and precision in the results. This works purposes a better classification of research papers, the architecture works with a database of knowledge related with the topics of programming, databases and operating s...

A text mining algorithm named HMM-TFM (Hidden Markov Model based transcription factor name mining) is presented. The proposed algorithm does not need a dictionary of transcription factor names. A small verb set is defined to filter sentences. Transcription factor names are mined according to the part of speech tagged by hidden Markov model. Experim...

Semantic Web technologies have been applied in educational settings for different purposes in recent years, with the type of application being mainly defined by the way in which knowledge is represented and exploited. The basic technology for knowledge representation in Semantic Web settings is the ontology, which represents a common, shareable and...

Background Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the...

Information and Communication Technologies are changing educational processes in several ways and making possible new options for longlife learning. One important issue is to provide mechanisms for the design of contents adapted to the needs and preferences of individuals, that is, providing personalized courses. In this paper we present a recommen...

Social Networks constitute the key ingredient for the huge success of the so called Social Web or Web 2.0. In social networks, a user has the possibility to interact with other users without the need of meeting them. The value of social applications benefit from the network effect, which states that the value of a service to a user arises from the...

The semantic interoperability of electronic healthcare record systems is a major issue given that it would increase the quality of healthcare and patient safety. in this chapter, different solutions based on the use of semantic models for representing clinical knowledge are presented. the aim of the research presented here is to contribute to the a...

Some modern Electronic Healthcare Record (EHR) architectures and standards are based on the dual model-based architecture, which defines two conceptual levels: reference model and archetype model. Such architectures represent EHR domain knowledge by means of archetypes, which are considered by many researchers to play a fundamental role for the ach...