PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data.

Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer (PCa), large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches. A formal representation of PCa-associated knowledge will be essential to the diverse data standardization, data sharing and the future knowledge graph extraction, deep phenotyping and explainable artificial intelligence developing. In this study, we constructed an updated PCa ontology (PCAO2) based on the ontology development life cycle. An online information retrieval system was designed to ensure the usability of the ontology. The PCAO2 with a subclass-based taxonomic hierarchy covers the major biomedical concepts for PCa-associated genotypic, phenotypic and lifestyle data. The current version of the PCAO2 contains 633 concepts organized under three biomedical viewpoints, namely, epidemiology, diagnosis and treatment. These concepts are enriched by the addition of definition, synonym, relationship and reference. For the precision diagnosis and treatment, the PCa-associated genes and lifestyles are integrated in the viewpoint of epidemiological aspects of PCa. PCAO2 provides a standardized and systematized semantic framework for studying large amounts of heterogeneous PCa data and knowledge, which can be further, edited and enriched by the scientific community. The PCAO2 is freely available at https://bioportal.bioontology.org/ontologies/PCAO, http://pcaontology.net/ and http://pcaontology.net/mobile/.

Developing an Ontology Representing Fall Risk Management Domain Knowledge.

Ontologies serve as comprehensive frameworks for organizing domain-specific knowledge, offering significant benefits for managing clinical data. This study presents the development of the Fall Risk Management Ontology (FRMO), designed to enhance clinical text mining, facilitate integration and interoperability between disparate data sources, and streamline clinical data analysis. By representing major entities within the fall risk management domain, the FRMO supports the unification of clinical language and decision-making processes, ultimately contributing to the prevention of falls among older adults. We used Ontology Web Language (OWL) to build the FRMO in Protégé. Of the seven steps of the Stanford approach, six steps were utilized in the development of the FRMO: (1) defining the domain and scope of the ontology, (2) reusing existing ontologies when possible, (3) enumerating ontology terms, (4) specifying the classes and their hierarchy, (5) defining the properties of the classes, and (6) defining the facets of the properties. We evaluated the FRMO using four main criteria: consistency, completeness, accuracy, and clarity. The developed ontology comprises 890 classes arranged in a hierarchical structure, including six top-level classes with a total of 43 object properties and 28 data properties. FRMO is the first comprehensively described semantic ontology for fall risk management. Healthcare providers can use the ontology as the basis of clinical decision technology for managing falls among older adults.

Ontology-based decision support systems for diabetes nutrition therapy: A systematic literature review.

Diabetes is a non-communicable disease that has reached epidemic proportions, affecting 537 million people globally. Artificial Intelligence can support patients or clinicians in diabetes nutrition therapy - the first medical therapy in most cases of Type 1 and Type 2 diabetes. In particular, ontology-based recommender and decision support systems can deliver a computable representation of experts' knowledge, thus delivering patient-tailored nutritional recommendations or supporting clinical personnel in identifying the most suitable diet. This work proposes a systematic literature review of the domain ontologies describing diabetes in such systems, identifying their underlying conceptualizations, the users targeted by the systems, the type(s) of diabetes tackled, and the nutritional recommendations provided. This review also delves into the structure of the domain ontologies, highlighting several aspects that may hinder (or foster) their adoption in recommender and decision support systems for diabetes nutrition therapy. The results of this review process allow to underline how recommendations are formulated and the role of clinical experts in developing domain ontologies, outlining the research trends characterizing this research area. The results also allow for identifying research directions that can foster a preeminent role for clinical experts and clinical guidelines in a cooperative effort to make ontologies more interoperable - thus enabling them to play a significant role in the decision-making processes about diabetes nutrition therapy.

Bayesian-knowledge driven ontologies: A framework for fusion of semantic knowledge under uncertainty and incompleteness.

The modeling of uncertain information is an open problem in ontology research and is a theoretical obstacle to creating a truly semantic web. Currently, ontologies often do not model uncertainty, so stochastic subject matter must either be normalized or rejected entirely. Because uncertainty is omnipresent in the real world, knowledge engineers are often faced with the dilemma of performing prohibitively labor-intensive research or running the risk of rejecting correct information and accepting incorrect information. It would be preferable if ontologies could explicitly model real-world uncertainty and incorporate it into reasoning. We present an ontology framework which is based on a seamless synthesis of description logic and probabilistic semantics. This synthesis is powered by a link between ontology assertions and random variables that allows for automated construction of a probability distribution suitable for inferencing. Furthermore, our approach defines how to represent stochastic, uncertain, or incomplete subject matter. Additionally, this paper describes how to fuse multiple conflicting ontologies into a single knowledge base that can be reasoned with using the methods of both description logic and probabilistic inferencing. This is accomplished by using probabilistic semantics to resolve conflicts between assertions, eliminating the need to delete potentially valid knowledge and perform consistency checks. In our framework, emergent inferences can be made from a fused ontology that were not present in any of the individual ontologies, producing novel insights in a given domain.

Development and application of Chinese medical ontology for diabetes mellitus.

OBJECTIVE: To develop a Chinese Diabetes Mellitus Ontology (CDMO) and explore methods for constructing high-quality Chinese biomedical ontologies. MATERIALS AND METHODS: We used various data sources, including Chinese clinical practice guidelines, expert consensus, literature, and hospital information system database schema, to build the CDMO. We combined top-down and bottom-up strategies and integrated text mining and cross-lingual ontology mapping. The ontology was validated by clinical experts and ontology development tools, and its application was validated through clinical decision support and Chinese natural language medical question answering. RESULTS: The current CDMO consists of 3,752 classes, 182 fine-grained object properties with hierarchical relationships, 108 annotation properties, and over 12,000 mappings to other well-known medical ontologies in English. Based on the CDMO and clinical practice guidelines, we developed 200 rules for diabetes diagnosis, treatment, diet, and medication recommendations using the Semantic Web Rule Language. By injecting ontology knowledge, CDMO enhances the performance of the T5 model on a real-world Chinese medical question answering dataset related to diabetes. CONCLUSION: CDMO has fine-grained semantic relationships and extensive annotation information, providing a foundation for medical artificial intelligence applications in Chinese contexts, including the construction of medical knowledge graphs, clinical decision support systems, and automated medical question answering. Furthermore, the development process incorporated natural language processing and cross-lingual ontology mapping to improve the quality of the ontology and improved development efficiency. This workflow offers a methodological reference for the efficient development of other high-quality Chinese as well as non-English medical ontologies.

Developing an ontology of non-pharmacological treatment for emotional and mood disturbances in dementia.

Emotional and mood disturbances are common in people with dementia. Non-pharmacological interventions are beneficial for managing these disturbances. However, effectively applying these interventions, particularly in the person-centred approach, is a complex and knowledge-intensive task. Healthcare professionals need the assistance of tools to obtain all relevant information that is often buried in a vast amount of clinical data to form a holistic understanding of the person for successfully applying non-pharmacological interventions. A machine-readable knowledge model, e.g., ontology, can codify the research evidence to underpin these tools. For the first time, this study aims to develop an ontology entitled Dementia-Related Emotional And Mood Disturbance Non-Pharmacological Treatment Ontology (DREAMDNPTO). DREAMDNPTO consists of 1258 unique classes (concepts) and 70 object properties that represent relationships between these classes. It meets the requirements and quality standards for biomedical ontology. As DREAMDNPTO provides a computerisable semantic representation of knowledge specific to non-pharmacological treatment for emotional and mood disturbances in dementia, it will facilitate the application of machine learning to this particular and important health domain of emotional and mood disturbance management for people with dementia.

Coordinating virus research: The Virus Infectious Disease Ontology.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

HeNeCOn: An ontology for integrative research in Head and Neck cancer.

BACKGROUND: Head and Neck Cancer (HNC) has a high incidence and prevalence in the worldwide population. The broad terminology associated with these diseases and their multimodality treatments generates large amounts of heterogeneous clinical data, which motivates the construction of a high-quality harmonization model to standardize this multi-source clinical data in terms of format and semantics. The use of ontologies and semantic techniques is a well-known approach to face this challenge. OBJECTIVE: This work aims to provide a clinically reliable data model for HNC processes during all phases of the disease: prognosis, treatment, and follow-up. Therefore, we built the first ontology specifically focused on the HNC domain, named HeNeCOn (Head and Neck Cancer Ontology). METHODS: First, an annotated dataset was established to provide a formal reference description of HNC. Then, 170 clinical variables were organized into a taxonomy, and later expanded and mapped to formalize and integrate multiple databases into the HeNeCOn ontology. The outcomes of this iterative process were reviewed and validated by clinicians and statisticians. RESULTS: HeNeCOn is an ontology consisting of 502 classes, a taxonomy with a hierarchical structure, semantic definitions of 283 medical terms and detailed relations between them, which can be used as a tool for information extraction and knowledge management. CONCLUSION: HeNeCOn is a reusable, extendible and standardized ontology which establishes a reference data model for terminology structure and standard definitions in the Head and Neck Cancer domain. This ontology allows handling both current and newly generated knowledge in Head and Neck cancer research, by means of data linking and mapping with other public ontologies.

The PACIFIC ontology for heterogeneous data management in cardiology.

With the emergence of health data warehouses and major initiatives to collect and analyze multi-modal and multisource data, data organization becomes central. In the PACIFIC-PRESERVED (PhenomApping, ClassIFication, and Innovation for Cardiac Dysfunction - Heart Failure with PRESERVED LVEF Study, NCT04189029) study, a data driven research project aiming at redefining and profiling the Heart Failure with preserved Ejection Fraction (HFpEF), an ontology was developed by different data experts in cardiology to enable better data management in a complex study context (multisource, multiformat, multimodality, multipartners). The PACIFIC ontology provides a cardiac data management framework for the phenomapping of patients. It was built upon the BMS-LM (Biomedical Study -Lifecycle Management) core ontology and framework, proposed in a previous work to ensure data organization and provenance throughout the study lifecycle (specification, acquisition, analysis, publication). The BMS-LM design pattern was applied to the PACIFIC multisource variables. In addition, data was structured using a subset of MeSH headings for diseases, technical procedures, or biological processes, and using the Uberon ontology anatomical entities. A total of 1372 variables were organized and enriched with annotations and description from existing ontologies and taxonomies such as LOINC to enable later semantic interoperability. Both, data structuring using the BMS-LM framework, and its mapping with published standards, foster interoperability of multimodal cardiac phenomapping datasets.

Design of the formalized and integrated Alzheimer's Disease Ontology and its application in retrieving textual data via text mining.

As one of the leading causes for dementia in the population, it is imperative that we discern exactly why Alzheimer's disease (AD) has a strong molecular association with beta-amyloid and tau. Although a clear understanding about etiology and pathogenesis of AD remains unsolved, scientists worldwide have dedicated significant efforts to discovering the molecular interactions linked to the pathological characteristics and potential treatments. Knowledge representations, such as domain ontologies encompassing our current understanding about AD, could greatly assist and contribute to disease research. This paper describes the construction and application of the integrated Alzheimer's Disease Ontology (ADO), combining selected concepts from the former version of the ADO and the Alzheimer's Disease Mapping Ontology (ADMO). In addition to the existing entities available from these knowledge models, essential knowledge about AD from public sources, such as newly discovered risk factor genes and novel treatments, was also integrated. The ADO can also be leveraged in text mining scenarios given that it is conceptually enriched with domain-specific knowledge as well as their relations. The integrated ADO consists of 39 855 total axioms. The ontology covers many aspects of the AD domain, including risk factor genes, clinical features, treatments and experimental models. The ontology complies with the Open Biological and Biomedical Ontology principles and was accepted by the foundry. In this paper, we illustrate the role of the presented ontology in extracting textual information from the SCAIView database and key measures in an ADO-based corpus. Database URL:  https://academic.oup.com/database.

The use of foundational ontologies in biomedical research.

BACKGROUND: The FAIR principles recommend the use of controlled vocabularies, such as ontologies, to define data and metadata concepts. Ontologies are currently modelled following different approaches, sometimes describing conflicting definitions of the same concepts, which can affect interoperability. To cope with that, prior literature suggests organising ontologies in levels, where domain specific (low-level) ontologies are grounded in domain independent high-level ontologies (i.e., foundational ontologies). In this level-based organisation, foundational ontologies work as translators of intended meaning, thus improving interoperability. Despite their considerable acceptance in biomedical research, there are very few studies testing foundational ontologies. This paper describes a systematic literature mapping that was conducted to understand how foundational ontologies are used in biomedical research and to find empirical evidence supporting their claimed (dis)advantages. RESULTS: From a set of 79 selected papers, we identified that foundational ontologies are used for several purposes: ontology construction, repair, mapping, and ontology-based data analysis. Foundational ontologies are claimed to improve interoperability, enhance reasoning, speed up ontology development and facilitate maintainability. The complexity of using foundational ontologies is the most commonly cited downside. Despite being used for several purposes, there were hardly any experiments (1 paper) testing the claims for or against the use of foundational ontologies. In the subset of 49 papers that describe the development of an ontology, it was observed a low adherence to ontology construction (16 papers) and ontology evaluation formal methods (4 papers). CONCLUSION: Our findings have two main implications. First, the lack of empirical evidence about the use of foundational ontologies indicates a need for evaluating the use of such artefacts in biomedical research. Second, the low adherence to formal methods illustrates how the field could benefit from a more systematic approach when dealing with the development and evaluation of ontologies. The understanding of how foundational ontologies are used in the biomedical field can drive future research towards the improvement of ontologies and, consequently, data FAIRness. The adoption of formal methods can impact the quality and sustainability of ontologies, and reusing these methods from other fields is encouraged.

The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease.

BACKGROUND: Navigating the clinical literature to determine the optimal clinical management for rare diseases presents significant challenges. We introduce the Medical Action Ontology (MAxO), an ontology specifically designed to organize medical procedures, therapies, and interventions. METHODS: MAxO incorporates logical structures that link MAxO terms to numerous other ontologies within the OBO Foundry. Term development involves a blend of manual and semi-automated processes. Additionally, we have generated annotations detailing diagnostic modalities for specific phenotypic abnormalities defined by the Human Phenotype Ontology (HPO). We introduce a web application, POET, that facilitates MAxO annotations for specific medical actions for diseases using the Mondo Disease Ontology. FINDINGS: MAxO encompasses 1,757 terms spanning a wide range of biomedical domains, from human anatomy and investigations to the chemical and protein entities involved in biological processes. These terms annotate phenotypic features associated with specific disease (using HPO and Mondo). Presently, there are over 16,000 MAxO diagnostic annotations that target HPO terms. Through POET, we have created 413 MAxO annotations specifying treatments for 189 rare diseases. CONCLUSIONS: MAxO offers a computational representation of treatments and other actions taken for the clinical management of patients. Its development is closely coupled to Mondo and HPO, broadening the scope of our computational modeling of diseases and phenotypic features. We invite the community to contribute disease annotations using POET (https://poet.jax.org/). MAxO is available under the open-source CC-BY 4.0 license (https://github.com/monarch-initiative/MAxO). FUNDING: NHGRI 1U24HG011449-01A1 and NHGRI 5RM1HG010860-04.

Patient safety classifications, taxonomies and ontologies, part 2: A systematic review on content coverage.

BACKGROUND: Content coverage of patient safety ontology and classification systems should be evaluated to provide a guide for users to select appropriate ones for specific applications. In this review, we identified and compare content coverage of patient safety classifications and ontologies. METHODS: We searched different databases and ontology/classification repositories to identify these classifications and ontologies. We included patient safety-related taxonomies, ontologies, classifications, and terminologies. We identified and extracted different concepts covered by these systems and mapped these concepts to international classification for patient safety (ICPS) and finally compared the content of these systems. RESULTS: Finally, 89 papers (77 classifications or ontologies) were analyzed. Thirteen classifications have been developed to cover all medical domains. Among specific domain systems, most systems cover medication (16), surgery (8), medical devices (3), general practice (3), and primary care (3). The most common patient safety-related concepts covered in these systems include incident types (41), contributing factors/hazards (31), patient outcomes (29), degree of harm (25), and action (18). However, stage/phase (6), incident characteristics (5), detection (5), people involved (5), organizational outcomes (4), error type (4), and care setting (3) are some of the less covered concepts in these classifications/ontologies. CONCLUSION: Among general systems, ICPS, World Health Organization's Adverse Reaction Terminology (WHO-ART), and Ontology of Adverse Events (OAE) cover most patient safety concepts and can be used as a gold standard for all medical domains. As a result, reporting systems could make use of these broad classifications, but the majority of their covered concepts are related to patient outcomes, with the exception of ICPS, which covers other patient safety concepts. However, the ICPS does not cover specialized domain concepts. For specific medical domains, MedDRA, NCC MERP, OPAE, ADRO, PPST, OCCME, TRTE, TSAHI, and PSIC-PC provide the broadest coverage of concepts. Many of the patient safety classifications and ontologies are not formally registered or available as formal classification/ontology in ontology repositories such as BioPortal. This study may be used as a guide for choosing appropriate classifications for various applications or expanding less developed patient safety classifications/ontologies. Furthermore, the same concepts are not represented by the same terms; therefore, the current study could be used to guide a harmonization process for existing or future patient safety classifications/ontologies.

Strategy maintenance in smart healthcare systems.

BACKGROUNDS: The size of medical strategies is expected to grow in conjunction with the expansion of modern diseases' complexity. When a strategy includes more than ten statements, its manual management becomes very challenging, and in some cases, impossible. As a result, the updates they get may result in the unavoidable appearance of anomalies. This causes an interruption in the outflow of imperfect knowledge. METHODS: In this paper, we propose an approach called TAnom-HS to verify healthcare strategies. We focus on the management and maintenance, in a convenient and automatic way, of a large strategy to guarantee knowledge accuracy and enhance the efficiency of the inference process in healthcare systems. RESULTS: We developed a prototype of our proposal and we applied it on some cases from the BioPortal repository. The evaluation of both steps of TAnom-HS proved the efficiency of our proposal. CONCLUSION: To increase ontologies expressiveness, a set of rules called strategy is added to it. TAnom-HS is a two-step approach that treats anomalies in healthcare strategies. Such a task helps to take automatic and efficient healthcare decisions.

Context-based refinement of mappings in evolving life science ontologies.

BACKGROUND: Biomedical computational systems benefit from ontologies and their associated mappings. Indeed, aligned ontologies in life sciences play a central role in several semantic-enabled tasks, especially in data exchange. It is crucial to maintain up-to-date alignments according to new knowledge inserted in novel ontology releases. Refining ontology mappings in place, based on adding concepts, demands further research. RESULTS: This article studies the mapping refinement phenomenon by proposing techniques to refine a set of established mappings based on the evolution of biomedical ontologies. In our first analysis, we investigate ways of suggesting correspondences with the new ontology version without applying a matching operation to the whole set of ontology entities. In the second analysis, the refinement technique enables deriving new mappings and updating the semantic type of the mapping beyond equivalence. Our study explores the neighborhood of concepts in the alignment process to refine mapping sets. CONCLUSION: Experimental evaluations with several versions of aligned biomedical ontologies were conducted. Those experiments demonstrated the usefulness of ontology evolution changes to support the process of mapping refinement. Furthermore, using context in ontological concepts was effective in our techniques.

Analysis and implementation of the DynDiff tool when comparing versions of ontology.

BACKGROUND: Ontologies play a key role in the management of medical knowledge because they have the properties to support a wide range of knowledge-intensive tasks. The dynamic nature of knowledge requires frequent changes to the ontologies to keep them up-to-date. The challenge is to understand and manage these changes and their impact on depending systems well in order to handle the growing volume of data annotated with ontologies and the limited documentation describing the changes. METHODS: We present a method to detect and characterize the changes occurring between different versions of an ontology together with an ontology of changes entitled DynDiffOnto, designed according to Semantic Web best practices and FAIR principles. We further describe the implementation of the method and the evaluation of the tool with different ontologies from the biomedical domain (i.e. ICD9-CM, MeSH, NCIt, SNOMEDCT, GO, IOBC and CIDO), showing its performance in terms of time execution and capacity to classify ontological changes, compared with other state-of-the-art approaches. RESULTS: The experiments show a top-level performance of DynDiff for large ontologies and a good performance for smaller ones, with respect to execution time and capability to identify complex changes. In this paper, we further highlight the impact of ontology matchers on the diff computation and the possibility to parameterize the matcher in DynDiff, enabling the possibility of benefits from state-of-the-art matchers. CONCLUSION: DynDiff is an efficient tool to compute differences between ontology versions and classify these differences according to DynDiffOnto concepts. This work also contributes to a better understanding of ontological changes through DynDiffOnto, which was designed to express the semantics of the changes between versions of an ontology and can be used to document the evolution of an ontology.

Construção de uma ontologia de referência para o domínio da HIV/aids / Construction of a reference ontology for the domain of HIV/Aids / Construcción de una ontología de referencia para el dominio del VIH/sida

O uso da Tecnologia da Informação está presente nos mais diversos domínios, inclusive no da saúde, ao utilizar várias metodologias e ferramentas computacionais. O objetivo deste artigo é apresentar o modelo conceitual baseado em ontologia sobre o domínio HIV/aids denominado OntoHI. No processo para desenvol-ver a OntoHI adotam-se a metodologia SABiO e a ontologia de fundamentação UFO, além do conhecimento de especialistas da área da saúde, o que garante a representação da realidade. Artefatos da ontologia aqui apresentados: representação gráfica, glossário de termos, questões de competência. O controle de qualidade se dá através dos processos de validação e verificação das questões de competências. A OntoHI possibilita a integração com representações de outros domínios. Pode ser utilizado como artefato para a construção de ferramentas computacionais, principalmente sistemas de informações e aplicativos móveis para acompanhar o tratamento de pacientes, além de poder ser expandida para se adaptar a novas situações

The use of Information Technology is present in the most diverse domains, including health care, using various methodologies and computational tools. The goal of this work is to present an ontology-driven con-ceptual model on the HIV/AIDS domain called OntoHI. In the process of developing OntoHI, the SABiO methodology and the UFO foundational ontology are adopted, in addition to the specialist's knowledge in the field of health care, which guarantees a consistent representation of reality. Ontology artifacts that are presented here: graphical representation, glossary of terms, validation of competence questions. Quality control happens in the process of validation and verification of competency questions. OntoHI enables in-tegration with representations from other domains. It can be used as an artifact for building computational tools, mainly information systems and mobile applications to monitor patient treatment, in addition to being able to be expanded to adapt to new situations

El uso de las Tecnologías de la Información ocurre en los más diversos dominios, incluido el de la salud, uti-lizando diversas metodologías y herramientas computacionales. El objetivo de este trabajo es presentar el modelo conceptual basado en ontologías sobre el dominio del VIH/sida denominado OntoHI. En el proceso de desarrollo de OntoHI se adoptan la metodología SABiO y la ontología de fundamentos OVNI, además del conocimiento de especialistas en el campo de la salud, lo que garantiza la representación de la realidad. Artefactos ontológicos presentados: representación gráfica, glosario, temas competenciales. El control de calidad se lleva a cabo a través del proceso de validación y verificación de problemas de competencia. Onto-HI permite la integración con representaciones de otros dominios. Puede usarse como artefacto para cons-truir herramientas computacionales, principalmente sistemas de información y aplicaciones móviles para monitorear el tratamiento del paciente, además de poder expandirse para adaptarse a nuevas situaciones

Epistemología y ontología en Ciencia: el reto de la Inteligencia Artificial / Epistemology and ontology in Science: the challenge of Artificial Intelligence

La brecha entre predictibilidad y comprensibilidad amenaza todo el proyecto científico porque los modelos matemáticos de los procesos, alimentados por enormes cantidades de datos de origen muy diverso, proporcionan resultados excepcionalmente precisos pero, al mismo tiempo, ocultan la explicación de los procesos. El conocimiento de “qué sabemos” de la ontología es tan relevante en ciencia como el de “cómo sabemos” y el de “cuánto sabemos” de la epistemología. La inteligencia artificial (IA) implica la comprensión científica de los mecanismos que subyacen al pensamiento y la conducta inteligente, así como su encarnación en máquinas capacitadas por sus creadores de razonar en un sentido convencional. Su formulación “débil” se refiere al empleo de programas informáticos complejos, diseñados con el fin de complementar o auxiliar el razonamiento humano para resolver o completar complejos problemas de cálculo, de mantenimiento de sistemas, de reconocimiento de todo tipo de imágenes, de diseño, de análisis de patrones de datos, etc., muchos de los cuales serían prácticamente inabordables mediante procedimientos convencionales; pero todo ello sin incluir capacidades sentientes o éticas humanas, que sí serían objeto de una – por ahora – inexistente IA “fuerte”, aquella que igualaría o incluso excedería la inteligencia sentiente humana. La vulgarización de la IA “generativa”, desarrollada para crear contenido – texto, imágenes, música o vídeos, entre otras muchas áreas – a partir de información previa, está contribuyendo a consolidar popularmente la idea errónea de que la actual IA excede el razonamiento a nivel humano y exacerba el riesgo de transmisión de información falsa y estereotipos negativos a las personas. Los modelos de lenguaje de la inteligencia artificial no funcionan emulando un cerebro biológico sino que se fundamentan en la búsqueda de patrones lógicos a partir de grandes bases de datos procedentes de fuentes diversas, que no siempre están actualizadas ni depuradas de falsedades, de errores ni de sesgos conceptuales o factuales, tanto involuntarios como interesados. Y la IA empleada en ciencia no es ajena a estas limitaciones y sesgos. Una cuestión particularmente sensible es la posibilidad de utilizar la IA generativa para redactar o incluso inventarse artículos científicos que llegan a pasar desapercibidos por los revisores por pares de las revistas científicas más prestigiosas del mundo, apuntando a un problema más aún profundo: los revisores por pares de las revistas científicas a menudo no tienen tiempo para revisar los manuscritos a fondo en busca de señales de alerta y, en muchos casos, además carecen de recursos informáticos adecuados y formación especializada.(AU)

The gap between predictability and comprehensibility threatens the entire scientific project because mathematical models of processes, fed by enormous amounts of data of very diverse origin, provide exceptionally precise results but, at the same time, hide the explanation of the processes. The knowledge of “what we know” of ontology is as relevant in science as that of “how we know” and “how much we know” of epistemology. Artificial intelligence (AI) involves the scientific understanding of the mechanisms underlying intelligent thought and behavior, as well as their embodiment in machines trained by their creators to reason in a conventional sense. Its “weak” formulation refers to the use of complex computer programs, designed with the purpose of complementing or assisting human reasoning to solve or complete complex problems of calculation, system maintenance, recognition of all types of images, design, analysis of data patterns, etc., many of which would be practically unapproachable using conventional procedures; but all this without including human sentient or ethical capabilities, which would be the subject of a – at the moment – non-existent “strong” AI, that would equal or even exceed human sentient intelligence. The popularization of “generative” AI, developed to create content – text, images, music or videos, among many other areas – from previous information, is helping to popularly consolidate the erroneous idea that current AI exceeds reasoning human level and exacerbates the risk of transmitting false information and negative stereotypes to people. The language models of artificial intelligence do not work by emulating a biological brain but are based on the search for logical patterns from large databases from diverse sources, which are not always updated or purged of falsehoods, errors or errors. conceptual or factual biases, both involuntary and self-serving. And the AI used in science is no stranger to these limitations and biases. A particularly sensitive issue is the possibility of using generative AI to write or even invent scientific articles that go unnoticed by the peer reviewers of the most prestigious scientific journals in the world, pointing to an even deeper problem: peer reviewers. Reviewers often do not have the time to review manuscripts thoroughly for red flags and, in many cases, they also lack adequate computing resources and specialized training.(AU)

Infrastructure tools to support an effective Radiation Oncology Learning Health System.

PURPOSE: Radiation Oncology Learning Health System (RO-LHS) is a promising approach to improve the quality of care by integrating clinical, dosimetry, treatment delivery, research data in real-time. This paper describes a novel set of tools to support the development of a RO-LHS and the current challenges they can address. METHODS: We present a knowledge graph-based approach to map radiotherapy data from clinical databases to an ontology-based data repository using FAIR concepts. This strategy ensures that the data are easily discoverable, accessible, and can be used by other clinical decision support systems. It allows for visualization, presentation, and data analyses of valuable information to identify trends and patterns in patient outcomes. We designed a search engine that utilizes ontology-based keyword searching, synonym-based term matching that leverages the hierarchical nature of ontologies to retrieve patient records based on parent and children classes, connects to the Bioportal database for relevant clinical attributes retrieval. To identify similar patients, a method involving text corpus creation and vector embedding models (Word2Vec, Doc2Vec, GloVe, and FastText) are employed, using cosine similarity and distance metrics. RESULTS: The data pipeline and tool were tested with 1660 patient clinical and dosimetry records resulting in 504 180 RDF (Resource Description Framework) tuples and visualized data relationships using graph-based representations. Patient similarity analysis using embedding models showed that the Word2Vec model had the highest mean cosine similarity, while the GloVe model exhibited more compact embeddings with lower Euclidean and Manhattan distances. CONCLUSIONS: The framework and tools described support the development of a RO-LHS. By integrating diverse data sources and facilitating data discovery and analysis, they contribute to continuous learning and improvement in patient care. The tools enhance the quality of care by enabling the identification of cohorts, clinical decision support, and the development of clinical studies and machine learning programs in radiation oncology.