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The vision of IASIS project is to turn the wave of big biomedical data heading our way into actionable knowledge for decision makers. This is achieved by integrating data from disparate sources, including genomics, electronic health records and bibliography, and applying advanced analytics methods to discover useful patterns. The goal is to turn large amounts of available data into actionable information to authorities for planning public health activities and policies. The integration and analysis of these heterogeneous sources of information will enable the best decisions to be made, allowing for diagnosis and treatment to be personalised to each individual. The project offers a common representation schema for the heterogeneous data sources. The iASiS infrastructure is able to convert clinical notes into usable data, combine them with genomic data, related bibliography, image data and more, and create a global knowledge base. This facilitates the use of intelligent methods in order to discover useful patterns across different resources. Using semantic integration of data gives the opportunity to generate information that is rich, auditable and reliable. This information can be used to provide better care, reduce errors and create more confidence in sharing data, thus providing more insights and opportunities. Data resources for two different disease categories are explored within the iASiS use cases, dementia and lung cancer., Comment: 6 pages, 2 figures, accepted at 2019 IEEE 32nd International Symposium on Computer-Based Medical Systems (CBMS)

This is an overview of the eleventh edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2023. BioASQ is a series of international challenges promoting advances in large-scale biomedical semantic indexing and question answering. This year, BioASQ consisted of new editions of the two established tasks b and Synergy, and a new task (MedProcNER) on semantic annotation of clinical content in Spanish with medical procedures, which have a critical role in medical practice. In this edition of BioASQ, 28 competing teams submitted the results of more than 150 distinct systems in total for the three different shared tasks of the challenge. Similarly to previous editions, most of the participating systems achieved competitive performance, suggesting the continuous advancement of the state-of-the-art in the field., Comment: 24 pages, 12 tables, 3 figures. CLEF2023. arXiv admin note: text overlap with arXiv:2210.06852

Objective: Semantic indexing of biomedical literature is usually done at the level of MeSH descriptors with several related but distinct biomedical concepts often grouped together and treated as a single topic. This study proposes a new method for the automated refinement of subject annotations at the level of MeSH concepts. Methods: Lacking labelled data, we rely on weak supervision based on concept occurrence in the abstract of an article, which is also enhanced by dictionary-based heuristics. In addition, we investigate deep learning approaches, making design choices to tackle the particular challenges of this task. The new method is evaluated on a large-scale retrospective scenario, based on concepts that have been promoted to descriptors. Results: In our experiments concept occurrence was the strongest heuristic achieving a macro-F1 score of about 0.63 across several labels. The proposed method improved it further by more than 4pp. Conclusion: The results suggest that concept occurrence is a strong heuristic for refining the coarse-grained labels at the level of MeSH concepts and the proposed method improves it further., Comment: 26 pages, 5 figures, 4 tables. A more concise version

This paper presents an overview of the tenth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2022. BioASQ is an ongoing series of challenges that promotes advances in the domain of large-scale biomedical semantic indexing and question answering. In this edition, the challenge was composed of the three established tasks a, b, and Synergy, and a new task named DisTEMIST for automatic semantic annotation and grounding of diseases from clinical content in Spanish, a key concept for semantic indexing and search engines of literature and clinical records. This year, BioASQ received more than 170 distinct systems from 38 teams in total for the four different tasks of the challenge. As in previous years, the majority of the competing systems outperformed the strong baselines, indicating the continuous advancement of the state-of-the-art in this domain., Comment: 25 pages, 14 tables, 4 figures. arXiv admin note: substantial text overlap with arXiv:2106.14885

In this paper, we present Knowledge4COVID-19, a framework that aims to showcase the power of integrating disparate sources of knowledge to discover adverse drug effects caused by drug-drug interactions among COVID-19 treatments and pre-existing condition drugs. Initially, we focus on constructing the Knowledge4COVID-19 knowledge graph (KG) from the declarative definition of mapping rules using the RDF Mapping Language. Since valuable information about drug treatments, drug-drug interactions, and side effects is present in textual descriptions in scientific databases (e.g., DrugBank) or in scientific literature (e.g., the CORD-19, the Covid-19 Open Research Dataset), the Knowledge4COVID-19 framework implements Natural Language Processing. The Knowledge4COVID-19 framework extracts relevant entities and predicates that enable the fine-grained description of COVID-19 treatments and the potential adverse events that may occur when these treatments are combined with treatments of common comorbidities, e.g., hypertension, diabetes, or asthma. Moreover, on top of the KG, several techniques for the discovery and prediction of interactions and potential adverse effects of drugs have been developed with the aim of suggesting more accurate treatments for treating the virus. We provide services to traverse the KG and visualize the effects that a group of drugs may have on a treatment outcome. Knowledge4COVID-19 was part of the Pan-European hackathon#EUvsVirus in April 2020 and is publicly available as a resource through a GitHub repository (https://github.com/SDM-TIB/Knowledge4COVID-19) and a DOI (https://zenodo.org/record/4701817#.YH336-8zbol).

Advancing the state-of-the-art in large-scale biomedical semantic indexing and question answering is the main focus of the BioASQ challenge. BioASQ organizes respective tasks where different teams develop systems that are evaluated on the same benchmark datasets that represent the real information needs of experts in the biomedical domain. This paper presents an overview of the ninth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2021. In this year, a new question answering task, named Synergy, is introduced to support researchers studying the COVID-19 disease and measure the ability of the participating teams to discern information while the problem is still developing. In total, 42 teams with more than 170 systems were registered to participate in the four tasks of the challenge. The evaluation results, similarly to previous years, show a performance gain against the baselines which indicates the continuous improvement of the state-of-the-art in this field., Comment: 25 pages, 15 tables, 3 figures. arXiv admin note: text overlap with arXiv:2106.14618

In this paper, we present an overview of the eighth edition of the BioASQ challenge, which ran as a lab in the Conference and Labs of the Evaluation Forum (CLEF) 2020. BioASQ is a series of challenges aiming at the promotion of systems and methodologies for large-scale biomedical semantic indexing and question answering. To this end, shared tasks are organized yearly since 2012, where different teams develop systems that compete on the same demanding benchmark datasets that represent the real information needs of experts in the biomedical domain. This year, the challenge has been extended with the introduction of a new task on medical semantic indexing in Spanish. In total, 34 teams with more than 100 systems participated in the three tasks of the challenge. As in previous years, the results of the evaluation reveal that the top-performing systems managed to outperform the strong baselines, which suggests that state-of-the-art systems keep pushing the frontier of research through continuous improvements., Comment: 21 pages, 10 tables, 3 figures

In this document, we report an analysis of the Public MeSH Note field of the new descriptors introduced in the MeSH thesaurus between 2006 and 2020. The aim of this analysis was to extract information about the previous status of these new descriptors as Supplementary Concept Records. The Public MeSH Note field contains information in semi-structured text, meant to be read by humans. Therefore, we adopted a semi-automated approach, based on regular expressions, to extract information from it. In the large majority of cases, we managed to minimize the required manual effort for extracting the previous state of a new descriptor as a Supplementary Concept Record. The source code for this analysis is openly available on GitHub., Comment: 3 pages, 1 figure, 1 table. Technical report

The Medical Subject Headings (MeSH) thesaurus is a controlled vocabulary widely used in biomedical knowledge systems, particularly for semantic indexing of scientific literature. As the MeSH hierarchy evolves through annual version updates, some new descriptors are introduced that were not previously available. This paper explores the conceptual provenance of these new descriptors. In particular, we investigate whether such new descriptors have been previously covered by older descriptors and what is their current relation to them. To this end, we propose a framework to categorize new descriptors based on their current relation to older descriptors. Based on the proposed classification scheme, we quantify, analyse and present the different types of new descriptors introduced in MeSH during the last fifteen years. The results show that only about 25% of new MeSH descriptors correspond to new emerging concepts, whereas the rest were previously covered by one or more existing descriptors, either implicitly or explicitly. Most of them were covered by a single existing descriptor and they usually end up as descendants of it in the current hierarchy, gradually leading towards a more fine-grained MeSH vocabulary. These insights about the dynamics of the thesaurus are useful for the retrospective study of scientific articles annotated with MeSH, but could also be used to inform the policy of updating the thesaurus in the future., Comment: 18 pages, 14 figures, 2 tables

The results of the seventh edition of the BioASQ challenge are presented in this paper. The aim of the BioASQ challenge is the promotion of systems and methodologies through the organization of a challenge on the tasks of large-scale biomedical semantic indexing and question answering. In total, 30 teams with more than 100 systems participated in the challenge this year. As in previous years, the best systems were able to outperform the strong baselines. This suggests that state-of-the-art systems are continuously improving, pushing the frontier of research., Comment: 17 pages, 2 figures

In this work, we propose a method for the automated refinement of subject annotations in biomedical literature at the level of concepts. Semantic indexing and search of biomedical articles in MEDLINE/PubMed are based on semantic subject annotations with MeSH descriptors that may correspond to several related but distinct biomedical concepts. Such semantic annotations do not adhere to the level of detail available in the domain knowledge and may not be sufficient to fulfil the information needs of experts in the domain. To this end, we propose a new method that uses weak supervision to train a concept annotator on the literature available for a particular disease. We test this method on the MeSH descriptors for two diseases: Alzheimer's Disease and Duchenne Muscular Dystrophy. The results indicate that concept-occurrence is a strong heuristic for automated subject annotation refinement and its use as weak supervision can lead to improved concept-level annotations. The fine-grained semantic annotations can enable more precise literature retrieval, sustain the semantic integration of subject annotations with other domain resources and ease the maintenance of consistent subject annotations, as new more detailed entries are added in the MeSH thesaurus over time., Comment: 36 pages, 8 figures; Dictionary-based baselines added and conclusions updated

In biomedical research, unified access to up-to-date domain-specific knowledge is crucial, as such knowledge is continuously accumulated in scientific literature and structured resources. Identifying and extracting specific information is a challenging task and computational analysis of knowledge bases can be valuable in this direction. However, for disease-specific analyses researchers often need to compile their own datasets, integrating knowledge from different resources, or reuse existing datasets, that can be out-of-date. In this study, we propose a framework to automatically retrieve and integrate disease-specific knowledge into an up-to-date semantic graph, the iASiS Open Data Graph. This disease-specific semantic graph provides access to knowledge relevant to specific concepts and their individual aspects, in the form of concept relations and attributes. The proposed approach is implemented as an open-source framework and applied to three diseases (Lung Cancer, Dementia, and Duchenne Muscular Dystrophy). Exemplary queries are presented, investigating the potential of this automatically generated semantic graph as a basis for retrieval and analysis of disease-specific knowledge., Comment: 6 pages, 2 figures, accepted in IEEE 33rd International Symposium on Computer Based Medical Systems (CBMS2020)

Evaluation in empirical computer science is essential to show progress and assess technologies developed. Several research domains such as information retrieval have long relied on systematic evaluation to measure progress: here, the Cranfield paradigm of creating shared test collections, defining search tasks, and collecting ground truth for these tasks has persisted up until now. In recent years, however, several new challenges have emerged that do not fit this paradigm very well: extremely large data sets, confidential data sets as found in the medical domain, and rapidly changing data sets as often encountered in industry. Also, crowdsourcing has changed the way that industry approaches problem-solving with companies now organizing challenges and handing out monetary awards to incentivize people to work on their challenges, particularly in the field of machine learning. This white paper is based on discussions at a workshop on Evaluation-as-a-Service (EaaS). EaaS is the paradigm of not providing data sets to participants and have them work on the data locally, but keeping the data central and allowing access via Application Programming Interfaces (API), Virtual Machines (VM) or other possibilities to ship executables. The objective of this white paper are to summarize and compare the current approaches and consolidate the experiences of these approaches to outline the next steps of EaaS, particularly towards sustainable research infrastructures. This white paper summarizes several existing approaches to EaaS and analyzes their usage scenarios and also the advantages and disadvantages. The many factors influencing EaaS are overviewed, and the environment in terms of motivations for the various stakeholders, from funding agencies to challenge organizers, researchers and participants, to industry interested in supplying real-world problems for which they require solutions.