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  1. The high volume of research focusing on extracting patient information from electronic health records (EHRs) has led to an increase in the demand for annotated corpora, which are a precious resource for both t...

    Authors: Lucas Emanuel Silva e Oliveira, Ana Carolina Peters, Adalniza Moura Pucca da Silva, Caroline Pilatti Gebeluca, Yohan Bonescki Gumiel, Lilian Mie Mukai Cintho, Deborah Ribeiro Carvalho, Sadid Al Hasan and Claudia Maria Cabral Moro
    Citation: Journal of Biomedical Semantics 2022 13:13
  2. The COVID-19 pandemic has challenged healthcare systems and research worldwide. Data is collected all over the world and needs to be integrated and made available to other researchers quickly. However, the var...

    Authors: Núria Queralt-Rosinach, Rajaram Kaliyaperumal, César H. Bernabé, Qinqin Long, Simone A. Joosten, Henk Jan van der Wijk, Erik L.A. Flikkenschild, Kees Burger, Annika Jacobsen, Barend Mons and Marco Roos
    Citation: Journal of Biomedical Semantics 2022 13:12
  3. In life sciences, there has been a long-standing effort of standardization and integration of reference datasets and databases. Despite these efforts, many studies data are provided using specific and non-stan...

    Authors: Marine Louarn, Fabrice Chatonnet, Xavier Garnier, Thierry Fest, Anne Siegel, Catherine Faron and Olivier Dameron
    Citation: Journal of Biomedical Semantics 2022 13:11
  4. Health data from different specialties or domains generallly have diverse formats and meanings, which can cause semantic communication barriers when these data are exchanged among heterogeneous systems. As suc...

    Authors: Zhe Yang, Kun Jiang, Miaomiao Lou, Yang Gong, Lili Zhang, Jing Liu, Xinyu Bao, Danhong Liu and Peng Yang
    Citation: Journal of Biomedical Semantics 2022 13:10
  5. The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating re...

    Authors: Rajaram Kaliyaperumal, Mark D. Wilkinson, Pablo Alarcón Moreno, Nirupama Benis, Ronald Cornet, Bruna dos Santos Vieira, Michel Dumontier, César Henrique Bernabé, Annika Jacobsen, Clémence M. A. Le Cornec, Mario Prieto Godoy, Núria Queralt-Rosinach, Leo J. Schultze Kool, Morris A. Swertz, Philip van Damme, K. Joeri van der Velde…
    Citation: Journal of Biomedical Semantics 2022 13:9
  6. Transfer learning is a common practice in image classification with deep learning where the available data is often limited for training a complex model with millions of parameters. However, transferring langu...

    Authors: Amara Tariq, Omar Kallas, Patricia Balthazar, Scott Jeffery Lee, Terry Desser, Daniel Rubin, Judy Wawira Gichoya and Imon Banerjee
    Citation: Journal of Biomedical Semantics 2022 13:8
  7. Population-based cancer registries are a critical reference source for the surveillance and control of cancer. Cancer registries work extensively with the internationally recognised TNM classification system u...

    Authors: Nicholas Charles Nicholson, Francesco Giusti, Manola Bettio, Raquel Negrao Carvalho, Nadya Dimitrova, Tadeusz Dyba, Manuela Flego, Luciana Neamtiu, Giorgia Randi and Carmen Martos
    Citation: Journal of Biomedical Semantics 2022 13:7
  8. Artificial intelligence methods applied to electronic medical records (EMRs) hold the potential to help physicians save time by sharpening their analysis and decisions, thereby improving the health of patients...

    Authors: Raphaël Gazzotti, Catherine Faron, Fabien Gandon, Virginie Lacroix-Hugues and David Darmon
    Citation: Journal of Biomedical Semantics 2022 13:6
  9. Text mining can be applied to automate knowledge extraction from unstructured data included in medical reports and generate quality indicators applicable for medical documentation. The primary objective of thi...

    Authors: Florent Baty, Jemima Hegermann, Tiziana Locatelli, Claudio Rüegg, Christian Gysin, Frank Rassouli and Martin Brutsche
    Citation: Journal of Biomedical Semantics 2022 13:5
  10. Electronic Laboratory Notebooks (ELNs) are used to document experiments and investigations in the wet-lab. Protocols in ELNs contain a detailed description of the conducted steps including the necessary inform...

    Authors: Max Schröder, Susanne Staehlke, Paul Groth, J. Barbara Nebe, Sascha Spors and Frank Krüger
    Citation: Journal of Biomedical Semantics 2022 13:4
  11. Drug repurposing can improve the return of investment as it finds new uses for existing drugs. Literature-based analyses exploit factual knowledge on drugs and diseases, e.g. from databases, and combine it wit...

    Authors: Bernd Müller, Leyla Jael Castro and Dietrich Rebholz-Schuhmann
    Citation: Journal of Biomedical Semantics 2022 13:3
  12. Melanoma is one of the least common but the deadliest of skin cancers. This cancer begins when the genes of a cell suffer damage or fail, and identifying the genes involved in melanoma is crucial for understan...

    Authors: Roberto Zanoli, Alberto Lavelli, Theresa Löffler, Nicolas Andres Perez Gonzalez and Fabio Rinaldi
    Citation: Journal of Biomedical Semantics 2022 13:2
  13. The advancement of science and technologies play an immense role in the way scientific experiments are being conducted. Understanding how experiments are performed and how results are derived has become signif...

    Authors: Sheeba Samuel and Birgitta König-Ries
    Citation: Journal of Biomedical Semantics 2022 13:1
  14. Image segmentation is a difficult and classic problem. It has a wide range of applications, one of which is skin lesion segmentation. Numerous researchers have made great efforts to tackle the problem, yet the...

    Authors: Dalei Jiang, Yin Wang, Feng Zhou, Hongtao Ma, Wenting Zhang, Weijia Fang, Peng Zhao and Zhou Tong
    Citation: Journal of Biomedical Semantics 2021 12:22
  15. The activation degree of the orbitofrontal cortex (OFC) functional area in drug abusers is directly related to the craving for drugs and the tolerance to punishment. Currently, among the clinical research on d...

    Authors: Xuelin Gu, Banghua Yang, Shouwei Gao, Lin Feng Yan, Ding Xu and Wen Wang
    Citation: Journal of Biomedical Semantics 2021 12:21
  16. The size, velocity, and heterogeneity of Big Data outclasses conventional data management tools and requires data and metadata to be fully machine-actionable (i.e., eScience-compliant) and thus findable, acces...

    Authors: Lars Vogt
    Citation: Journal of Biomedical Semantics 2021 12:20
  17. Medical experts in the domain of Diabetes Mellitus (DM) acquire specific knowledge from diabetic patients through monitoring and interaction. This allows them to know the disease and information about other co...

    Authors: Cecilia Reyes-Peña, Mireya Tovar, Maricela Bravo and Regina Motz
    Citation: Journal of Biomedical Semantics 2021 12:19
  18. With COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span of time, we often lose an integrative and...

    Authors: Anthony Huffman, Anna Maria Masci, Jie Zheng, Nasim Sanati, Timothy Brunson, Guanming Wu and Yongqun He
    Citation: Journal of Biomedical Semantics 2021 12:18
  19. In recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotyp...

    Authors: Şenay Kafkas, Sara Althubaiti, Georgios V. Gkoutos, Robert Hoehndorf and Paul N. Schofield
    Citation: Journal of Biomedical Semantics 2021 12:17
  20. Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool...

    Authors: Shane Babcock, John Beverley, Lindsay G. Cowell and Barry Smith
    Citation: Journal of Biomedical Semantics 2021 12:13
  21. Recent advances in representation learning have enabled large strides in natural language understanding; However, verbal reasoning remains a challenge for state-of-the-art systems. External sources of structur...

    Authors: Olga Majewska, Charlotte Collins, Simon Baker, Jari Björne, Susan Windisch Brown, Anna Korhonen and Martha Palmer
    Citation: Journal of Biomedical Semantics 2021 12:12
  22. The limited availability of clinical texts for Natural Language Processing purposes is hindering the progress of the field. This article investigates the use of synthetic data for the annotation and automated ...

    Authors: Pål H. Brekke, Taraka Rama, Ildikó Pilán, Øystein Nytrø and Lilja Øvrelid
    Citation: Journal of Biomedical Semantics 2021 12:11
  23. Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unifi...

    Authors: Ayeh Naghizadeh, Mahdi Salamat, Donya Hamzeian, Shaghayegh Akbari, Hossein Rezaeizadeh, Mahdi Alizadeh Vaghasloo, Reza Karbalaei, Mehdi Mirzaie, Mehrdad Karimi and Mohieddin Jafari
    Citation: Journal of Biomedical Semantics 2021 12:9
  24. A wide array of existing instruments are commonly used to assess childhood behavior and development for the evaluation of social, emotional and behavioral disorders such as Autism Spectrum Disorder (ASD), atte...

    Authors: Alyson Maslowski, Halim Abbas, Kelley Abrams, Sharief Taraman, Ford Garberson and Susan Segar
    Citation: Journal of Biomedical Semantics 2021 12:8
  25. Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the ...

    Authors: Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf and Georgios V Gkoutos
    Citation: Journal of Biomedical Semantics 2021 12:7
  26. Medical texts such as radiology reports or electronic health records are a powerful source of data for researchers. Anonymization methods must be developed to de-identify documents containing personal informat...

    Authors: Irene Pérez-Díez, Raúl Pérez-Moraga, Adolfo López-Cerdán, Jose-Maria Salinas-Serrano and María de la Iglesia-Vayá
    Citation: Journal of Biomedical Semantics 2021 12:6
  27. The amount of available data, which can facilitate answering scientific research questions, is growing. However, the different formats of published data are expanding as well, creating a serious challenge when...

    Authors: Andreea Grigoriu, Amrapali Zaveri, Gerhard Weiss and Michel Dumontier
    Citation: Journal of Biomedical Semantics 2021 12:5
  28. Incorporating the feedback of expert stakeholders in ontology development is important to ensure content is appropriate, comprehensive, meets community needs and is interoperable with other ontologies and clas...

    Authors: Emma Norris, Janna Hastings, Marta M. Marques, Ailbhe N. Finnerty Mutlu, Silje Zink and Susan Michie
    Citation: Journal of Biomedical Semantics 2021 12:4
  29. Mortality prediction is an important task to achieve smart healthcare, especially for the management of intensive care unit. It can provide a reference for doctors to quickly predict the course of disease and ...

    Authors: Haiyang Yang, Li Kuang and FengQiang Xia
    Citation: Journal of Biomedical Semantics 2021 12:3
  30. Accurate and precise information about the therapeutic uses (indications) of a drug is essential for applications in drug repurposing and precision medicine. Leading online drug resources such as DrugCentral a...

    Authors: Kody Moodley, Linda Rieswijk, Tudor I. Oprea and Michel Dumontier
    Citation: Journal of Biomedical Semantics 2021 12:2
  31. Population-based cancer registries constitute an important information source in cancer epidemiology. Studies collating and comparing data across regional and national boundaries have proved important for depl...

    Authors: Nicholas Charles Nicholson, Francesco Giusti, Manola Bettio, Raquel Negrao Carvalho, Nadya Dimitrova, Tadeusz Dyba, Manuela Flego, Luciana Neamtiu, Giorgia Randi and Carmen Martos
    Citation: Journal of Biomedical Semantics 2021 12:1
  32. The successful determination and analysis of phenotypes plays a key role in the diagnostic process, the evaluation of risk factors and the recruitment of participants for clinical and epidemiological studies. ...

    Authors: Alexandr Uciteli, Christoph Beger, Toralf Kirsten, Frank A. Meineke and Heinrich Herre
    Citation: Journal of Biomedical Semantics 2020 11:15
  33. Free-text descriptions in electronic health records (EHRs) can be of interest for clinical research and care optimization. However, free text cannot be readily interpreted by a computer and, therefore, has lim...

    Authors: Martijn G. Kersloot, Florentien J. P. van Putten, Ameen Abu-Hanna, Ronald Cornet and Derk L. Arts
    Citation: Journal of Biomedical Semantics 2020 11:14
  34. The Genetic and Rare Diseases (GARD) Information Center was established by the National Institutes of Health (NIH) to provide freely accessible consumer health information on over 6500 genetic and rare disease...

    Authors: Qian Zhu, Dac-Trung Nguyen, Ivan Grishagin, Noel Southall, Eric Sid and Anne Pariser
    Citation: Journal of Biomedical Semantics 2020 11:13
  35. Medical knowledge is accumulated in scientific research papers along time. In order to exploit this knowledge by automated systems, there is a growing interest in developing text mining methodologies to extrac...

    Authors: Patricio Wolff, Sebastián Ríos, David Clavijo, Manuel Graña and Miguel Carrasco
    Citation: Journal of Biomedical Semantics 2020 11:12
  36. Recently, more electronic data sources are becoming available in the healthcare domain. Electronic health records (EHRs), with their vast amounts of potentially available data, can greatly improve healthcare. ...

    Authors: Kohei Kajiyama, Hiromasa Horiguchi, Takashi Okumura, Mizuki Morita and Yoshinobu Kano
    Citation: Journal of Biomedical Semantics 2020 11:11
  37. Up to 35% of nurses’ working time is spent on care documentation. We describe the evaluation of a system aimed at assisting nurses in documenting patient care and potentially reducing the documentation workloa...

    Authors: Hans Moen, Kai Hakala, Laura-Maria Peltonen, Hanna-Maria Matinolli, Henry Suhonen, Kirsi Terho, Riitta Danielsson-Ojala, Maija Valta, Filip Ginter, Tapio Salakoski and Sanna Salanterä
    Citation: Journal of Biomedical Semantics 2020 11:10
  38. Knowledge graphs can represent the contents of biomedical literature and databases as subject-predicate-object triples, thereby enabling comprehensive analyses that identify e.g. relationships between diseases...

    Authors: Wytze J. Vlietstra, Rein Vos, Marjan van den Akker, Erik M. van Mulligen and Jan A. Kors
    Citation: Journal of Biomedical Semantics 2020 11:9
  39. A key challenge for improving the quality of health care is to be able to use a common framework to work with patient information acquired in any of the health and life science disciplines. Patient information...

    Authors: William D. Duncan, Thankam Thyvalikakath, Melissa Haendel, Carlo Torniai, Pedro Hernandez, Mei Song, Amit Acharya, Daniel J. Caplan, Titus Schleyer and Alan Ruttenberg
    Citation: Journal of Biomedical Semantics 2020 11:8
  40. Textual corpora are extremely important for various NLP applications as they provide information necessary for creating, setting and testing those applications and the corresponding tools. They are also crucia...

    Authors: Natalia Grabar, Clément Dalloux and Vincent Claveau
    Citation: Journal of Biomedical Semantics 2020 11:7
  41. Sharing sensitive data across organizational boundaries is often significantly limited by legal and ethical restrictions. Regulations such as the EU General Data Protection Rules (GDPR) impose strict requireme...

    Authors: Lars Christoph Gleim, Md Rezaul Karim, Lukas Zimmermann, Oliver Kohlbacher, Holger Stenzhorn, Stefan Decker and Oya Beyan
    Citation: Journal of Biomedical Semantics 2020 11:6
  42. Health 2.0 allows patients and caregivers to conveniently seek medical information and advice via e-portals and online discussion forums, especially regarding potential drug side effects. Although online healt...

    Authors: Van-Hoang Nguyen, Kazunari Sugiyama, Min-Yen Kan and Kishaloy Halder
    Citation: Journal of Biomedical Semantics 2020 11:5
  43. Most tutorial ontologies focus on illustrating one aspect of ontology development, notably language features and automated reasoners, but ignore ontology development factors, such as emergent modelling guideli...

    Authors: C. Maria Keet
    Citation: Journal of Biomedical Semantics 2020 11:4
  44. Scientific activity for 3D bioprinting has increased over the past years focusing mainly on fully functional biological constructs to overcome issues related to organ transplants. This research performs a scie...

    Authors: Leonardo Azael García-García and Marisela Rodríguez-Salvador
    Citation: Journal of Biomedical Semantics 2020 11:3
  45. Duration of untreated psychosis (DUP) is an important clinical construct in the field of mental health, as longer DUP can be associated with worse intervention outcomes. DUP estimation requires knowledge about wh...

    Authors: Natalia Viani, Joyce Kam, Lucia Yin, André Bittar, Rina Dutta, Rashmi Patel, Robert Stewart and Sumithra Velupillai
    Citation: Journal of Biomedical Semantics 2020 11:2
  46. Ontologies are widely used across biology and biomedicine for the annotation of databases. Ontology development is often a manual, time-consuming, and expensive process. Automatic or semi-automatic identificat...

    Authors: Sara Althubaiti, Şenay Kafkas, Marwa Abdelhakim and Robert Hoehndorf
    Citation: Journal of Biomedical Semantics 2020 11:1

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