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  1. 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

    Content type: Research

    Published on:

  2. 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

    Content type: Research

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  6. 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

    Content type: Research

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  7. 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

    Content type: Database

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  8. 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

    Content type: Research

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  10. 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

    Content type: Database

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  11. 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

    Content type: Research

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  12. 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

    Content type: Research

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  13. 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

    Content type: Research

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  14. 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

    Content type: Research

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  15. 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

    Content type: Review

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  16. 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

    Content type: Research

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  17. 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

    Content type: Short Report

    Published on:

  18. 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

    Content type: Software

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  19. 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

    Content type: Research

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  20. 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

    Content type: Review

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  21. 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

    Content type: Research

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  22. 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

    Content type: Research

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  23. 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

    Content type: Research

    Published on:

  24. 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

    Content type: Research

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  25. 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

    Content type: Research

    Published on:

  26. 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

    Content type: Research

    Published on:

  27. 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

    Content type: Research

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  28. 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

    Content type: Research

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  29. 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

    Content type: Research

    Published on:

  30. 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

    Content type: Database

    Published on:

  31. 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

    Content type: Research

    Published on:

  32. 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

    Content type: Research

    Published on:

  33. 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

    Content type: Research

    Published on:

  34. Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases. Extensive HMI studies have generated large amounts of data. We propose that...

    Authors: Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Barry Smith, Alexander V. Alekseyenko and Jihad S. Obeid

    Citation: Journal of Biomedical Semantics 2019 10:25

    Content type: Research

    Published on:

  35. Knee injury and Osteoarthritis Outcome Score (KOOS) is an instrument used to quantify patients’ perceptions about their knee condition and associated problems. It is administered as a 42-item closed-ended ques...

    Authors: Irena Spasić, David Owen, Andrew Smith and Kate Button

    Citation: Journal of Biomedical Semantics 2019 10(Suppl 1):24

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  36. With the improvements to text mining technology and the availability of large unstructured Electronic Healthcare Records (EHR) datasets, it is now possible to extract structured information from raw text conta...

    Authors: Beatrice Alex, Claire Grover, Richard Tobin, Cathie Sudlow, Grant Mair and William Whiteley

    Citation: Journal of Biomedical Semantics 2019 10(Suppl 1):23

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  37. Deep Learning opens up opportunities for routinely scanning large bodies of biomedical literature and clinical narratives to represent the meaning of biomedical and clinical terms. However, the validation and ...

    Authors: Mercedes Arguello-Casteleiro, Robert Stevens, Julio Des-Diz, Chris Wroe, Maria Jesus Fernandez-Prieto, Nava Maroto, Diego Maseda-Fernandez, George Demetriou, Simon Peters, Peter-John M. Noble, Phil H. Jones, Jo Dukes-McEwan, Alan D. Radford, John Keane and Goran Nenadic

    Citation: Journal of Biomedical Semantics 2019 10(Suppl 1):22

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  38. Significant amounts of health data are stored as free-text within clinical reports, letters, discharge summaries and notes. Busy clinicians have limited time to read such large amounts of free-text and are at ...

    Authors: Alicja Piotrkowicz, Owen Johnson and Geoff Hall

    Citation: Journal of Biomedical Semantics 2019 10(Suppl 1):21

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  39. Free text in electronic health records (EHR) may contain additional phenotypic information beyond structured (coded) information. For major health events – heart attack and death – there is a lack of studies e...

    Authors: Anoop D. Shah, Emily Bailey, Tim Williams, Spiros Denaxas, Richard Dobson and Harry Hemingway

    Citation: Journal of Biomedical Semantics 2019 10(Suppl 1):20

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  40. There is an increasing amount of unstructured medical data that can be analysed for different purposes. However, information extraction from free text data may be particularly inefficient in the presence of sp...

    Authors: Hegler Tissot and Richard Dobson

    Citation: Journal of Biomedical Semantics 2019 10(Suppl 1):17

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  41. Readmission after discharge from a hospital is disruptive and costly, regardless of the reason. However, it can be particularly problematic for psychiatric patients, so predicting which patients may be readmit...

    Authors: Eben Holderness, Nicholas Miller, Philip Cawkwell, Kirsten Bolton, Marie Meteer, James Pustejovsky and Mei-Hua Hall

    Citation: Journal of Biomedical Semantics 2019 10:19

    Content type: Research

    Published on:

  42. Although the mouse is widely used to model human lung development, function, and disease, our understanding of the molecular mechanisms involved in alveolarization of the peripheral lung is incomplete. Recentl...

    Authors: Huaqin Pan, Gail H. Deutsch and Susan E. Wert

    Citation: Journal of Biomedical Semantics 2019 10:18

    Content type: Database

    Published on:

  45. Information in Electronic Health Records is largely stored as unstructured free text. Natural language processing (NLP), or Medical Language Processing (MLP) in medicine, aims at extracting structured informat...

    Authors: Martijn G. Kersloot, Francis Lau, Ameen Abu-Hanna, Derk L. Arts and Ronald Cornet

    Citation: Journal of Biomedical Semantics 2019 10:14

    Content type: Research

    Published on:

  46. Microbial genetics has formed a foundation for understanding many aspects of biology. Systematic annotation that supports computational data mining should reveal further insights for microbes, microbiomes, and...

    Authors: Deborah A. Siegele, Sandra A. LaBonte, Peter I-Fan Wu, Marcus C. Chibucos, Suvarna Nandendla, Michelle G. Giglio and James C. Hu

    Citation: Journal of Biomedical Semantics 2019 10:13

    Content type: Research

    Published on:

  48. To improve the outcomes of biological pathway analysis, a better way of integrating pathway data is needed. Ontologies can be used to organize data from disparate sources, and we leverage the Pathway Ontology ...

    Authors: Lucy Lu Wang, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Mary E. Shimoyama and John H. Gennari

    Citation: Journal of Biomedical Semantics 2019 10:11

    Content type: Research

    Published on:

  49. We introduce TranScriptML, a semantic representation schema for prescription regimens allowing various properties of prescriptions (e.g. dose, frequency, route) to be specified separately and applied (manually or...

    Authors: John Aberdeen, Samuel Bayer, Cheryl Clark, Meredith Keybl and David Tresner-Kirsch

    Citation: Journal of Biomedical Semantics 2019 10:10

    Content type: Research

    Published on:

  50. The vigilant observation of medical devices during post-market surveillance (PMS) for identifying safety-relevant incidents is a non-trivial task. A wide range of sources has to be monitored in order to integr...

    Authors: Alexandr Uciteli, Stefan Kropf, Timo Weiland, Stefanie Meese, Klaus Graef, Sabrina Rohrer, Marc O. Schurr, Wolfram Bartussek, Christoph Goller, Philipp Blohm, Robin Seidel, Christian Bayer, Manuel Kernenbach, Kathrin Pfeiffer, Wolfgang Lauer, Jörg-Uwe Meyer…

    Citation: Journal of Biomedical Semantics 2019 10:9

    Content type: Research

    Published on:

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