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  1. 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:

  2. 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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  3. 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

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  4. 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

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  5. 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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  6. 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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  7. 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:

  8. 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

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  9. 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

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  10. 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

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  11. 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

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  12. 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

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  13. 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

  14. 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

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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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:

  20. 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

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  23. 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

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  24. 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

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  26. 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

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  27. 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

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  28. 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:

  29. The ability to express the same meaning in different ways is a well-known property of natural language. This amazing property is the source of major difficulties in natural language processing. Given the const...

    Authors: Oscar Lithgow-Serrano, Socorro Gama-Castro, Cecilia Ishida-Gutiérrez, Citlalli Mejía-Almonte, Víctor H. Tierrafría, Sara Martínez-Luna, Alberto Santos-Zavaleta, David Velázquez-Ramírez and Julio Collado-Vides

    Citation: Journal of Biomedical Semantics 2019 10:8

    Content type: Research

    Published on:

  31. Social risk factors are important dimensions of health and are linked to access to care, quality of life, health outcomes and life expectancy. However, in the Electronic Health Record, data related to many soc...

    Authors: Mike Conway, Salomeh Keyhani, Lee Christensen, Brett R. South, Marzieh Vali, Louise C. Walter, Danielle L. Mowery, Samir Abdelrahman and Wendy W. Chapman

    Citation: Journal of Biomedical Semantics 2019 10:6

    Content type: Software

    Published on:

  34. A Cardiac-centered Frailty Ontology can be an important foundation for using NLP to assess patient frailty. Frailty is an important consideration when making patient treatment decisions, particularly in older ...

    Authors: Kristina Doing-Harris, Bruce E. Bray, Anne Thackeray, Rashmee U. Shah, Yijun Shao, Yan Cheng, Qing Zeng-Treitler, Jennifer H. Garvin and Charlene Weir

    Citation: Journal of Biomedical Semantics 2019 10:3

    Content type: Research

    Published on:

  35. VerbNet, an extensive computational verb lexicon for English, has proved useful for supporting a wide range of Natural Language Processing tasks requiring information about the behaviour and meaning of verbs. ...

    Authors: Billy Chiu, Olga Majewska, Sampo Pyysalo, Laura Wey, Ulla Stenius, Anna Korhonen and Martha Palmer

    Citation: Journal of Biomedical Semantics 2019 10:2

    Content type: Database

    Published on:

  37. Structured electronic health records are a rich resource for identifying novel correlations, such as co-morbidities and adverse drug reactions. For drug development and better understanding of biomedical pheno...

    Authors: Thomas C. Rindflesch, Catherine L. Blake, Michael J. Cairelli, Marcelo Fiszman, Caroline J. Zeiss and Halil Kilicoglu

    Citation: Journal of Biomedical Semantics 2018 9:25

    Content type: Research

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  38. Even though several high-quality clinical terminologies, such as SNOMED CT and LOINC, are readily available, uptake in clinical systems has been slow and many continue to capture information in plain text or u...

    Authors: Alejandro Metke-Jimenez, Jim Steel, David Hansen and Michael Lawley

    Citation: Journal of Biomedical Semantics 2018 9:24

    Content type: Software

    Published on:

  39. Biomedical knowledge graphs have become important tools to computationally analyse the comprehensive body of biomedical knowledge. They represent knowledge as subject-predicate-object triples, in which the pre...

    Authors: Wytze J. Vlietstra, Rein Vos, Anneke M. Sijbers, Erik M. van Mulligen and Jan A. Kors

    Citation: Journal of Biomedical Semantics 2018 9:23

    Content type: Research

    Published on:

  40. In this paper, we discuss the design and development of a formal ontology to describe misinformation about vaccines. Vaccine misinformation is one of the drivers leading to vaccine hesitancy in patients. While...

    Authors: Muhammad Amith and Cui Tao

    Citation: Journal of Biomedical Semantics 2018 9:22

    Content type: Research

    Published on:

  41. While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has f...

    Authors: Prodromos Kolyvakis, Alexandros Kalousis, Barry Smith and Dimitris Kiritsis

    Citation: Journal of Biomedical Semantics 2018 9:21

    Content type: Research

    Published on:

  42. Entropy has become increasingly popular in computer science and information theory because it can be used to measure the predictability and redundancy of knowledge bases, especially ontologies. However, curren...

    Authors: Ying Shen, Daoyuan Chen, Buzhou Tang, Min Yang and Kai Lei

    Citation: Journal of Biomedical Semantics 2018 9:20

    Content type: Research

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  43. Vaccine has been one of the most successful public health interventions to date. However, vaccines are pharmaceutical products that carry risks so that many adverse events (AEs) are reported after receiving va...

    Authors: Junxiang Wang, Liang Zhao, Yanfang Ye and Yuji Zhang

    Citation: Journal of Biomedical Semantics 2018 9:19

    Content type: Research

    Published on:

  44. In recent years, Twitter has been applied to monitor diseases through its facility to monitor users’ comments and concerns in real-time. The analysis of tweets for disease mentions should reflect not only user...

    Authors: Joana M. Barros, Jim Duggan and Dietrich Rebholz-Schuhmann

    Citation: Journal of Biomedical Semantics 2018 9:18

    Content type: Research

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  45. Adverse drug reactions (ADRs), also called as drug adverse events (AEs), are reported in the FDA drug labels; however, it is a big challenge to properly retrieve and analyze the ADRs and their potential relati...

    Authors: Junguk Hur, Arzucan Özgür and Yongqun He

    Citation: Journal of Biomedical Semantics 2018 9:17

    Content type: Research

    Published on:

  46. Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of usin...

    Authors: Stefan Kropf, Alexandr Uciteli, Katrin Schierle, Peter Krücken, Kerstin Denecke and Heinrich Herre

    Citation: Journal of Biomedical Semantics 2018 9:16

    Content type: Research

    Published on:

  47. Prompted by the frequency of concomitant use of prescription drugs with natural products, and the lack of knowledge regarding the impact of pharmacokinetic-based natural product-drug interactions (PK-NPDIs), t...

    Authors: John Judkins, Jessica Tay-Sontheimer, Richard D. Boyce and Mathias Brochhausen

    Citation: Journal of Biomedical Semantics 2018 9:15

    Content type: Research

    Published on:

  48. Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides i...

    Authors: Elena Solovieva, Toshihide Shikanai, Noriaki Fujita and Hisashi Narimatsu

    Citation: Journal of Biomedical Semantics 2018 9:14

    Content type: Research

    Published on:

  49. Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardio...

    Authors: Mercedes Arguello Casteleiro, George Demetriou, Warren Read, Maria Jesus Fernandez Prieto, Nava Maroto, Diego Maseda Fernandez, Goran Nenadic, Julie Klein, John Keane and Robert Stevens

    Citation: Journal of Biomedical Semantics 2018 9:13

    Content type: Research

    Published on:

  50. Natural language processing applied to clinical text or aimed at a clinical outcome has been thriving in recent years. This paper offers the first broad overview of clinical Natural Language Processing (NLP) f...

    Authors: Aurélie Névéol, Hercules Dalianis, Sumithra Velupillai, Guergana Savova and Pierre Zweigenbaum

    Citation: Journal of Biomedical Semantics 2018 9:12

    Content type: Review

    Published on:

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ISSN: 2041-1480