Skip to main content

Articles

Page 1 of 11

  1. 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 describin...

    Authors: César H. Bernabé, Núria Queralt-Rosinach, Vítor E. Silva Souza, Luiz Olavo Bonino da Silva Santos, Barend Mons, Annika Jacobsen and Marco Roos
    Citation: Journal of Biomedical Semantics 2023 14:21
  2. Knowledge graphs (KGs) are an important tool for representing complex relationships between entities in the biomedical domain. Several methods have been proposed for learning embeddings that can be used to pre...

    Authors: Daniel Daza, Dimitrios Alivanistos, Payal Mitra, Thom Pijnenburg, Michael Cochez and Paul Groth
    Citation: Journal of Biomedical Semantics 2023 14:20
  3. Healthcare data and the knowledge gleaned from it play a key role in improving the health of current and future patients. These knowledge sources are regularly represented as ‘linked’ resources based on the Re...

    Authors: Shuxin Zhang, Nirupama Benis and Ronald Cornet
    Citation: Journal of Biomedical Semantics 2023 14:19
  4. Multiple studies have investigated bibliometric features and uncategorized scholarly documents for the influential scholarly document prediction task. In this paper, we describe our work that attempts to go be...

    Authors: Gollam Rabby, Jennifer D’Souza, Allard Oelen, Lucie Dvorackova, Vojtěch Svátek and Sören Auer
    Citation: Journal of Biomedical Semantics 2023 14:18
  5. Open Science Graphs (OSGs) are scientific knowledge graphs representing different entities of the research lifecycle (e.g. projects, people, research outcomes, institutions) and the relationships among them. T...

    Authors: Elli Papadopoulou, Alessia Bardi, George Kakaletris, Diamadis Tziotzios, Paolo Manghi and Natalia Manola
    Citation: Journal of Biomedical Semantics 2023 14:17
  6. 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 exc...

    Authors: Victor Eiti Yamamoto, Juliana Medeiros Destro and Julio Cesar dos Reis
    Citation: Journal of Biomedical Semantics 2023 14:16
  7. 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 change...

    Authors: Sara Diaz Benavides, Silvio D. Cardoso, Marcos Da Silveira and Cédric Pruski
    Citation: Journal of Biomedical Semantics 2023 14:15
  8. Clinical early warning scoring systems, have improved patient outcomes in a range of specializations and global contexts. These systems are used to predict patient deterioration. A multitude of patient-level p...

    Authors: Cilia E. Zayas, Justin M. Whorton, Kevin W. Sexton, Charles D. Mabry, S. Clint Dowland and Mathias Brochhausen
    Citation: Journal of Biomedical Semantics 2023 14:14
  9. Current animal protection laws require replacement of animal experiments with alternative methods, whenever such methods are suitable to reach the intended scientific objective. However, searching for alternat...

    Authors: Mariana Neves, Antonina Klippert, Fanny Knöspel, Juliane Rudeck, Ailine Stolz, Zsofia Ban, Markus Becker, Kai Diederich, Barbara Grune, Pia Kahnau, Nils Ohnesorge, Johannes Pucher, Gilbert Schönfelder, Bettina Bert and Daniel Butzke
    Citation: Journal of Biomedical Semantics 2023 14:13
  10. With the capacity to produce and record data electronically, Scientific research and the data associated with it have grown at an unprecedented rate. However, despite a decent amount of data now existing in an...

    Authors: Steve Penn, Jane Lomax, Anneli Karlsson, Vincent Antonucci, Carl-Dieter Zachmann, Samantha Kanza, Stephan Schurer and John Turner
    Citation: Journal of Biomedical Semantics 2023 14:10
  11. Clinical decision support systems have been widely deployed to guide healthcare decisions on patient diagnosis, treatment choices, and patient management through evidence-based recommendations. These recommend...

    Authors: Oshani Seneviratne, Amar K. Das, Shruthi Chari, Nkechinyere N. Agu, Sabbir M. Rashid, Jamie McCusker, Jade S. Franklin, Miao Qi, Kristin P. Bennett, Ching-Hua Chen, James A. Hendler and Deborah L. McGuinness
    Citation: Journal of Biomedical Semantics 2023 14:8
  12. The current rise of Open Science and Reproducibility in the Life Sciences requires the creation of rich, machine-actionable metadata in order to better share and reuse biological digital resources such as data...

    Authors: Alban Gaignard, Thomas Rosnet, Frédéric De Lamotte, Vincent Lefort and Marie-Dominique Devignes
    Citation: Journal of Biomedical Semantics 2023 14:7
  13. The Findable, Accessible, Interoperable and Reusable(FAIR) Principles explicitly require the use of FAIR vocabularies, but what precisely constitutes a FAIR vocabulary remains unclear. Being able to define FAI...

    Authors: Fuqi Xu, Nick Juty, Carole Goble, Simon Jupp, Helen Parkinson and Mélanie Courtot
    Citation: Journal of Biomedical Semantics 2023 14:6
  14. Drug-drug interaction (DDI) information retrieval (IR) is an important natural language process (NLP) task from the PubMed literature. For the first time, active learning (AL) is studied in DDI IR analysis. DD...

    Authors: Weixin Xie, Kunjie Fan, Shijun Zhang and Lang Li
    Citation: Journal of Biomedical Semantics 2023 14:5
  15. The majority of available datasets in open government data are statistical. They are widely published by various governments to be used by the public and data consumers. However, most open government data port...

    Authors: Enayat Rajabi, Rishi Midha and Jairo Francisco de Souza
    Citation: Journal of Biomedical Semantics 2023 14:4
  16. Evaluating the impact of environmental exposures on organism health is a key goal of modern biomedicine and is critically important in an age of greater pollution and chemicals in our environment. Environmenta...

    Authors: Lauren E. Chan, Anne E. Thessen, William D. Duncan, Nicolas Matentzoglu, Charles Schmitt, Cynthia J. Grondin, Nicole Vasilevsky, Julie A. McMurry, Peter N. Robinson, Christopher J. Mungall and Melissa A. Haendel
    Citation: Journal of Biomedical Semantics 2023 14:3
  17. Information pertaining to mechanisms, management and treatment of disease-causing pathogens including viruses and bacteria is readily available from research publications indexed in MEDLINE. However, identifyi...

    Authors: Antonio Jose Jimeno Yepes and Karin Verspoor
    Citation: Journal of Biomedical Semantics 2023 14:1
  18. The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and saf...

    Authors: Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah…
    Citation: Journal of Biomedical Semantics 2022 13:25
  19. Vaccine information in European electronic health record (EHR) databases is represented using various clinical and database-specific coding systems and drug vocabularies. The lack of harmonization constitutes ...

    Authors: Benedikt FH Becker, Jan A Kors, Erik M van Mulligen and Miriam CJM Sturkenboom
    Citation: Journal of Biomedical Semantics 2022 13:24
  20. Health data analytics is an area that is facing rapid change due to the acceleration of digitization of the health sector, and the changing landscape of health data and clinical terminology standards. Our rese...

    Authors: John Grimes, Piotr Szul, Alejandro Metke-Jimenez, Michael Lawley and Kylynn Loi
    Citation: Journal of Biomedical Semantics 2022 13:23
  21. The Vaccine Ontology (VO) is a biomedical ontology that standardizes vaccine annotation. Errors in VO will affect a multitude of applications that it is being used in. Quality assurance of VO is imperative to ...

    Authors: Warren Manuel, Rashmie Abeysinghe, Yongqun He, Cui Tao and Licong Cui
    Citation: Journal of Biomedical Semantics 2022 13:22
  22. The concept of Data Management Plan (DMP) has emerged as a fundamental tool to help researchers through the systematical management of data. The Research Data Alliance DMP Common Standard (DCS) working group d...

    Authors: João Cardoso, Leyla J. Castro, Fajar J. Ekaputra, Marie C. Jacquemot, Marek Suchánek, Tomasz Miksa and José Borbinha
    Citation: Journal of Biomedical Semantics 2022 13:21
  23. Ontology matching should contribute to the interoperability aspect of FAIR data (Findable, Accessible, Interoperable, and Reusable). Multiple data sources can use different ontologies for annotating their data...

    Authors: Philip van Damme, Jesualdo Tomás Fernández-Breis, Nirupama Benis, Jose Antonio Miñarro-Gimenez, Nicolette F. de Keizer and Ronald Cornet
    Citation: Journal of Biomedical Semantics 2022 13:19
  24. In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eS...

    Authors: Lars Vogt, István Mikó and Thomas Bartolomaeus
    Citation: Journal of Biomedical Semantics 2022 13:18
  25. Adverse events induced by drug-drug interactions are a major concern in the United States. Current research is moving toward using electronic health record (EHR) data, including for adverse drug events discove...

    Authors: Samar Binkheder, Heng-Yi Wu, Sara K. Quinney, Shijun Zhang, Md. Muntasir Zitu, Chien‐Wei Chiang, Lei Wang, Josette Jones and Lang Li
    Citation: Journal of Biomedical Semantics 2022 13:17

    The Correction to this article has been published in Journal of Biomedical Semantics 2022 13:20

  26. Evidence-based medicine propagates that medical/clinical decisions are made by taking into account high-quality evidence, most notably in the form of randomized clinical trials. Evidence-based decision-making ...

    Authors: Olivia Sanchez-Graillet, Christian Witte, Frank Grimm, Steffen Grautoff, Basil Ell and Philipp Cimiano
    Citation: Journal of Biomedical Semantics 2022 13:16
  27. Most previous relation extraction (RE) studies have focused on intra sentence relations and have ignored relations that span sentences, i.e. inter sentence relations. Such relations connect entities at the doc...

    Authors: Hoang-Quynh Le, Duy-Cat Can and Nigel Collier
    Citation: Journal of Biomedical Semantics 2022 13:15
  28. The evidence-based medicine paradigm requires the ability to aggregate and compare outcomes of interventions across different trials. This can be facilitated and partially automatized by information extraction...

    Authors: Olivia Sanchez-Graillet, Christian Witte, Frank Grimm and Philipp Cimiano
    Citation: Journal of Biomedical Semantics 2022 13:14
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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

Annual Journal Metrics

  • 2022 Citation Impact
    1.9 - 2-year Impact Factor
    2.6 - 5-year Impact Factor
    0.870 - SNIP (Source Normalized Impact per Paper)
    0.697 - SJR (SCImago Journal Rank)

    2023 Speed
    14 days submission to first editorial decision for all manuscripts (Median)
    265 days submission to accept (Median)

    2022 Usage 
    248,663 downloads
    3,363 Altmetric mentions