Skip to main content


Page 3 of 11

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed...

    Authors: Mengyi Zhao, Songmao Zhang, Weizhuo Li and Guowei Chen
    Citation: Journal of Biomedical Semantics 2018 9:11
  19. The Gene Ontology (GO) consists of over 40,000 terms for biological processes, cell components and gene product activities linked into a graph structure by over 90,000 relationships. It has been used to annota...

    Authors: David J. Osumi-Sutherland, Enrico Ponta, Melanie Courtot, Helen Parkinson and Laura Badi
    Citation: Journal of Biomedical Semantics 2018 9:10
  20. Pathogenesis of inflammatory diseases can be tracked by studying the causality relationships among the factors contributing to its development. We could, for instance, hypothesize on the connections of the pat...

    Authors: Asan Agibetov, Ernesto Jiménez-Ruiz, Marta Ondrésik, Alessandro Solimando, Imon Banerjee, Giovanna Guerrini, Chiara E. Catalano, Joaquim M. Oliveira, Giuseppe Patanè, Rui L. Reis and Michela Spagnuolo
    Citation: Journal of Biomedical Semantics 2018 9:9
  21. Treatment of type 2 diabetes mellitus (T2DM) is a complex problem. A clinical decision support system (CDSS) based on massive and distributed electronic health record data can facilitate the automation of this...

    Authors: Shaker El-Sappagh, Daehan Kwak, Farman Ali and Kyung-Sup Kwak
    Citation: Journal of Biomedical Semantics 2018 9:8
  22. Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineeri...

    Authors: Nagesh C. Panyam, Karin Verspoor, Trevor Cohn and Kotagiri Ramamohanarao
    Citation: Journal of Biomedical Semantics 2018 9:7
  23. The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the ba...

    Authors: Viktor Senderov, Kiril Simov, Nico Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert A. Morris and Lyubomir Penev
    Citation: Journal of Biomedical Semantics 2018 9:5
  24. Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies themselves. The biomedical tracks in the Onto...

    Authors: Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto and Isabel F. Cruz
    Citation: Journal of Biomedical Semantics 2018 9:4
  25. Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interop...

    Authors: Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton and Edison Ong
    Citation: Journal of Biomedical Semantics 2018 9:3
  26. Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers (“pre-coordinated concepts”). Less frequently, normalization corpora have used concepts with multiple id...

    Authors: John D. Osborne, Matthew B. Neu, Maria I. Danila, Thamar Solorio and Steven J. Bethard
    Citation: Journal of Biomedical Semantics 2018 9:2
  27. Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomica...

    Authors: Miguel Ángel Rodríguez-García, Georgios V. Gkoutos, Paul N. Schofield and Robert Hoehndorf
    Citation: Journal of Biomedical Semantics 2017 8:58
  28. One important type of information contained in biomedical research literature is the newly discovered relationships between phenotypes and genotypes. Because of the large quantity of literature, a reliable aut...

    Authors: Maryam Khordad and Robert E. Mercer
    Citation: Journal of Biomedical Semantics 2017 8:57
  29. The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important f...

    Authors: Ian Harrow, Ernesto Jiménez-Ruiz, Andrea Splendiani, Martin Romacker, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, James Malone and Arild Waaler
    Citation: Journal of Biomedical Semantics 2017 8:55
  30. There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, ...

    Authors: Aisha Blfgeh, Jennifer Warrender, Catharien M. U. Hilkens and Phillip Lord
    Citation: Journal of Biomedical Semantics 2017 8:54
  31. High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires ...

    Authors: Vincent J. Henry, Anne Goelzer, Arnaud Ferré, Stephan Fischer, Marc Dinh, Valentin Loux, Christine Froidevaux and Vincent Fromion
    Citation: Journal of Biomedical Semantics 2017 8:53
  32. An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protoco...

    Authors: Olga Giraldo, Alexander García, Federico López and Oscar Corcho
    Citation: Journal of Biomedical Semantics 2017 8:52
  33. One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has a...

    Authors: Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung…
    Citation: Journal of Biomedical Semantics 2017 8:50
  34. Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to hete...

    Authors: Freddy Priyatna, Raul Alonso-Calvo, Sergio Paraiso-Medina and Oscar Corcho
    Citation: Journal of Biomedical Semantics 2017 8:49
  35. In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists.

    Authors: Claudia Mazo, Liliana Salazar, Oscar Corcho, Maria Trujillo and Enrique Alegre
    Citation: Journal of Biomedical Semantics 2017 8:47
  36. Regional and epidemiological cancer registries are important for cancer research and the quality management of cancer treatment. Many technological solutions are available to collect and analyse data for cance...

    Authors: Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis and Martin Boeker
    Citation: Journal of Biomedical Semantics 2017 8:46
  37. The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such text...

    Authors: Jelena Jovanović and Ebrahim Bagheri
    Citation: Journal of Biomedical Semantics 2017 8:44
  38. In this paper we present the approach that we employed to deal with large scale multi-label semantic indexing of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge (...

    Authors: Yannis Papanikolaou, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos and Ioannis Vlahavas
    Citation: Journal of Biomedical Semantics 2017 8:43
  39. While a large number of well-known knowledge bases (KBs) in life science have been published as Linked Open Data, there are few KBs in Chinese. However, KBs in Chinese are necessary when we want to automatical...

    Authors: Tong Ruan, Mengjie Wang, Jian Sun, Ting Wang, Lu Zeng, Yichao Yin and Ju Gao
    Citation: Journal of Biomedical Semantics 2017 8(Suppl 1):33

    This article is part of a Supplement: Volume 8 Supplement 1

  40. Functional similarity between molecules results in similar phenotypes, such as diseases. Therefore, it is an effective way to reveal the function of molecules based on their induced diseases. However, the lack...

    Authors: Yang Hu, Lingling Zhao, Zhiyan Liu, Hong Ju, Hongbo Shi, Peigang Xu, Yadong Wang and Liang Cheng
    Citation: Journal of Biomedical Semantics 2017 8(Suppl 1):28

    This article is part of a Supplement: Volume 8 Supplement 1

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)

    2022 Speed
    14 days submission to first editorial decision for all manuscripts (Median)
    363 days submission to accept (Median)

    2022 Usage 
    3,363 Altmetric mentions