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  1. 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:

  2. 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

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  3. 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

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  4. 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

    Content type: Research

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  5. 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

    Content type: Research

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  6. 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

    Content type: Research

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  7. 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

    Content type: Research

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  8. 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

    Content type: Research

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  9. 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

    Content type: Research

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  10. 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

    Content type: Research

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  11. 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

    Content type: Review

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  12. 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

    Content type: Research

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  13. 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

    Content type: Research

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  14. 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

    Content type: Research

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  15. 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

    Content type: Research

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  16. 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

    Content type: Research

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  17. 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

    Content type: Research

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  18. 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

    Content type: Research

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  19. 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

    Content type: Research

    Published on:

  20. 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

    Content type: Research

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  21. 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

    Content type: Research

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  22. 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

    Content type: Research

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  23. 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

    Content type: Review

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  24. 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

    Content type: Research

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  25. There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semanti...

    Authors: Marija Djokic-Petrovic, Vladimir Cvjetkovic, Jeremy Yang, Marko Zivanovic and David J. Wild

    Citation: Journal of Biomedical Semantics 2017 8:42

    Content type: Software

    Published on:

  26. Automatic extracting protein entity interaction information from biomedical literature can help to build protein relation network and design new drugs. There are more than 20 million literature abstracts inclu...

    Authors: Xu Dongliang, Pan Jingchang and Wang Bailing

    Citation: Journal of Biomedical Semantics 2017 8(Suppl 1):38

    Content type: Research

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

  27. Although disease diagnosis has greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis purely based on sequencing technologies for many diseases with c...

    Authors: Jiajie Peng, Qianqian Li and Xuequn Shang

    Citation: Journal of Biomedical Semantics 2017 8(Suppl 1):34

    Content type: Research

    Published on:

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

  28. 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

    Content type: Research

    Published on:

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

  29. Discovering novel genes that are involved human diseases is a challenging task in biomedical research. In recent years, several computational approaches have been proposed to prioritize candidate disease genes...

    Authors: Zhen Tian, Maozu Guo, Chunyu Wang, LinLin Xing, Lei Wang and Yin Zhang

    Citation: Journal of Biomedical Semantics 2017 8(Suppl 1):32

    Content type: Research

    Published on:

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

  30. Biological environment is uncertain and its dynamic is similar to the multiagent environment, thus the research results of the multiagent system area can provide valuable insights to the understanding of biolo...

    Authors: Chengwei Zhang, Xiaohong Li, Shuxin Li and Zhiyong Feng

    Citation: Journal of Biomedical Semantics 2017 8(Suppl 1):31

    Content type: Research

    Published on:

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

  31. More than 1/3 of human genes are regulated by microRNAs. The identification of microRNA (miRNA) is the precondition of discovering the regulatory mechanism of miRNA and developing the cure for genetic diseases...

    Authors: Tianyi Zhao, Ningyi Zhang, Ying Zhang, Jun Ren, Peigang Xu, Zhiyan Liu, Liang Cheng and Yang Hu

    Citation: Journal of Biomedical Semantics 2017 8(Suppl 1):30

    Content type: Research

    Published on:

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

  32. 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

    Content type: Research

    Published on:

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

  33. In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they inter...

    Authors: Zhixia Teng, Maozu Guo, Xiaoyan Liu, Zhen Tian and Kai Che

    Citation: Journal of Biomedical Semantics 2017 8(Suppl 1):27

    Content type: Research

    Published on:

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

  34. Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing a massive amount of sequencing datasets. Often, ...

    Authors: Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann and Ratnesh Sahay

    Citation: Journal of Biomedical Semantics 2017 8:40

    Content type: Research

    Published on:

  35. Bio-ontologies are becoming increasingly important in knowledge representation and in the machine learning (ML) fields. This paper presents a ML approach that incorporates bio-ontologies and its application to...

    Authors: Hua Min, Hedyeh Mobahi, Katherine Irvin, Sanja Avramovic and Janusz Wojtusiak

    Citation: Journal of Biomedical Semantics 2017 8:39

    Content type: Research

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  36. Knowledge representation frameworks are essential to the understanding of complex biomedical processes, and to the analysis of biomedical texts that describe them. Combined with natural language processing (NL...

    Authors: Louise Deléger, Leonardo Campillos, Anne-Laure Ligozat and Aurélie Névéol

    Citation: Journal of Biomedical Semantics 2017 8:37

    Content type: Research

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  37. Medical personnel in hospitals often works under great physical and mental strain. In medical decision-making, errors can never be completely ruled out. Several studies have shown that between 50 and 60% of ad...

    Authors: Alexandr Uciteli, Juliane Neumann, Kais Tahar, Kutaiba Saleh, Stephan Stucke, Sebastian Faulbrück-Röhr, André Kaeding, Martin Specht, Tobias Schmidt, Thomas Neumuth, Andreas Besting, Dominik Stegemann, Frank Portheine and Heinrich Herre

    Citation: Journal of Biomedical Semantics 2017 8:36

    Content type: Research

    Published on:

  38. Biological sciences are characterised not only by an increasing amount but also the extreme complexity of its data. This stresses the need for efficient ways of integrating these data in a coherent description...

    Authors: Samuel Lampa, Egon Willighagen, Pekka Kohonen, Ali King, Denny Vrandečić, Roland Grafström and Ola Spjuth

    Citation: Journal of Biomedical Semantics 2017 8:35

    Content type: Software

    Published on:

  39. Patient data, such as electronic health records or adverse event reporting systems, constitute an essential resource for studying Adverse Drug Events (ADEs). We explore an original approach to identify frequen...

    Authors: Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone and Adrien Coulet

    Citation: Journal of Biomedical Semantics 2017 8:29

    Content type: Research

    Published on:

  40. Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be auto...

    Authors: Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney and Mark A. Musen

    Citation: Journal of Biomedical Semantics 2017 8:26

    Content type: Software

    Published on:

  41. Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understand...

    Authors: Jisoo Park, Benjamin J. Hescott and Donna K. Slonim

    Citation: Journal of Biomedical Semantics 2017 8:25

    Content type: Research

    Published on:

  42. Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a d...

    Authors: Filipe Santana da Silva, Ludger Jansen, Fred Freitas and Stefan Schulz

    Citation: Journal of Biomedical Semantics 2017 8:24

    Content type: Research

    Published on:

  43. High-throughput methods in molecular biology provided researchers with abundance of experimental data that need to be interpreted in order to understand the experimental results. Manual methods of functional g...

    Authors: Aleksandra Gruca and Marek Sikora

    Citation: Journal of Biomedical Semantics 2017 8:23

    Content type: Research

    Published on:

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