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  1. Content type: Research

    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

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  2. Content type: Research

    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

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  3. Content type: Research

    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

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  4. Content type: Review

    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

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  5. Content type: Research

    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

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  6. Content type: Software

    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

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  7. Content type: Research

    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

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

  8. Content type: Research

    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

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

  9. Content type: Research

    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

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

  10. Content type: Research

    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

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

  11. Content type: Research

    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

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

  12. Content type: Research

    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

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

  13. Content type: Research

    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

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

  14. Content type: Research

    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

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

  15. Content type: Research

    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

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  16. Content type: Research

    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

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  17. Content type: Research

    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

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  18. Content type: Research

    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

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  19. Content type: Software

    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

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  20. Content type: Research

    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

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  21. Content type: Software

    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

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  22. Content type: Research

    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

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  23. Content type: Research

    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

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  24. Content type: Research

    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

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  25. Content type: Research

    Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated...

    Authors: Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai and Kazuhiko Ohe

    Citation: Journal of Biomedical Semantics 2017 8:22

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  26. Content type: Research

    Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and in...

    Authors: Marcos Martínez-Romero, Clement Jonquet, Martin J. O’Connor, John Graybeal, Alejandro Pazos and Mark A. Musen

    Citation: Journal of Biomedical Semantics 2017 8:21

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  27. Content type: Software

    We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-...

    Authors: Şenay Kafkas, Ian Dunham and Johanna McEntyre

    Citation: Journal of Biomedical Semantics 2017 8:20

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  28. Content type: Research

    Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing...

    Authors: Deepak K. Sharma, Harold R. Solbrig, Cui Tao, Chunhua Weng, Christopher G. Chute and Guoqian Jiang

    Citation: Journal of Biomedical Semantics 2017 8:19

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  29. Content type: Software

    Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automat...

    Authors: David Osumi-Sutherland, Melanie Courtot, James P. Balhoff and Christopher Mungall

    Citation: Journal of Biomedical Semantics 2017 8:18

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  30. Content type: Research

    Research for ontology evaluation is scarce. If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the on...

    Authors: Muhammad Amith and Cui Tao

    Citation: Journal of Biomedical Semantics 2017 8:17

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  31. Content type: Research

    A standard task in pharmacogenomics research is identifying genes that may be involved in drug response variability, i.e., pharmacogenes. Because genomic experiments tended to generate many false positives, co...

    Authors: Kevin Dalleau, Yassine Marzougui, Sébastien Da Silva, Patrice Ringot, Ndeye Coumba Ndiaye and Adrien Coulet

    Citation: Journal of Biomedical Semantics 2017 8:16

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  32. Content type: Research

    Single Nucleotide Polymorphisms (SNPs) are among the most important types of genetic variations influencing common diseases and phenotypes. Recently, some corpora and methods have been developed with the purpo...

    Authors: Behrouz Bokharaeian, Alberto Diaz, Nasrin Taghizadeh, Hamidreza Chitsaz and Ramyar Chavoshinejad

    Citation: Journal of Biomedical Semantics 2017 8:14

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  33. Content type: Research

    Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to b...

    Authors: Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude Warren Jr, Durre Zehra, Stefan Decker and Dietrich Rebholz-Schuhmann

    Citation: Journal of Biomedical Semantics 2017 8:13

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  34. Content type: Software

    Integrating multiple sources of pharmacovigilance evidence has the potential to advance the science of safety signal detection and evaluation. In this regard, there is a need for more research on how to integr...

    Authors:

    Citation: Journal of Biomedical Semantics 2017 8:11

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  35. Content type: Research

    The Drug Ontology (DrOn) is an OWL2-based representation of drug products and their ingredients, mechanisms of action, strengths, and dose forms. We originally created DrOn for use cases in comparative effecti...

    Authors: William R. Hogan, Josh Hanna, Amanda Hicks, Samira Amirova, Baxter Bramblett, Matthew Diller, Rodel Enderez, Timothy Modzelewski, Mirela Vasconcelos and Chris Delcher

    Citation: Journal of Biomedical Semantics 2017 8:10

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  36. Content type: Research

    Analysing public opinions on HPV vaccines on social media using machine learning based approaches will help us understand the reasons behind the low vaccine coverage and come up with corresponding strategies t...

    Authors: Jingcheng Du, Jun Xu, Hsingyi Song, Xiangyu Liu and Cui Tao

    Citation: Journal of Biomedical Semantics 2017 8:9

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  37. Content type: Research

    Identifying incident cancer cases within a population remains essential for scientific research in oncology. Data produced within electronic health records can be useful for this purpose. Due to the multiplici...

    Authors: Vianney Jouhet, Fleur Mougin, Bérénice Bréchat and Frantz Thiessard

    Citation: Journal of Biomedical Semantics 2017 8:6

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  38. Content type: Research

    Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stake...

    Authors: Yasar Khan, Muhammad Saleem, Muntazir Mehdi, Aidan Hogan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann and Ratnesh Sahay

    Citation: Journal of Biomedical Semantics 2017 8:5

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  39. Content type: Research

    Ectopic pregnancy is a frequent early complication of pregnancy associated with significant rates of morbidly and mortality. The positive diagnosis of this condition is established through transvaginal ultraso...

    Authors: Ferdinand Dhombres, Paul Maurice, Stéphanie Friszer, Lucie Guilbaud, Nathalie Lelong, Babak Khoshnood, Jean Charlet, Nicolas Perrot, Eric Jauniaux, Davor Jurkovic and Jean-Marie Jouannic

    Citation: Journal of Biomedical Semantics 2017 8:4

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  40. Content type: Research

    Drug product data is available on the Web in a distributed fashion. The reasons lie within the regulatory domains, which exist on a national level. As a consequence, the drug data available on the Web are inde...

    Authors: Milos Jovanovik and Dimitar Trajanov

    Citation: Journal of Biomedical Semantics 2017 8:3

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  41. Content type: Research

    Biomedical ontologies aim at providing the most exhaustive and rigorous representation of reality as described by biomedical sciences. A large part of medical reasoning deals with diagnosis and is essentially ...

    Authors: Adrien Barton, Jean-François Ethier, Régis Duvauferrier and Anita Burgun

    Citation: Journal of Biomedical Semantics 2017 8:1

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  42. Content type: Research

    Semantic relatedness is a measure that quantifies the strength of a semantic link between two concepts. Often, it can be efficiently approximated with methods that operate on words, which represent these conce...

    Authors: Maciej Rybinski and José Francisco Aldana-Montes

    Citation: Journal of Biomedical Semantics 2016 7:67

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