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  1. Research

    Dynamically analyzing cell interactions in biological environments using multiagent social learning framework

    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...

    Chengwei Zhang, Xiaohong Li, Shuxin Li and Zhiyong Feng

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

    Published on: 20 September 2017

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

  2. Research

    Constructing an integrated gene similarity network for the identification of disease genes

    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...

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

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

    Published on: 20 September 2017

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

  3. Research

    Revealing protein functions based on relationships of interacting proteins and GO terms

    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...

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

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

    Published on: 20 September 2017

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

  4. Research

    Investigations on factors influencing HPO-based semantic similarity calculation

    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...

    Jiajie Peng, Qianqian Li and Xuequn Shang

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

    Published on: 20 September 2017

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

  5. Research

    Multiple kernels learning-based biological entity relationship extraction method

    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...

    Xu Dongliang, Pan Jingchang and Wang Bailing

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

    Published on: 20 September 2017

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

  6. Research

    A novel method to identify pre-microRNA in various species knowledge base on various species

    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...

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

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

    Published on: 20 September 2017

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

  7. Research

    An automatic approach for constructing a knowledge base of symptoms in Chinese

    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...

    Tong Ruan, Mengjie Wang, Jian Sun, Ting Wang, Lu Zeng, Yichao Yin and Ju Gao

    Journal of Biomedical Semantics 2017 8(Suppl 1):33

    Published on: 20 September 2017

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

  8. Research

    DisSetSim: an online system for calculating similarity between disease sets

    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...

    Yang Hu, Lingling Zhao, Zhiyan Liu, Hong Ju, Hongbo Shi, Peigang Xu, Yadong Wang and Liang Cheng

    Journal of Biomedical Semantics 2017 8(Suppl 1):28

    Published on: 20 September 2017

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

  9. Research

    Towards achieving semantic interoperability of clinical study data with FHIR

    Observational clinical studies play a pivotal role in advancing medical knowledge and patient healthcare. To lessen the prohibitive costs of conducting these studies and support evidence-based medicine, result...

    Hugo Leroux, Alejandro Metke-Jimenez and Michael J. Lawley

    Journal of Biomedical Semantics 2017 8:41

    Published on: 19 September 2017

  10. Research

    Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data

    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, ...

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

    Journal of Biomedical Semantics 2017 8:40

    Published on: 19 September 2017

  11. Research

    Predicting activities of daily living for cancer patients using an ontology-guided machine learning methodology

    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...

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

    Journal of Biomedical Semantics 2017 8:39

    Published on: 16 September 2017

  12. Research

    Design of an extensive information representation scheme for clinical narratives

    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...

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

    Journal of Biomedical Semantics 2017 8:37

    Published on: 11 September 2017

  13. Research

    Ontology-based specification, identification and analysis of perioperative risks

    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...

    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

    Journal of Biomedical Semantics 2017 8:36

    Published on: 6 September 2017

  14. Software

    RDFIO: extending Semantic MediaWiki for interoperable biomedical data management

    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...

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

    Journal of Biomedical Semantics 2017 8:35

    Published on: 4 September 2017

  15. Research

    Discovering associations between adverse drug events using pattern structures and ontologies

    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...

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

    Journal of Biomedical Semantics 2017 8:29

    Published on: 22 August 2017

  16. Software

    An ontology-driven tool for structured data acquisition using Web forms

    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...

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

    Journal of Biomedical Semantics 2017 8:26

    Published on: 1 August 2017

  17. Research

    Towards a more molecular taxonomy of disease

    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...

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

    Journal of Biomedical Semantics 2017 8:25

    Published on: 27 July 2017

  18. Research

    Ontological interpretation of biomedical database content

    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...

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

    Journal of Biomedical Semantics 2017 8:24

    Published on: 26 June 2017

  19. Research

    NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation

    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...

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

    Journal of Biomedical Semantics 2017 8:21

    Published on: 7 June 2017

  20. Software

    Literature evidence in open targets - a target validation platform

    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-...

    Şenay Kafkas, Ian Dunham and Johanna McEntyre

    Journal of Biomedical Semantics 2017 8:20

    Published on: 6 June 2017

  21. Software

    Dead simple OWL design patterns

    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...

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

    Journal of Biomedical Semantics 2017 8:18

    Published on: 5 June 2017

  22. Research

    Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies

    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...

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

    Journal of Biomedical Semantics 2017 8:19

    Published on: 5 June 2017

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