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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...
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
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...
Journal of Biomedical Semantics 2017 8:42
Published on: 20 September 2017
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...
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
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...
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
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...
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
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...
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
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...
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
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...
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
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...
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
Research
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...
Journal of Biomedical Semantics 2017 8:41
Published on: 19 September 2017
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, ...
Journal of Biomedical Semantics 2017 8:40
Published on: 19 September 2017
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...
Journal of Biomedical Semantics 2017 8:39
Published on: 16 September 2017
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...
Journal of Biomedical Semantics 2017 8:37
Published on: 11 September 2017
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...
Journal of Biomedical Semantics 2017 8:36
Published on: 6 September 2017
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...
Journal of Biomedical Semantics 2017 8:35
Published on: 4 September 2017
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...
Journal of Biomedical Semantics 2017 8:29
Published on: 22 August 2017
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...
Journal of Biomedical Semantics 2017 8:26
Published on: 1 August 2017
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...
Journal of Biomedical Semantics 2017 8:25
Published on: 27 July 2017
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...
Journal of Biomedical Semantics 2017 8:24
Published on: 26 June 2017
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...
Journal of Biomedical Semantics 2017 8:23
Published on: 26 June 2017
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...
Journal of Biomedical Semantics 2017 8:22
Published on: 19 June 2017
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...
Journal of Biomedical Semantics 2017 8:21
Published on: 7 June 2017
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-...
Journal of Biomedical Semantics 2017 8:20
Published on: 6 June 2017
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...
Journal of Biomedical Semantics 2017 8:18
Published on: 5 June 2017
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...
Journal of Biomedical Semantics 2017 8:19
Published on: 5 June 2017
