Abstract:
BACKGROUND:Drug discovery is the process through which potential new medicines are identified. High-throughput screening and computer-aided drug discovery/design are the two main drug discovery methods for now, which have successfully discovered a series of drugs. However, development of new drugs is still an extremely time-consuming and expensive process. Biomedical literature contains important clues for the identification of potential treatments. It could support experts in biomedicine on their way towards new discoveries. METHODS:Here, we propose a biomedical knowledge graph-based drug discovery method called SemaTyP, which discovers candidate drugs for diseases by mining published biomedical literature. We first construct a biomedical knowledge graph with the relations extracted from biomedical abstracts, then a logistic regression model is trained by learning the semantic types of paths of known drug therapies' existing in the biomedical knowledge graph, finally the learned model is used to discover drug therapies for new diseases. RESULTS:The experimental results show that our method could not only effectively discover new drug therapies for new diseases, but also could provide the potential mechanism of action of the candidate drugs. CONCLUSIONS:In this paper we propose a novel knowledge graph based literature mining method for drug discovery. It could be a supplementary method for current drug discovery methods.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Sang S,Yang Z,Wang L,Liu X,Lin H,Wang Jdoi
10.1186/s12859-018-2167-5subject
Has Abstractpub_date
2018-05-30 00:00:00pages
193issue
1issn
1471-2105pii
10.1186/s12859-018-2167-5journal_volume
19pub_type
杂志文章abstract:BACKGROUND:In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell surface shedding is an exemplary application area of this approach. RESULTS:We developed ImproViser...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-207
更新日期:2014-06-19 00:00:00
abstract:BACKGROUND:Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order t...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-480
更新日期:2008-11-13 00:00:00
abstract:BACKGROUND:Cancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation are equally likely. When the fixation of some mutations depends on the presence of previous ones, identifying restrictions in the order of accumulation of mutations can lead to the discovery of therap...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0466-7
更新日期:2015-02-12 00:00:00
abstract:BACKGROUND:Because common complex diseases are affected by multiple genes and environmental factors, it is essential to investigate gene-gene and/or gene-environment interactions to understand genetic architecture of complex diseases. After the great success of large scale genome-wide association (GWA) studies using th...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S9-S5
更新日期:2012-06-11 00:00:00
abstract:BACKGROUND:SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Understanding the binding mode of SARS CoVMpro with a specific substrate is useful and contributes to struc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S1-S48
更新日期:2009-01-30 00:00:00
abstract:BACKGROUND:Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when building and installing the run programs required for these analyses. For scientists that may not be as...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2964-5
更新日期:2019-06-28 00:00:00
abstract:BACKGROUND:Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3293-4
更新日期:2019-12-27 00:00:00
abstract:BACKGROUND:Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembled onto a single support - ty...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2111-8
更新日期:2018-04-19 00:00:00
abstract:BACKGROUND:Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed for predicting their locations in archaeal, bacterial and eukaryotic genomes. However, a prediction method designed for a particular kind o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-163
更新日期:2007-05-21 00:00:00
abstract:BACKGROUND:Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-108
更新日期:2005-04-27 00:00:00
abstract:BACKGROUND:Phosphorylated histone H2AX, also known as γH2AX, forms μm-sized nuclear foci at the sites of DNA double-strand breaks (DSBs) induced by ionizing radiation and other agents. Due to their specificity and sensitivity, γH2AX immunoassays have become the gold standard for studying DSB induction and repair. One o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3370-8
更新日期:2020-01-28 00:00:00
abstract:BACKGROUND:Infectious disease modeling and computational power have evolved such that large-scale agent-based models (ABMs) have become feasible. However, the increasing hardware complexity requires adapted software designs to achieve the full potential of current high-performance workstations. RESULTS:We have found l...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0612-2
更新日期:2015-06-02 00:00:00
abstract:BACKGROUND:Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-112
更新日期:2010-03-01 00:00:00
abstract:BACKGROUND:Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, integrative analysis have been performed by using genomics, transcriptomics, epigenomics, proteomics an...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03691-3
更新日期:2020-09-30 00:00:00
abstract:BACKGROUND:Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as "molecular switches" in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S1-S3
更新日期:2011-02-15 00:00:00
abstract::In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a re...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S19-S1
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable binding pose of a ligand, when bound to a receptor protein, from among a large set of candidate poses. Des...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-16-S6-S3
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Ubiquitylation plays an important role in regulating protein functions. Recently, experimental methods were developed toward effective identification of ubiquitylation sites. To efficiently explore more undiscovered ubiquitylation sites, this study aims to develop an accurate sequence-based prediction method...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-310
更新日期:2008-07-15 00:00:00
abstract:BACKGROUND:Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a class of small, non-coding RNAs that attract great attention because of their role in regulation of...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0836-1
更新日期:2015-12-10 00:00:00
abstract:BACKGROUND:Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2390-0
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but h...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-108
更新日期:2010-02-25 00:00:00
abstract:BACKGROUND:The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-cou...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-7-254
更新日期:2006-05-15 00:00:00
abstract:BACKGROUND:Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-478
更新日期:2010-09-23 00:00:00
abstract:BACKGROUND:Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex structures, protein-DNA docking can be used to predict native or near-native...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2538-y
更新日期:2018-12-21 00:00:00
abstract:BACKGROUND:Protein-protein interactions (PPIs) play crucial roles in virtually every aspect of cellular function within an organism. Over the last decade, the development of novel high-throughput techniques has resulted in enormous amounts of data and provided valuable resources for studying protein interactions. Howev...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S7-S3
更新日期:2012-05-08 00:00:00
abstract:BACKGROUND:Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutations and other genomic events (copies, deletions, captures) during transposition. The identification ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-474
更新日期:2010-09-22 00:00:00
abstract:BACKGROUND:Protein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic analysis. RESULTS:In thi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-252
更新日期:2014-07-25 00:00:00
abstract:BACKGROUND:To infer gene regulatory networks from time series gene profiles, two important tasks that are related to biological systems must be undertaken. One task is to determine a valid network structure that has topological properties that can influence the network dynamics profoundly. The other task is to optimize...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S15-S8
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Hidden variability is a fundamentally important issue in the context of gene expression studies. Collected tissue samples may have a wide variety of hidden effects that may alter their transcriptional landscape significantly. As a result their actual differential expression pattern can be potentially distort...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-236
更新日期:2013-07-24 00:00:00
abstract:BACKGROUND:Understanding the community structure of microbes is typically accomplished by sequencing 16S ribosomal RNA (16S rRNA) genes. These community data can be represented by constructing a phylogenetic tree and comparing it with other samples using statistical methods. However, owing to high computational complex...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-332
更新日期:2010-06-18 00:00:00