Abstract:
BACKGROUND:Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure image recognition and text mining together. RESULTS:We have developed ChemEx, a chemical information extraction system. ChemEx processes both text and images in publications. Text annotator is able to extract compound, organism, and assay entities from text content while structure image recognition enables translation of chemical raster images to machine readable format. A user can view annotated text along with summarized information of compounds, organism that produces those compounds, and assay tests. CONCLUSIONS:ChemEx facilitates and speeds up chemical data curation by extracting compounds, organisms, and assays from a large collection of publications. The software and corpus can be downloaded from http://www.biotec.or.th/isl/ChemEx.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Tharatipyakul A,Numnark S,Wichadakul D,Ingsriswang Sdoi
10.1186/1471-2105-13-S17-S9subject
Has Abstractpub_date
2012-01-01 00:00:00pages
S9issn
1471-2105pii
1471-2105-13-S17-S9journal_volume
13 Suppl 17pub_type
杂志文章abstract:BACKGROUND:Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes. However, deep coverage variations in short-read data sets and high sequencing error rates o...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0357-3
更新日期:2014-11-19 00:00:00
abstract::Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic networks has been considered in the past, the computational complexity of the existing solutions has so far lim...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S3-S2
更新日期:2012-03-21 00:00:00
abstract:BACKGROUND:Ribosomal 16S DNA sequences are an essential tool for identifying and classifying microbes. High-throughput DNA sequencing now makes it economically possible to produce very large datasets of 16S rDNA sequences in short time periods, necessitating new computer tools for analyses. Here we describe FastGroup, ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-2-9
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1678-9
更新日期:2017-05-18 00:00:00
abstract:BACKGROUND:With the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available, the assembly of a template sequence is usually challenging because of repeats and the short length of reads. When NGS reads cannot be mapped onto a r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S9-S1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Genome-wide transcriptional profiling of patient blood samples offers a powerful tool to investigate underlying disease mechanisms and personalized treatment decisions. Most studies are based on analysis of total peripheral blood mononuclear cells (PBMCs), a mixed population. In this case, accuracy is inhere...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-258
更新日期:2011-06-24 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:Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., conti...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-11-275
更新日期:2010-05-21 00:00:00
abstract:BACKGROUND:Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff bet...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1518-y
更新日期:2017-02-23 00:00:00
abstract:BACKGROUND:In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functional antibody sequences to their sourcing germline gene segments is vital not only for understanding...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S12-S20
更新日期:2008-12-12 00:00:00
abstract:BACKGROUND:Abruptness of pigment patterns at the periphery of a skin lesion is one of the most important dermoscopic features for detection of malignancy. In current clinical setting, abrupt cutoff of a skin lesion determined by an examination of a dermatologist. This process is subjective, nonquantitative, and error-p...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1892-5
更新日期:2017-12-28 00:00:00
abstract:BACKGROUND:For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significant...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-471
更新日期:2007-12-03 00:00:00
abstract:BACKGROUND:The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and ass...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-6
更新日期:2011-01-05 00:00:00
abstract:BACKGROUND AND GOAL:The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown to a standard classification approach competing with logistic regression in many innovation-friendly scientific fields. RESULTS:In this conte...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2264-5
更新日期:2018-07-17 00:00:00
abstract:BACKGROUND:RNA-seq is a powerful tool for measuring transcriptomes, especially for identifying differentially expressed genes or transcripts (DEGs) between sample groups. A number of methods have been developed for this task, and several evaluation studies have also been reported. However, those evaluations so far have...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0794-7
更新日期:2015-11-04 00:00:00
abstract:BACKGROUND:Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new m...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1943-y
更新日期:2017-11-28 00:00:00
abstract:BACKGROUND:Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. Even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. Identifying sequencing errors fr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-14-367
更新日期:2013-12-18 00:00:00
abstract:BACKGROUND:The aberrant expression of microRNAs is closely connected to the occurrence and development of a great deal of human diseases. To study human diseases, numerous effective computational models that are valuable and meaningful have been presented by researchers. RESULTS:Here, we present a computational framew...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-3409-x
更新日期:2020-02-18 00:00:00
abstract:BACKGROUND:Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-253
更新日期:2008-05-29 00:00:00
abstract:BACKGROUND:A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Si...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-017-1466-6
更新日期:2017-03-14 00:00:00
abstract:BACKGROUND:Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3020-1
更新日期:2019-08-13 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:Interest in de novo genome assembly has been renewed in the past decade due to rapid advances in high-throughput sequencing (HTS) technologies which generate relatively short reads resulting in highly fragmented assemblies consisting of contigs. Additional long-range linkage information is typically used to ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-15-S9-S9
更新日期:2014-01-01 00:00:00
abstract::Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by an op...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-13-S16-S8
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning models using gene expression data from patients' primary tumor tissues to predict whether a patient wi...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-020-03690-4
更新日期:2020-09-30 00:00:00
abstract:BACKGROUND:Automatic quantification of neuronal morphology from images of fluorescence microscopy plays an increasingly important role in high-content screenings. However, there exist very few freeware tools and methods which provide automatic neuronal morphology quantification for pharmacological discovery. RESULTS:T...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-230
更新日期:2011-06-08 00:00:00
abstract:BACKGROUND:This paper summarises the lessons and experiences gained from a case study of the application of semantic web technologies to the integration of data from the bacterial species Francisella tularensis novicida (Fn). Fn data sources are disparate and heterogeneous, as multiple laboratories across the world, us...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S10-S3
更新日期:2009-10-01 00:00:00
abstract:BACKGROUND:Fluorescent reporter genes have become widely used for monitoring gene expression in living cells. When a microbial strain carrying a reporter gene is grown in a microplate reader, the fluorescence and the absorbance (optical density) of the culture can be automatically measured every few minutes in a highly...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-2920-4
更新日期:2019-06-11 00:00:00
abstract:BACKGROUND:Recent studies in computational primary protein sequence analysis have leveraged the power of unlabeled data. For example, predictive models based on string kernels trained on sequences known to belong to particular folds or superfamilies, the so-called labeled data set, can attain significantly improved acc...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S4-S2
更新日期:2009-04-29 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