检索结果-内蒙古大学图书馆

MBA: a literature mining system for extracting biomedical abbreviations

BMC BIOINFORMATICS 2009年第1期10卷 1-10页

作者： Xu, Yun Wang, ZhiHao Lei, YiMing Zhao, YuZhong Xue, Yu Univ Sci & Technol China Dept Comp Sci & Technol Hefei 230027 Anhui Peoples R China Anhui Prov MOST Cokey Lab High Performance Comp & Hefei 230027 Anhui Peoples R China Univ Sci & Technol China Sch Life Sci Hefei 230027 Anhui Peoples R China

Background: The exploding growth of the biomedical literature presents many challenges for biological researchers. One such challenge is from the use of a great deal of abbreviations. Extracting abbreviations and their definitions accurately is very helpful to biologists and also facilitates biomedical text analysis. Existing approaches fall into four broad categories: rule based, machine learning based, text alignment based and statistically based. State of the art methods either focus exclusively on acronym-type abbreviations, or could not recognize rare abbreviations. We propose a systematic method to extract abbreviations effectively. At first a scoring method is used to classify the abbreviations into acronym-type and non-acronym-type abbreviations, and then their corresponding definitions are identified by two different methods: text alignment algorithm for the former, statistical method for the latter. Results: A literature mining system MBA was constructed to extract both acronym-type and non-acronym-type abbreviations. An abbreviation-tagged literature corpus, called Medstract gold standard corpus, was used to evaluate the system. MBA achieved a recall of 88% at the precision of 91% on the Medstract gold-standard EVALUATION Corpus. Conclusion: We present a new literature mining system MBA for extracting biomedical abbreviations. Our evaluation demonstrates that the MBA system performs better than the others. It can identify the definition of not only acronym-type abbreviations including a little irregular acronym-type abbreviations (e. g., < CNS1, cyclophilin seven suppressor >), but also non-acronym-type abbreviations (e. g., < Fas, CD95 >).

关键词： Short Form alignment algorithm Suprachiasmatic Nucleus Longe Common Subsequence Biomedical Text

来源：评论

学校读者我要写书评

暂无评论

A comprehensive two-dimensional retention time alignment algorithm to enhance chemometric analysis of comprehensive two-dimensional separation data

引用

ANALYTICAL CHEMISTRY 2005年第23期77卷 7735-7743页

作者： Pierce, KM Wood, LF Wright, BW Synovec, RE Univ Washington Dept Chem Seattle WA 98195 USA Pacific NW Natl Lab Richland WA 99352 USA

A comprehensive two-dimensional (21)) retention time alignment algorithm was developed using a novel indexing scheme. The algorithm is termed comprehensive because it functions to correct the entire chromatogram in both dimensions and it preserves the separation information in both dimensions. Although the algorithm is demonstrated by correcting comprehensive two-dimensional gas chromatography (GC x GC) data, the algorithm is designed to correct shifting in all forms of 2D separations, such as LC x LC, LC x CE, CE x CE, and LC x GC. This 2D alignment algorithm was applied to three different data sets composed of replicate GC x GC separations of (1) three 22-component control mixtures, (2) three gasoline samples, and (3) three diesel samples. The three data sets were collected using slightly different temperature or pressure programs to engender significant retention time shifting in the raw data and then demonstrate subsequent corrections of that shifting upon comprehensive 2D alignment of the data sets. Thirty 12-min GC x GC separations from three 22-component control mixtures were used to evaluate the 2D alignment performance (10 runs/mixture). The average standard deviation of first column retention time improved 5-fold from 0.020 min (before alignment) to 0.004 min (after alignment). Concurrently, the average standard deviation of second column retention time improved 4-fold from 3.5 ms (before alignment) to 0.8 ms (after alignment). alignment of the 30 control mixture chromatograms took 20 min. The quantitative integrity of the GC x GC data following 2D alignment was also investigated. The mean integrated signal was determined for all components in the three 22-component mixtures for all 30 replicates. The average percent difference in the integrated signal for each component before and after alignment was 2.6%. Singular value decomposition (SVD) was applied to the 22-component control mixture data before and after alignment to show the restoration of trilinear

关键词： .retention time Comprehensive Two-dimensional Chemometric Analysis gasoline samples alignment algorithm diesel samples Separation Data novel indexing entire chromatogram LC CE LC GC GC GC separations control mixtures GC GC data

来源：评论

学校读者我要写书评

暂无评论

Splign: algorithms for computing spliced alignments with identification of paralogs

引用

BIOLOGY DIRECT 2008年第1期3卷 20-20页

作者： Kapustin, Yuri Souvorov, Alexander Tatusova, Tatiana Lipman, David Natl Inst Hlth Natl Ctr Biotechnol Informat Natl Lib Med Bethesda MD 20814 USA

Background: The computation of accurate alignments of cDNA sequences against a genome is at the foundation of modern genome annotation pipelines. Several factors such as presence of paralogs, small exons, non-consensus splice signals, sequencing errors and polymorphic sites pose recognized difficulties to existing spliced alignment algorithms. Results: We describe a set of algorithms behind a tool called Splign for computing cDNA-to-Genome alignments. The algorithms include a high-performance preliminary alignment, a compartment identification based on a formally defined model of adjacent duplicated regions, and a refined sequence alignment. In a series of tests, Splign has produced more accurate results than other tools commonly used to compute spliced alignments, in a reasonable amount of time. Conclusion: Splign's ability to deal with various issues complicating the spliced alignment problem makes it a helpful tool in eukaryotic genome annotation processes and alternative splicing studies. Its performance is enough to align the largest currently available pools of cDNA data such as the human EST set on a moderate-sized computing cluster in a matter of hours. The duplications identification (compartmentization) algorithm can be used independently in other areas such as the study of pseudogenes. Reviewers: This article was reviewed by: Steven Salzberg, Arcady Mushegian and Andrey Mironov (nominated by Mikhail Gelfand).

关键词： Local alignment mRNA Sequence alignment algorithm Query Coverage Author Response

来源：评论

学校读者我要写书评

暂无评论

Use artificial neural network to align biological ontologies

引用

BMC GENOMICS 2008年第2-Sup期9卷 S16-S16页

作者： Huang, Jingshan Dang, Jiangbo Huhns, Michael N. Zheng, W. Jim Med Univ S Carolina Dept Biostat Bioinformat & Epidemiol Charleston SC 29425 USA Univ S Carolina Dept Comp Sci & Engn Columbia SC 29208 USA Siemens Corp Res Princeton NJ 08540 USA

Background: Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. Results: In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. Conclusion: The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore,

关键词： Machine Learning Technique alignment algorithm Ontology Concept Concept Property Semantic Aspect

来源：评论

学校读者我要写书评

暂无评论

alignment of laboratory-scale soft X-ray microscope using laser plasma

引用

JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS 2007年第1期46卷 394-399页

作者： Kang, Dongwoo Kang, Sunghoon Kwon, Youngman Kim, Kyongwoo Yu, Hongki Kim, Tachun Gweon, Daegab Rah, Seungyu Min, Jinyoung Yoon, Kwonha Korea Adv Inst Sci & Technol Dept Mech Engn Nanooptomechatron Lab Taejon 305701 South Korea Wonkwang Univ Inst Radiol Imaging Sci Iksan 570749 Jeonbuk South Korea POSTECH Pohang Accelerator Lab Pohang 790784 Kyungbuk South Korea LISTEM Corp Inchon 403032 South Korea

We demonstrate an alignment method for a laboratory-scale soft X-ray microscope, which utilizes a liquid-jet laser-produced plasma source in combination with a tandem ellipsoidal condenser mirror and a diffiractive micro zone plate. Because the intensity of the laser-produced plasma source is relatively low, we developed the tandem ellipsoidal condenser mirror to increase the photon density in the objective plane and to obtain a high-resolution image within a short exposure time. But, aligning the tandem ellipsoidal condenser mirror is a difficult task because it has 5 degrees of freedom (DOF) alignment tolerances and there is a connection among these tolerances. We performed its tolerance analysis and developed a new fully automated alignment algorithm via computer control. As a result, a 12.5-mu m-pitch gold mesh image was measured using 700x magnification and a 5 min exposure and the resultant edge detection resolution was about 70 nm.

关键词： soft X-ray microscope laser-produced plasma source X-ray optics grazing incidence reflective mirror tandem ellipsoidal condenser mirror alignment algorithm precision stage nanotechnology

来源：评论

学校读者我要写书评

暂无评论

Quantification of the variation in percentage identity for protein sequence alignments

引用

BMC BIOINFORMATICS 2006年第1期7卷 415-415页

作者： Raghava, G. P. S. Barton, Geoffrey J. Univ Dundee Sch Life Sci Res Dundee DD1 5EH Scotland Bioinformat Ctr Inst Microbial Technol Chandigarh India Univ Oxford Mol Biophys Lab Oxford OX1 3QU England

Background: Percentage Identity (PID) is frequently quoted in discussion of sequence alignments since it appears simple and easy to understand. However, although there are several different ways to calculate percentage identity and each may yield a different result for the same alignment, the method of calculation is rarely reported. Accordingly, quantification of the variation in PID caused by the different calculations would help in interpreting PID values in the literature. In this study, the variation in PID was quantified systematically on a reference set of 1028 alignments generated by comparison of the protein three-dimensional structures. Since the alignment algorithm may also affect the range of PID, this study also considered the effect of algorithm, and the combination of algorithm and PID method. Results: The maximum variation in PID due to the calculation method was 11.5% while the effect of alignment algorithm on PID was up to 14.6% across three popular alignment methods. The combined effect of alignment algorithm and PID calculation gave a variation of up to 22% on the test data, with an average of 5.3% +/- 2.8% for sequence pairs with < 30% identity. In order to see which PID method was most highly correlated with structural similarity, four different PID calculations were compared to similarity scores (Sc) from the comparison of the corresponding protein three-dimensional structures. The highest correlation coefficient for a PID calculation was 0.80. In contrast, the more sophisticated Z-score calculated by reference to randomized sequences gave a correlation coefficient of 0.84. Conclusion: Although it is well known amongst expert sequence analysts that PID is a poor score for discriminating between protein sequences, the apparent simplicity of the percentage identity score encourages its widespread use in establishing cutoffs for structural similarity. This paper illustrates that not only is PID a poor measure of sequence similarity when compared

关键词： Structural alignment alignment algorithm Percentage Identity alignment Method Reference alignment

来源：评论

学校读者我要写书评

暂无评论

Automated generation of heuristics for biological sequence comparison

引用

BMC BIOINFORMATICS 2005年第1期6卷 31-31页

作者： Slater, GS Birney, E EMBL European Bioinformat Inst Ensembl Grp Cambridge CB10 1SD England

Background: Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement. We introduce bounded sparse dynamic programming (BSDP) to allow rapid approximation to exhaustive alignment. This is used within a framework whereby the alignment algorithms are described in terms of their underlying model, to allow automated development of efficient heuristic implementations which may be applied to a general set of sequence comparison problems. Results: The speed and accuracy of this approach compares favourably with existing methods. Examples of its use in the context of genome annotation are given. Conclusions: This system allows rapid implementation of heuristics approximating to many complex alignment models, and has been incorporated into the freely available sequence alignment program, exonerate.

关键词： Dynamic Programming Finite State Machine Priority Queue alignment algorithm Heuristic Model

来源：评论

学校读者我要写书评

暂无评论

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

引用

BMC BIOINFORMATICS 2005年第1期6卷 70-70页

作者： Brown, CT Xie, Y Davidson, EH Cameron, RA CALTECH Div Biol Sci Pasadena CA 91125 USA CALTECH Ctr Computat Regulatory Genom Pasadena CA 91125 USA

Background: Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes. Results: We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at http:// family. caltech. edu/. Conclusion: These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.

关键词： Regulatory Region alignment algorithm Comparative Sequence Analysis Gapped alignment Tuple Space

来源：评论

学校读者我要写书评

暂无评论

High-performance liquid chromatographic method with quantitative comparisons of whole chromatograms of raw and steamed Panax notoginseng

引用

JOURNAL OF CHROMATOGRAPHY A 2004年第1-2期1057卷 141-149页

作者： Lau, AJ Seo, BH Woo, SO Koh, HL Natl Univ Singapore Fac Sci Dept Pharm Singapore 117643 Singapore Waters Asia Ltd Singapore 119954 Singapore Univ Tunku Abdul Rahman Fac Sci & Engn Salangor Darul Ehsan Malaysia

A high-performance liquid chromatographic (HPLC) method coupled with chromatographic pattern matching was developed to differentiate whole chromatograms of raw and steamed Panax notoginseng objectively and quantitatively. The major peaks differentiating chromatograms of raw and steamed samples were also identified for the first time in this herb. The raw and steamed P. notoginseng roots and its products were successfully differentiated. The quantitative differences between the chromatograms were correlated to the duration of steaming. Chromatographic pattern matching allows rapid, simple, automated, and quantitative comparisons of complex chromatograms. It is a useful tool in ensuring safety and quality of herbal products. (C) 2004 Elsevier B.V. All rights reserved.

关键词： chromatographic pattern matching Panax notoginseng medicinal herbs ginsenosides chemical fingerprinting alignment algorithm

来源：评论

学校读者我要写书评

暂无评论

Searching algorithm for alignment automation between a laser diode and a single-mode fiber

引用

Guofang Keji Daxue Xuebao/Journal of National University of Defense Technology 2004年第6期26卷 44-48页

作者： Chun, Jing Wu, Yu-Lie Dai, Yi-Fan Li, Sheng-Yi Coll. of Mech. Eng. and Auto. Natl. Univ. of Defense Technol. Changsha 410073 China

The five-dimension searching algorithm is presented for the alignment automation between a laser diode and a single-mode fiber. The searching path and the parameters are discussed in detail. The novel exponential function approximation algorithm for XY plane searching is also presented first. The experimental results with these algorithms are finally presented. It is confirmed that the searching efficiency of the exponential function approximation algorithm is better than the hill-climbing algorithm. The main reason is that the sample points are reduced. Thus the alignment speed is improved notably.

关键词： alignment algorithm Laser diode Single-mode fiber

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：