Review of "Biomedical Informatics; Computer Applications in Health Care and Biomedicine" by Edward H. Shortliffe and James J. Cimino

This article is an invited review of the third edition of "Biomedical Informatics; Computer Applications in Health Care and Biomedicine", one of thirty-six volumes in Springer's 'Health Informatics Series', edited by E. Shortliffe and J. Cimino. This book spans most of the current methods and issues in health informatics, ranging through subjects as varied as data acquisition and storage, standards, natural language processing, imaging, electronic health records, decision support, teaching methods and ethics. The book is aimed at 'healthcare professionals', and is certainly appropriate for the non-technical informatics user. However, this book is also excellent background reading for the technical engineer who may be interested in the possible problems that confront the users in this field.     

Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education

Some of the latest trends in cheminformatics, computation, and the world wide web are reviewed with predictions of how these are likely to impact the field of cheminformatics in the next five years. The vision and some of the work of the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University are described, which we base around the core concepts of e-Science and cyberinfrastructure that have proven successful in other fields. Our chemical informatics cyberinfrastructure is realized by building a flexible, generic infrastructure for cheminformatics tools and databases, exporting "best of breed" methods as easily-accessible web APIs for cheminformaticians, scientists, and researchers in other disciplines, and hosting a unique chemical informatics education program aimed at scientists and cheminformatics practitioners in academia and industry.     

国外公众健康信息学发展研究

通过分析国外公众健康信息学研究的年代分布特点、核心期刊、重要作者和研究热点,探索国外公众健康信息学研究的历史、现状和发展趋势,为国内公众健康信息学领域的研究与实践提供理论参考。利用TDA、Excel等工具,从时间、期刊和作者分布三方面对SCIE数据库收录的公众健康信息学领域的研究文献进行时空维度分析,再进行关键词和高频被引文献分析。从发文量来看国外公众健康信息学研究的发展比较平缓,核心期刊包括医学互联网研究杂志与国际医学信息学杂志,重要作者有Eysenbach Gunther、Keselman Alla等。1994~2013年公众健康信息学研究热点包括基本问题、卫生系统和个人健康记录、健康传播和患者教育以及医学信息学相关学科。高频被引文献内容涵盖公众健康信息学科,公众健康信息系统,电子病历和个人健康记录,互联网对公众健康行为的影响等几个方面。     

Genomics meets informatics

A report on the 11th Workshop on Genome Informatics, the annual meeting on genome informatics and related subjects supported by the Genome Informatics Society of Japan, Tokyo, Japan, 18-19 December, 2000.     

Informatics for peptide retention properties in proteomic LC-MS

Retention times in HPLC yield valuable information for the identification of various analytes and the prediction of peptide retention is useful for the identification of peptides/proteins in LC-MS-based proteomics. Informatics methods such as artificial neural networks and support vector machines capable of solving nonlinear problems made possible the accurate modeling of quantitative structure-retention relationships of peptides (including large polymers) up to 5 kDa to which classical linear models cannot be applied, as well as the proteome-wide prediction of peptide retention. Proteome-wide retention prediction and accurate mass-information facilitate the identification of peptides in complex proteomic samples. In this review, we address recent developments in solid informatics methods and their application to peptide-retention properties in 'bottom-up' shotgun proteomics. We also describe future prospects for the standardization and application of retention times.     

GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group.

The Gene Expression Database (GXD) is a community resource that stores and integrates expression information for the laboratory mouse, with a particular emphasis on mouse development, and makes these data freely available in formats appropriate for comprehensive analysis. GXD is implemented as a relational database and integrated with the Mouse Genome Database (MGD) to enable global analysis of genotype, expression and phenotype information. Interconnections with sequence databases and with databases from other species further extend GXD's utility for the analysis of gene expression data. GXD is available through the Mouse Genome Informatics Web Site at http://www.informatics.jax.org/     

The dental informatics online community

Dental Informatics (DI) is the application of computer and information science to improve dental practice, research, education, and program administration. To support the growth of this emerging discipline, we created the Dental Informatics Online Community (DIOC). The DIOC provides a dedicated professional home for DI researchers and serves as an open, common, and worldwide forum for all individuals interested in the field. It was created and is maintained by the Center for Dental Informatics at the University of Pittsburgh School of Dental Medicine, independent from any professional association, corporate interest or funding source. The DIOC's Website provides many useful features, such as a learning center, publication archive, member and project directories, and the Current Awareness Service (CAS). The CAS automatically notifies members about new information added to the Community. Notifications are individualized according to a member's profile and activities on the site. The DIOC is a research-oriented online community which provides resources in the dental informatics and dental technology field, as well as a way to establish social connections to share ideas, problems and research opportunities. Member and activity growth since the community's inception in 2005 have been steady, but future sustainability of the community depends on many factors.     

The dental informatics online community

Dental Informatics (DI) is the application of computer and information science to improve dental practice, research, education, and program administration. To support the growth of this emerging discipline, we created the Dental Informatics Online Community (DIOC). The DIOC provides a dedicated professional home for DI researchers and serves as an open, common, and worldwide forum for all individuals interested in the field. It was created and is maintained by the Center for Dental Informatics at the University of Pittsburgh School of Dental Medicine, independent from any professional association, corporate interest or funding source. The DIOC''s Website provides many useful features, such as a learning center, publication archive, member and project directories, and the Current Awareness Service (CAS). The CAS automatically notifies members about new information added to the Community. Notifications are individualized according to a member''s profile and activities on the site. The DIOC is a research-oriented online community which provides resources in the dental informatics and dental technology field, as well as a way to establish social connections to share ideas, problems and research opportunities. Member and activity growth since the community''s inception in 2005 have been steady, but future sustainability of the community depends on many factors.     

Mouse tumor biology database (MTB): enhancements and current status

The Mouse Tumor Biology Database (MTB) is a Web-based resource that provides access to information on tumor frequency and latency, genetics and pathology in genetically defined mice (transgenics, targeted mutations and inbred strains). MTB is designed to serve as an information resource for cancer genetics researchers who use the laboratory mouse as a model system for understanding human disease processes. Data in MTB are obtained from the primary scientific literature and direct submissions by the research community. MTB is accessible from the Mouse Genome Informatics Web site (http://www. informatics.jax.org). User support is available for MTB via Email at mgi-help@informatics.jax.org     

The Mouse Gene Expression Database (GXD)

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is integrated with the Mouse Genome Database (MGD). Extensive interconnections with sequence databases and with databases from other species, and the development and use of shared controlled vocabularies extend GXD's utility for the analysis of gene expression information. GXD is accessible through the Mouse Genome Informatics web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu. shtml.     

<Emphasis Type="BoldItalic">Digital Humanitarians: How Big Data Is Changing the Face of Humanitarian Response</Emphasis>

This is a review of Patrick Meier’s 2015 book, Digital Humanitarians: How Big Data Is Changing the Face of Humanitarian Response. The book explores the role of technologies such as high-resolution satellite imagery, online social media, drones, and artificial intelligence in humanitarian responses during disasters such as the 2010 Haiti earthquake. In this analysis, the book is examined using a humanitarian health ethics perspective.     

生物多样性信息学研究进展

生物多样性信息学是一门蓬勃发展的新学科。它将现代的信息技术带入生物多样性及其相关学科的研究领域。它在生物多样性基础数据的数字化、模型工具和各种工具软件的开发、数据整合, 以及全球、地区和国家尺度生物多样性信息网络等多个方面的发展, 向我们展示了未来在全球范围内自由、免费共享生物多样性数据和信息, 以及人们行动起来共同关注、调查与监测野外生物多样性的前景。目前, 已有大量数字化的物种编目、标本馆标本、多媒体影像、研究文献等生物多样性基础信息可以通过互联网检索和利用。其中, 最值得关注的是一些成功的国际性研究项目, 如物种2000、全球生物多样性信息网络、生命条形码以及网络生命大百科全书。这些项目的成功不仅体现在对大量基础信息和数据的发布, 而且它们通过与生物多样性信息标准TDWG(Biodiversity Information Standards: TDWG)的合作, 推动了达尔文核心标准(Darwin Core)等一些重要的生物多样性信息标准的应用, 以及地区和国家性生物多样性信息节点的建立, 这些都为将来全球范围生物多样性信息的共享和数据交换奠定了重要基础。在数字化信息的基础上, 研究人员也开发了一些在特定研究领域应用的数据挖掘和模型工具, 例如基于数字化标本的地理分布预测工具MAXENT, 分类学专家知识管理的LifeDesk。公民科学理念的发展则向我们展示了公众和科学爱好者广泛参与以互联网为基础的生物多样性信息学研究活动。因此, 生物多样性信息学的发展前景广阔, 它将为我们实现全球保护战略目标, 应对生物多样性危机, 解决全球气候变化条件下生物多样性资源管理和利用建立坚实的信息基础。     

流感疫情中的医学信息学

在应对当前甲型流感暴发的疾病控制过程中,医学信息学发挥着不可替代的重要作用．本文结合多种信息学数据库来源的最新资料,在介绍甲型流感病毒的生物学知识和生物信息学分析手段的同时,对本次甲型流感病毒的来源、进化、传播和预防等一系列重要问题,结合信息学分析的结果做了深入的分析和探讨．并且突出介绍和评论了医学信息学在疾病控制中的前景和潜力,希望能有助于多种相关学科的生物医学研究人员．     

ISART: A Generic Framework for Searching Books with Social Information

Effective book search has been discussed for decades and is still future-proof in areas as diverse as computer science, informatics, e-commerce and even culture and arts. A variety of social information contents (e.g, ratings, tags and reviews) emerge with the huge number of books on the Web, but how they are utilized for searching and finding books is seldom investigated. Here we develop an Integrated Search And Recommendation Technology (IsArt), which breaks new ground by providing a generic framework for searching books with rich social information. IsArt comprises a search engine to rank books with book contents and professional metadata, a Generalized Content-based Filtering model to thereafter rerank books with user-generated social contents, and a learning-to-rank technique to finally combine a wide range of diverse reranking results. Experiments show that this technology permits embedding social information to promote book search effectiveness, and IsArt, by making use of it, has the best performance on CLEF/INEX Social Book Search Evaluation datasets of all 4 years (from 2011 to 2014), compared with some other state-of-the-art methods.     

Shipley, B. Cause and correlation in Biology

As indicated by the title, this book seeks to address the relationshipbetween correlation and causation, with application to biologicaltopics. The book begins with a statement of three objectives:(1) to persuade biologists that it is possible to infer causationwith observational (non-experimental) data; (2) to describecertain methods that can assist in this process; and (3) toillustrate the methods presented using biological examples. A philosophical discussion of causation is potentially confusingand can often evoke debate, which necessitates some carefullycrafted effort at the beginning of the book to address the meaningof causation. Fortunately for all involved, the methods presenteddo not depend on any one particular definition     

BioGPS and GXD: mouse gene expression data—the benefits and challenges of data integration

Mouse gene expression data are complex and voluminous. To maximize the utility of these data, they must be made readily accessible through databases, and those resources need to place the expression data in the larger biological context. Here we describe two community resources that approach these problems in different but complementary ways: BioGPS and the Mouse Gene Expression Database (GXD). BioGPS connects its large and homogeneous microarray gene expression reference data sets via plugins with a heterogeneous collection of external gene centric resources, thus casting a wide but loose net. GXD acquires different types of expression data from many sources and integrates these data tightly with other types of data in the Mouse Genome Informatics (MGI) resource, with a strong emphasis on consistency checks and manual curation. We describe and contrast the “loose” and “tight” data integration strategies employed by BioGPS and GXD, respectively, and discuss the challenges and benefits of data integration. BioGPS is freely available at http://biogps.org. GXD is freely available through the MGI web site (www.informatics.jax.org) or directly at www.informatics.jax.org/expression.shtml.     

Bioinformatics and Computational Biology Solutions Using R and Bioconductor. * Edited by Robert Gentleman, Wolfgang Huber, Vincent J. Carey, Rafael A. Irizarry and Sandrine Dudoit

This book guides through practical bioinformatics data analysisusing the Bioconductor toolkit, which is based on the statisticallanguage R. R itself is an open-source recreation of the languageS-Plus. The Bioconductor is a collection of R-packages for theanalysis of genomic and molecular biological data generatedin high-throughput experiments. High-throughput experimentsare characterized by large amounts of data generated in shortperiods of time on a sizable number of samples. This poses newchallenges to the analysis such as assessing and adjusting fornoise, exploration using cluster-analysis, visualization, andlinking to (or ‘annotating with’) biomedical knowledgebases. The book focuses on gene expression microarrays, the high-throughputtechnology for which statistical methods are best developedtoday. In addition, a     

Exploring frontiers in the DNA landscape: an introduction to the symposium "Genome Analysis and the Molecular Systematics of Retroelements"

The emerging field of phylogenomics is influencing both the amount and type of characters being brought to bear on long-standing problems in systematic biology. Moreover, the proliferation of sequence information from genome projects in concert with the development of new informatics tools is widening access to comparative data on retroelements to a broad cross section of investigators. Motivated by this, the Society of Systematic Biologists sponsored a symposium entitled "Genome Analysis and the Molecular Systematics of Retroelements," and the resulting papers illustrate this theme of new discoveries and cover three basic areas of research: (i) the taxonomic distribution and phylogenetic structure of families of retroelements; (II) the use of SINE and LINE insertions for phylogenetic inference; and (III) the informatics and classification of repetitive elements. Contributions of each article are briefly discussed in this context and particularly fruitful directions for future research illuminated by results of this symposium are reviewed.