Protein structure databases with new web services for structural biology and biomedical research

The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes approximately 25-30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, eF-site, as well as a search service for similar molecular surfaces, eF-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the utility of these tools in recognizing remote homologies between pairs of protein structures and in assigning putative biochemical functions to newly determined targets from structural genomics projects.     

A package of computer programs for handling taxonomic databases

A package of programs is described which processes taxonomicdata, suitable to use when preparing monographs, handbooks,Floras or Faunas, in which species or other taxa are describedand identified. There is also an interactive program for specimenidentification, and conversion routines which prepare data fornumerical taxonomy (clustering and cladistics). The programsare equally suitable for botany or for zoology, or even fornon-biological data. Received on September 20, 1985; accepted on November 11, 1985     

Experience using web services for biological sequence analysis

Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed.     

A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

BioText Search Engine: beyond abstract search

The BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. One novel feature is the ability to search and browse article figures and their captions. A grid view juxtaposes many different figures associated with the same keywords, providing new insight into the literature. An abstract/title search and list view shows at a glance many of the figures associated with each article. The interface is carefully designed according to usability principles and techniques. The search engine is a work in progress, and more functionality will be added over time. Availability: http://biosearch.berkeley.edu.     

A Real-Time All-Atom Structural Search Engine for Proteins

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

This is a PLOS Computational Biology Software Article

     

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services

Background  

SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies.     

BioMOBY: an open source biological web services proposal

BioMOBY is an Open Source research project which aims to generate an architecture for the discovery and distribution of biological data through web services; data and services are decentralised, but the availability of these resources, and the instructions for interacting with them, are registered in a central location called MOBY Central. BioMOBY adds to the web services paradigm, as exemplified by Universal Data Discovery and Integration (UDDI), by having an object-driven registry query system with object and service ontologies. This allows users to traverse expansive and disparate data sets where each possible next step is presented based on the data object currently in-hand. Moreover, a path from the current data object to a desired final data object could be automatically discovered using the registry. Native BioMOBY objects are lightweight XML, and make up both the query and the response of a simple object access protocol (SOAP) transaction.     

A bibliometric investigation of life cycle assessment research in the web of science databases

Purpose

Over the past few decades, life cycle assessment (LCA) methodologies have been developed extensively, and there has been a growing interest in LCA research. However, as attested by scientific literature, few systematic, synthesizing, and visualizing studies have been found on LCA research which show how this field has evolved over time. The goal of this mainly bibliometric, empirical study is to get insight into publication performance of global LCA research, characterize its intellectual structure, and trace its evolution by using the bibliometric method with visual mapping.

Methods

Based on the data from the ISI Web of Science databases Science Citation Index Expanded (SCI-EXPANDED), Social Sciences Citation Index (SSCI), Conference Proceedings Citation Index—Science (CPCI-S) and Conference Proceedings Citation Index —Social Science & Humanities (CPCI-SSH) in the period of 1998–2013, bibliometric methods are used to investigate general development profiles of LCA research, while knowledge domain visualization technologies are employed to conduct a further co-citation analysis.

Results and discussion

The results and discussions of this research mainly shed light on (1) basic statistics of significant publication performances, (2) research focuses and their intellectual base in LCA research, (3) how the streams of research evolved during the whole period of interest.

Conclusions

A new work on systematic and synthesizing study is conducted in this research to evaluate and map LCA research-related context. Some salient scholarly journals and institutions are identified that have shown a significant impact during the exponential growth of LCA research in the past 16 years. Biofuel, process design, solid waste management, and livestock production-related LCA researches are the main areas where interest is surging, confirmed by the active citers in each specialty. Furthermore, from the perspective of science mapping, evolution of LCA research is traced and some pivot publications are identified, which work as structural holes for the LCA-research development in the given time window.     

基于文献计量分析的生态系统服务研究现状及热点

生态系统服务是生态学研究的核心和热点议题。近年来,各国和各相关机构对生态系统服务的研究力度不断加大。基于SCI-E和CNKI数据库,利用文献计量方法,分析了国内外生态系统服务研究的发展特征和变化趋势。研究结果表明:(1)国内外生态系统服务研究的发文量不断增加,发展态势良好。(2)发达国家是生态系统服务领域的主要研究力量,美国占据绝对领先地位;美国的加利福尼亚大学是主要研究机构;总体来看,国家和机构间的合作正在不断增强。(3)当前该领域的8类研究热点分别是生态系统服务机理研究,保护管理及可持续性、生物多样性、脆弱性、土地利用及景观变化、评估与模型、气候变化、政策与决策分析。从各个时期国内外研究热点整体分布情况来看,国际更侧重于生态系统服务及生态系统服务与人类福祉的依存关系的研究,国内则更加关注生态系统服务评估。(4)近年来中国在生态系统服务研究领域的国际地位有所提升,科研产出量显著增加,累积发文量居世界第5位,中国科学院是全球主要研究机构之一,但论文被引频次相对偏低,国际合作亟待加强和提升。     

uBioRSS: tracking taxonomic literature using RSS

Web content syndication through standard formats such as RSS and ATOM has become an increasingly popular mechanism for publishers, news sources and blogs to disseminate regularly updated content. These standardized syndication formats deliver content directly to the subscriber, allowing them to locally aggregate content from a variety of sources instead of having to find the information on multiple websites. The uBioRSS application is a 'taxonomically intelligent' service customized for the biological sciences. It aggregates syndicated content from academic publishers and science news feeds, and then uses a taxonomic Named Entity Recognition algorithm to identify and index taxonomic names within those data streams. The resulting name index is cross-referenced to current global taxonomic datasets to provide context for browsing the publications by taxonomic group. This process, called taxonomic indexing, draws upon services developed specifically for biological sciences, collectively referred to as 'taxonomic intelligence'. Such value-added enhancements can provide biologists with accelerated and improved access to current biological content. AVAILABILITY: http://names.ubio.org/rss/     

KBWS: an EMBOSS associated package for accessing bioinformatics web services

The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from and GitHub repository . Users can utilize the SOAP services implemented in Perl directly via WSDL file at (RPC Encoded) and (Document/literal).     

Magallanes: a web services discovery and automatic workflow composition tool

Background  

To aid in bioinformatics data processing and analysis, an increasing number of web-based applications are being deployed. Although this is a positive circumstance in general, the proliferation of tools makes it difficult to find the right tool, or more importantly, the right set of tools that can work together to solve real complex problems.     

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

Background  

Metagenomics is a new field of research on natural microbial communities. High-throughput sequencing techniques like 454 or Solexa-Illumina promise new possibilities as they are able to produce huge amounts of data in much shorter time and with less efforts and costs than the traditional Sanger technique. But the data produced comes in even shorter reads (35-100 basepairs with Illumina, 100-500 basepairs with 454-sequencing). CARMA is a new software pipeline for the characterisation of species composition and the genetic potential of microbial samples using short, unassembled reads.