Web resources for the carbohydrate chemist

Bioinformatics has played a pivotal role in advancing genetics and protein sciences. The large amount of information generated by genomics, and now proteomics, has been a driving force. By comparison, glycobiology still generates small amounts of data. The need to organize our knowledge about carbohydrates is however growing constantly and has given rise to an increasing number of public databases and freely available tools. This review gives an overview of the carbohydrate-oriented resources currently available on the Internet. Many of the resources are seldom referred to in the literature and difficult to find, in part because of the constant flux of the net itself, but also because many efforts have been lead by a single individual. As the World Wide Web has matured the number of 'permanent' resources, maintained by organizations rather than individuals, has increased. In this paper, we present some of the more useful and accessible public tools and databases. There are also a few commercial initiatives but these have not been reviewed.     

糖类的生物信息学资源

生物信息学在推动遗传学和蛋白质科学的研究领域中,已发挥了举足轻重的作用.相比较而 言,糖科学产生的信息还比较有限,随着人们对糖类分子的关注,糖生物学的发展也出现新 的契机,其信息正在飞速地增长.对已经获得的糖类相关知识进行系统整合就显得越来越有 必要,许多研究型数据库和免费工具已应运而生,并且数目在不断扩大,正成为科学工作者 非常便利的工具.但到目前为止,许多数据库或者网络预测工具在文献中很少提及或难以找 到,给研究者带来了不少的麻烦.部分原因是数据库资源本身数据不断在更新,人机界面也 变得越方便和人性化,另外就是人们对于这些新型的研究工具了解较少.这篇综述介绍了 目前网络上最常用的糖类生物信息学资源,包括糖的一级结构,分析测试数据、构象,酶, 凝集素,糖蛋白等方面的各种数据库.     

PLATCOM: a Platform for Computational Comparative Genomics

MOTIVATION: As more whole genome sequences become available, comparing multiple genomes at the sequence level can provide insight into new biological discovery. However, there are significant challenges for genome comparison. The challenge includes requirement for computational resources owing to the large volume of genome data. More importantly, since the choice of genomes to be compared is entirely subjective, there are too many choices for genome comparison. For these reasons, there is pressing need for bioinformatics systems for comparing multiple genomes where users can choose genomes to be compared freely. RESULTS: PLATCOM (Platform for Computational Comparative Genomics) is an integrated system for the comparative analysis of multiple genomes. The system is built on several public databases and a suite of genome analysis applications are provided as exemplary genome data mining tools over these internal databases. Researchers are able to visually investigate genomic sequence similarities, conserved gene neighborhoods, conserved metabolic pathways and putative gene fusion events among a set of selected multiple genomes. AVAILABILITY: http://platcom.informatics.indiana.edu/platcom     

The NIDDK Information Network: A Community Portal for Finding Data,Materials, and Tools for Researchers Studying Diabetes,Digestive, and Kidney Diseases

The NIDDK Information Network (dkNET; http://dknet.org) was launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources that advance the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). By research resources, we mean the multitude of data, software tools, materials, services, projects and organizations available to researchers in the public domain. Most of these are accessed via web-accessible databases or web portals, each developed, designed and maintained by numerous different projects, organizations and individuals. While many of the large government funded databases, maintained by agencies such as European Bioinformatics Institute and the National Center for Biotechnology Information, are well known to researchers, many more that have been developed by and for the biomedical research community are unknown or underutilized. At least part of the problem is the nature of dynamic databases, which are considered part of the “hidden” web, that is, content that is not easily accessed by search engines. dkNET was created specifically to address the challenge of connecting researchers to research resources via these types of community databases and web portals. dkNET functions as a “search engine for data”, searching across millions of database records contained in hundreds of biomedical databases developed and maintained by independent projects around the world. A primary focus of dkNET are centers and projects specifically created to provide high quality data and resources to NIDDK researchers. Through the novel data ingest process used in dkNET, additional data sources can easily be incorporated, allowing it to scale with the growth of digital data and the needs of the dkNET community. Here, we provide an overview of the dkNET portal and its functions. We show how dkNET can be used to address a variety of use cases that involve searching for research resources.     

MPtopo: A database of membrane protein topology

The reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vast majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the prediction of MP structure. We have therefore created MPtopo, a database of MPs whose topologies have been verified experimentally by means of crystallography, gene fusion, and other methods. Tests using MPtopo strongly validated four existing MP topology-prediction algorithms. MPtopo is freely available over the internet and can be queried by means of an SQL-based search engine.     

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

The availability of user‐friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols ) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open‐source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog .     

CDK-Taverna: an open workflow environment for cheminformatics

Background  

Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone.     

GARNet, the Genomic Arabidopsis Resource Network

GARNet, the Genomic Arabidopsis Resource Network, was created to establish UK-based facilities for functional genomic research on Arabidopsis thaliana. In addition, GARNet provides a platform for international Arabidopsis research and for research on other plant species. To use the GARNet facilities apply via the website: http://garnet.arabidopsis.org.uk. All GARNet services and resources are publicly available, and data created using the GARNet resources will be freely distributed via databases held at the Nottingham Arabidopsis Stock Centre and the John Innes Centre.     

Evolution and applications of plant pathway resources and databases

Plants are important sources of food and plant products are essential for modern human life. Plants are increasingly gaining importance as drug and fuel resources, bioremediation tools and as tools for recombinant technology. Considering these applications, database infrastructure for plant model systems deserves much more attention. Study of plant biological pathways, the interconnection between these pathways and plant systems biology on the whole has in general lagged behind human systems biology. In this article we review plant pathway databases and the resources that are currently available. We lay out trends and challenges in the ongoing efforts to integrate plant pathway databases and the applications of database integration. We also discuss how progress in non-plant communities can serve as an example for the improvement of the plant pathway database landscape and thereby allow quantitative modeling of plant biosystems. We propose Good Database Practice as a possible model for collaboration and to ease future integration efforts.     

Design and utilization of epitope-based databases and predictive tools

In the last decade, significant progress has been made in expanding the scope and depth of publicly available immunological databases and online analysis resources, which have become an integral part of the repertoire of tools available to the scientific community for basic and applied research. Herein, we present a general overview of different resources and databases currently available. Because of our association with the Immune Epitope Database and Analysis Resource, this resource is reviewed in more detail. Our review includes aspects such as the development of formal ontologies and the type and breadth of analytical tools available to predict epitopes and analyze immune epitope data. A common feature of immunological databases is the requirement to host large amounts of data extracted from disparate sources. Accordingly, we discuss and review processes to curate the immunological literature, as well as examples of how the curated data can be used to generate a meta-analysis of the epitope knowledge currently available for diseases of worldwide concern, such as influenza and malaria. Finally, we review the impact of immunological databases, by analyzing their usage and citations, and by categorizing the type of citations. Taken together, the results highlight the growing impact and utility of immunological databases for the scientific community.     

An ontology for cell types

We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA.     

Storing biological sequence databases in relational form

SUMMARY: We have created a set of applications using Perl and Java in combination with XML technology to install biological sequence databases into an Oracle RDBMS. An easy-to-use interface using Java has been created for database query and other tools developed to integrate with our in-house bioinformatics applications. AVAILIBILITY: The database schema, DTD file, and source codes are available from the authors via email. CONTACT: guochun_ xie@merck. com     

ORBIT: an integrated environment for user-customized bioinformatics tools

MOTIVATION: There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. RESULTS: We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.     

Open source tools and toolkits for bioinformatics: significance, and where are we?

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.     

A community-based annotation framework for linking solanaceae genomes with phenomes

The amount of biological data available in the public domain is growing exponentially, and there is an increasing need for infrastructural and human resources to organize, store, and present the data in a proper context. Model organism databases (MODs) invest great efforts to functionally annotate genomes and phenomes by in-house curators. The SOL Genomics Network (SGN; http://www.sgn.cornell.edu) is a clade-oriented database (COD), which provides a more scalable and comparative framework for biological information. SGN has recently spearheaded a new approach by developing community annotation tools to expand its curational capacity. These tools effectively allow some curation to be delegated to qualified researchers, while, at the same time, preserving the in-house curators' full editorial control. Here we describe the background, features, implementation, results, and development road map of SGN's community annotation tools for curating genotypes and phenotypes. Since the inception of this project in late 2006, interest and participation from the Solanaceae research community has been strong and growing continuously to the extent that we plan to expand the framework to accommodate more plant taxa. All data, tools, and code developed at SGN are freely available to download and adapt.     

An ontology for cell types

We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA.     

GeneCruiser: a web service for the annotation of microarray data

SUMMARY: GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers from databases, such as UniGene, while providing links to web resources, such as the UCSC Genome Browser. It relies on a regularly updated database that retrieves and indexes the mappings between microarray probes and genomic databases. Genes are identified using the Life Sciences Identifier standard. AVAILABILITY: GeneCruiser is freely available in the following forms: Web service and Web application, http://www.genecruiser.org; GenePattern, GeneCruiser access has been integrated into our microarray analysis platform, GenePattern. http://www.genepattern.org.     

The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server

Since it was launched in 1993, the ExPASy server has been and is still a reference in the proteomics world. ExPASy users access various databases, many dedicated tools, and lists of resources, among other services. A significant part of resources available is devoted to two-dimensional electrophoresis data. Our latest contribution to the expansion of the pool of on-line proteomics data is the World-2DPAGE Constellation, accessible at http://world-2dpage.expasy.org/. It is composed of the established WORLD-2DPAGE List of 2-D PAGE database servers, the World-2DPAGE Portal that queries simultaneously world-wide proteomics databases, and the recently created World-2DPAGE Repository. The latter component is a public standards-compliant repository for gel-based proteomics data linked to protein identifications published in the literature. It has been set up using the Make2D-DB package, a software tool that helps building SWISS-2DPAGE-like databases on one's own Web site. The lack of necessary informatics infrastructure to build and run a dedicated website is no longer an obstacle to make proteomics data publicly accessible on the Internet.     

Towards microbial data integration

There are currently 100–200 microbiology-related databases in existence, although it is impossible to find answers to queries that span even a few of these. The Center for Microbial Ecology (CME) at Michigan State University seeks to change this situation by coordinating the creation of an Integrated Microbial Database (IMD), accessible through the World Wide Web (WWW). Such a system will contain up-to-date phylogeny and taxonomy, gene sequences (including genomes), biochemical data, metabolic models, ecological and phenotypic data. Current main obstacles to creation of an IMD are the lack of a single freely available organismal nomenclature with synonyms and the availability of much critical data. An IMD will have major impacts on microbial biology: currently intractable fundamental questions might be answered, experiments could be refocused, and new commercial possibilities created. An IMD should remain freely available and be created under an open development model. Received 20 June 1996/ Accepted in revised form 02 November 1996     

Online resources for SNP analysis

The major online single nucleotide polymorphism (SNP) databases freely available as research tools for genetic analysis are explained, reviewed, and compared. An outline is given of the search strategies that can be used with the most extensive current SNP databases: National Centre for Biotechnology Information (NCBI) dbSNP and HapMap to help the user secure the most appropriate data for the research needs of clinical genetics and population genetics research. A range of online tools that can be useful in designing SNP genotyping assays are also detailed.