共查询到20条相似文献,搜索用时 647 毫秒
1.
Thomas J Lee Yannick Pouliot Valerie Wagner Priyanka Gupta David WJ Stringer-Calvert Jessica D Tenenbaum Peter D Karp 《BMC bioinformatics》2006,7(1):170-14
Background
This article addresses the problem of interoperation of heterogeneous bioinformatics databases. 相似文献2.
Background
The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration. 相似文献3.
Gregor Rot Anup Parikh Tomaz Curk Adam Kuspa Gad Shaulsky Blaz Zupan 《BMC bioinformatics》2009,10(1):265
Background
Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. 相似文献4.
Robert W Byrnes Dawn Cotter Andreia Maer Joshua Li David Nadeau Shankar Subramaniam 《BMC systems biology》2009,3(1):99-10
Background
Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. 相似文献5.
6.
Damian DG Gessler Gary S Schiltz Greg D May Shulamit Avraham Christopher D Town David Grant Rex T Nelson 《BMC bioinformatics》2009,10(1):309-21
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. 相似文献7.
Background
Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. 相似文献8.
Francisco J Lopez Armando Blanco Fernando Garcia Carlos Cano Antonio Marin 《BMC bioinformatics》2008,9(1):107
Background
Last years' mapping of diverse genomes has generated huge amounts of biological data which are currently dispersed through many databases. Integration of the information available in the various databases is required to unveil possible associations relating already known data. Biological data are often imprecise and noisy. Fuzzy set theory is specially suitable to model imprecise data while association rules are very appropriate to integrate heterogeneous data. 相似文献9.
Diogo FT Veiga Helena F Deus Caner Akdemir Ana Tereza R Vasconcelos Jonas S Almeida 《BMC systems biology》2009,3(1):109-9
Background
DAS is a widely adopted protocol for providing syntactic interoperability among biological databases. The popularity of DAS is due to a simplified and elegant mechanism for data exchange that consists of sources exposing their RESTful interfaces for data access. As a growing number of DAS services are available for molecular biology resources, there is an incentive to explore this protocol in order to advance data discovery and integration among these resources. 相似文献10.
Background
Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction of mobile phones that utilise the open source Android operating system, and which include (among other features) both GPS and Google Maps, provide new opportunities for developing mobile phone applications, which in conjunction with web applications, allow two-way communication between field workers and their project databases.Methodology
Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a web application located within www.spatialepidemiology.net. Data collected by multiple field workers can be submitted by phone, together with GPS data, to a common web database and can be displayed and analysed, along with previously collected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayed on the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individual field workers or, for example, those data within certain values of a measured variable or a time period.Conclusions
Data collection frameworks utilising mobile phones with data submission to and from central databases are widely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would have if viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection and display, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworks offer great potential for recruiting ‘citizen scientists’ to contribute data easily to central databases through their mobile phone. 相似文献11.
Wei Tan Ravi Madduri Alexandra Nenadic Stian Soiland-Reyes Dinanath Sulakhe Ian Foster Carole A Goble 《BMC bioinformatics》2010,11(1):542
Background
In biological and medical domain, the use of web services made the data and computation functionality accessible in a unified manner, which helped automate the data pipeline that was previously performed manually. Workflow technology is widely used in the orchestration of multiple services to facilitate in-silico research. Cancer Biomedical Informatics Grid (caBIG) is an information network enabling the sharing of cancer research related resources and caGrid is its underlying service-based computation infrastructure. CaBIG requires that services are composed and orchestrated in a given sequence to realize data pipelines, which are often called scientific workflows. 相似文献12.
Background
Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. 相似文献13.
Kevin Garwood Christopher Garwood Cornelia Hedeler Tony Griffiths Neil Swainston Stephen G Oliver Norman W Paton 《BMC bioinformatics》2006,7(1):532-14
Background
The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. 相似文献14.
Background
Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. 相似文献15.
Background
Current genomic research methods provide researchers with enormous amounts of data. Combining data from different high-throughput research technologies commonly available in biological databases can lead to novel findings and increase research efficiency. However, combining data from different heterogeneous sources is often a very arduous task. These sources can be different microarray technology platforms, genomic databases, or experiments performed on various species. Our aim was to develop a software program that could facilitate the combining of data from heterogeneous sources, and thus allow researchers to perform genomic cross-platform/cross-species studies and to use existing experimental data for compendium studies. 相似文献16.
17.
A number of biological data resources (i.e. databases and data analytical tools) are searchable and usable on-line thanks to the internet and the World Wide Web (WWW) servers. The output from the web server is easy for us to browse. However, it is laborious and sometimes impossible for us to write a computer program that finds a useful data resource, sends a proper query and processes the output. It is a serious obstacle to the integration of distributed heterogeneous data resources. To solve the issue, we have implemented a SOAP (Simple Object Access Protocol) server and web services that provide a program-friendly interface. The web services are accessible at http://www.xml.nig.ac.jp/. 相似文献
18.
Background
Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequence databases. However, this is usually not an easy task for the average bench scientist. 相似文献19.
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