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1.
Baxevanis AD 《Nucleic acids research》2001,29(1):1-10
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries of each of the databases included in the Collection are available through the Nucleic Acids Research Web site, at http://www. nar.oupjournals.org. 相似文献
2.
Andreas D. Baxevanis 《Nucleic acids research》2002,30(1):1-12
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org. 相似文献
3.
The molecular biology database collection: an online compilation of relevant database resources 总被引:6,自引:0,他引:6
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Baxevanis AD 《Nucleic acids research》2000,28(1):1-7
The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more accessible to biologists. This online resource, available at http://www.oup.co.uk/nar/Volume_28/Issue_01/html /gkd115_gml.html, is intended to serve as a searchable, up-to-date, centralized jumping-off point to individual Web sites. An emphasis has also been placed on including databases where new value is added to the underlying data by virtue of curation, new data connections, or other innovative approaches. 相似文献
4.
Active Sequences Collection (ASC) is a collection of amino acid sequences, with an unique feature: only short sequences are collected, with a demonstrated biological activity. The current version of ASC consists of three sections: DORRS, a collection of active RGD-containing peptides; TRANSIT, a collection of protein regions active as substrates of transglutaminase enzyme (TGase), and BAC, a collection of short peptides with demonstrated biological activity. Literature references for each entry are reported, as well as cross references to other databases, when available. The current version of ASC includes more than 800 different entries. The main scope of this collection is to offer a new tool to investigate the structural features of protein active sites, additionally to similarity searches against large protein databases or searching for known functional patterns. ASC database is available at the web address http://crisceb.unina2.it/ASC/ which also offers a dedicated query interface to compare user-defined protein sequences with the database, as well as an updating interface to allow contribution of new referenced active sequences. 相似文献
5.
《Journal of applied microbiology》1990,69(2):141-144
These quarterly literature reviews are a listing of selected references from various sources. The selection has been made by a panel of 'reviewers' and is compiled by S.P. Denyer, Department of Pharmaceutical Sciences, Nottingham University. This current selection includes some references published prior to this quarter which have only recently come to the attention of the 'reviewers'. The listing is not intended to be exhaustive. We regret that reprints and photocopies are not available from the Journal or from the 'review' panel. 相似文献
6.
《Journal of applied microbiology》1991,70(4):275-278
These quarterly literature reviews are a listing of selected references from various sources. The selection has been made by a panel of 'reviewers' and is compiled by S.P. Denyer, Department of Pharmacy, Brighton Polytechnic. This current selection includes some references published prior to this quarter which have only recently come to the attention of the 'reviewers'. The listing is not intended to be exhaustive. We regret that reprints and photocopies are not available from the Journal or from the 'review' panel. 相似文献
7.
The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations. 相似文献
8.
The documentation of biological control agents targeting arthropods in the United States has historically been subject to less regulation relative to weed biological control releases. This study reviews publicly available databases to track environmental releases of biological control agents targeting arthropods in the United States. It then presents available data for the states with the most releases between 1962 and 2005: Hawaii, California and Florida. These data indicate a clear decline in rates of introduction since 1982 or 1994, depending on the source. Existing record-keeping systems offer incomplete or inconsistent data for evaluation because they were designed with limited goals, attempt to capture excessive detail and are thus impractical, or are insufficiently resourced. Existing databases cannot be used to answer meaningful questions regarding non-target effects of introduced control agents. Current databases are inappropriately designed and insufficiently resourced to meet today's research and regulatory needs. We propose and describe a new database system for classical biological control of arthropods. 相似文献
9.
Public databases are essential to the development of multi-omics resources. The amount of data created by biological technologies needs a systematic and organized form of storage, that can quickly be accessed, and managed. This is the objective of a biological database. Here, we present an overview of human databases with web applications. The databases and tools allow the search of biological sequences, genes and genomes, gene expression patterns, epigenetic variation, protein-protein interactions, variant frequency, regulatory elements, and comparative analysis between human and model organisms. Our goal is to provide an opportunity for exploring large datasets and analyzing the data for users with little or no programming skills. Public user-friendly web-based databases facilitate data mining and the search for information applicable to healthcare professionals. Besides, biological databases are essential to improve biomedical search sensitivity and efficiency and merge multiple datasets needed to share data and build global initiatives for the diagnosis, prognosis, and discovery of new treatments for genetic diseases. To show the databases at work, we present a a case study using ACE2 as example of a gene to be investigated. The analysis and the complete list of databases is available in the following website <https://kur1sutaru.github.io/fantastic_databases_and_where_to_find_them/>. 相似文献
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A huge amount of important biomedical information is hidden in the bulk of research articles in biomedical fields. At the same time, the publication of databases of biological information and of experimental datasets generated by high-throughput methods is in great expansion, and a wealth of annotated gene databases, chemical, genomic (including microarray datasets), clinical and other types of data repositories are now available on the Web. Thus a current challenge of bioinformatics is to develop targeted methods and tools that integrate scientific literature, biological databases and experimental data for reducing the time of database curation and for accessing evidence, either in the literature or in the datasets, useful for the analysis at hand. Under this scenario, this article reviews the knowledge discovery systems that fuse information from the literature, gathered by text mining, with microarray data for enriching the lists of down and upregulated genes with elements for biological understanding and for generating and validating new biological hypothesis. Finally, an easy to use and freely accessible tool, GeneWizard, that exploits text mining and microarray data fusion for supporting researchers in discovering gene-disease relationships is described. 相似文献
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Schoof H 《Comparative and Functional Genomics》2003,4(2):255-258
Increasing numbers of whole-genome sequences are available, but to interpret them fully requires more than listing all genes. Genome databases are faced with the challenges of integrating heterogenous data and enabling data mining. In comparison to a data warehousing approach, where integration is achieved through replication of all relevant data in a unified schema, distributed approaches provide greater flexibility and maintainability. These are important in a field where new data is generated rapidly and our understanding of the data changes. Interoperability between distributed data sources allows data maintenance to be separated from integration and analysis. Simple ways to access the data can facilitate the development of new data mining tools and the transition from model genome analysis to comparative genomics. With the MIPS Arabidopsis thaliana genome database (MAtDB, http://mips.gsf.de/proj/thal/db) our aim is to go beyond a data repository towards creating an integrated knowledge resource. To this end, the Arabidopsis genome has been a backbone against which to structure and integrate heterogenous data. The challenges to be met are continuous updating of data, the design of flexible data models that can evolve with new data, the integration of heterogenous data, e.g. through the use of ontologies, comprehensive views and visualization of complex information, simple interfaces for application access locally or via the Internet, and knowledge transfer across species. 相似文献
14.
Enormous amounts of data result from genome sequencing projects and new experimental methods. Within this tremendous amount of genomic data 30-40 per cent of the genes being identified in an organism remain unknown in terms of their biological function. As a consequence of this lack of information the overall schema of all the biological functions occurring in a specific organism cannot be properly represented. To understand the functional properties of the genomic data more experimental data must be collected. A pathway database is an effort to handle the current knowledge of biochemical pathways and in addition can be used for interpretation of sequence data. Some of the existing pathway databases can be interpreted as detailed functional annotations of genomes because they are tightly integrated with genomic information. However, experimental data are often lacking in these databases. This paper summarises a list of pathway databases and some of their corresponding biological databases, and also focuses on information about the content and the structure of these databases, the organisation of the data and the reliability of stored information from a biological point of view. Moreover, information about the representation of the pathway data and tools to work with the data are given. Advantages and disadvantages of the analysed databases are pointed out, and an overview to biological scientists on how to use these pathway databases is given. 相似文献
15.
Sangket U Phongdara A Chotigeat W Nathan D Kim WY Bhak J Ngamphiw C Tongsima S Khan AM Lin H Tan TW 《Bioinformatics (Oxford, England)》2008,24(2):299-301
Bioinformatics involves the collection, organization and analysis of large amounts of biological data, using networks of computers and databases. Developing countries in the Asia-Pacific region are just moving into this new field of information-based biotechnology. However, the computational infrastructure and network bandwidths available in these countries are still at a basic level compared to that in developed countries. In this study, we assessed the utility of a BitTorrent-based Peer-to-Peer (btP2P) file distribution model for automatic synchronization and distribution of large amounts of biological data among developing countries. The initial country-level nodes in the Asia-Pacific region comprised Thailand, Korea and Singapore. The results showed a significant improvement in download performance using btP2P--three times faster overall download performance than conventional File Transfer Protocol (FTP). This study demonstrated the reliability of btP2P in the dissemination of continuously growing multi-gigabyte biological databases across the three Asia-Pacific countries. The download performance for btP2P can be further improved by including more nodes from other countries into the network. This suggests that the btP2P technology is appropriate for automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries in the Asia-Pacific region. AVAILABILITY: http://everest.bic.nus.edu.sg/p2p/ 相似文献
16.
The domesticated silkworm, Bombyx mori serves as an ideal representative of lepidopteran species for a variety of scientific studies. As a result, databases have been created to organize information pertaining to the silkworm genome that is subject to constant updating. Of these, four main databases are important for store nucleotide information in the form of genomic data, ESTs and microsatelites. These databases also store data related to other lepidoptera and important insects, which help in insect biological research. Though a considerable amount of nucleotide data is currently available, there is a paucity of data related to silkworm and other lepidopteran proteins. Hence, the focus of this article is to present the current status of nucleotide databases of silkworm, avenues for improvement and possibilities for databases that could be created in the future. 相似文献
17.
With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database. 相似文献
18.
This review of published in vitro and in vivo studies concerning the biological effects of ultraviolet A (UVA; 320-400 nm) radiation illustrates the evidence for combining UVA and UVB filters in sun-protection products. These data have led to the development of new sunscreens as well as methods to evaluate their efficacy. After listing the UVA filters available and briefly noting the requirements for a high SPF, broad-spectrum sunscreen, the methods for evaluating the level of UVA protection will be described. This article also summarizes several studies looking at the prevention of erythema, pigmentation, DNA damage, photoimmunosuppression, photoaging and photodermatoses. These data demonstrate in vitro and in vivo that only well-balanced UVA-UVB sunscreens, absorbing over the entire UV spectrum are able to prevent or significantly reduce the associated biological damage. 相似文献
19.
Collection of biological samples is the foundation of genetic studies ranging from estimation of genetic diversity to reconstruction of population history. Sample collections are intended to accurately represent the genetic, biological, ecological, cultural, geographic, and/or linguistic diversity of a particular region or population by providing a small, but representative, set of samples. In this study, we analyze human mitochondrial DNA variation in samples collected using four different sampling strategies to represent the same geographic region. Specifically, samples were collected from a village, a rural area, a regional clinic, and a national university in the governorate of Dhamar in Yemen. All samples were assayed for mitochondrial hypervariable region I DNA sequence variation and data were subjected to standard molecular genetic analyses. Our results suggest that analyses in which individual DNA sequences are explicitly compared or evaluated, e.g. phylogenetic and network analyses, may be more sensitive to sample collection design than analyses in which data are averaged across individuals or are analyzed more indirectly, e.g. summary statistics. 相似文献