Will a biological database be different from a biological journal?
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Journal Article↗
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Results for “Biological databases”
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Mobile access to biological databases on the Internet.
We have developed a new way of accessing biological databases and bioinformatics applications on the Internet. This new service, bioinformatics wireless application protocol (BioWAP) service, which is accessible by mobile devices makes it possible to access bioinformatics services, where normal PC or personal digital assistant (PDA) connections are not feasible. The BioWAP service includes major biological databases and applications demonstrating a simple method of implementing WAP interfaces to uncompliant applications, i.e. the applications that are not WAP or Internet based. The BioWAP service can be browsed with any WAP terminal.
Computational Biology↗
Biological database design and implementation.
We present our experience of building biological databases. Such databases have most aspects in common with other complex databases in other fields. We do not believe that biological data are that different from complex data in other fields. Our experience has led us to emphasise simplicity and conservative technology choices when building these databases. This is a short paper of advice that we hope is useful to people designing their own biological database.
Database Management Systems↗
Whither biological database research?
We consider how the landscape of biological databases may evolve in the future, and what research is needed to realize this evolution. We suggest today's dispersal of diverse resources will only increase as the number and size of those resources, driving the need for semantic interoperability even more strongly. Because the complexity of the questions biologists want answered automatically continues to rapidly escalate, we will need to draw upon high-performance computing resources such as the GRID to process complex queries. Finally, we still need data, and our ways of acquiring and curating data must improve by orders of magnitude.
Computational Biology↗
Supporting the curation of biological databases with reusable text mining.
Curators of biological databases transfer knowledge from scientific publications, a laborious and expensive manual process. Machine learning algorithms can reduce the workload of curators by filtering relevant biomedical literature, though their widespread adoption will depend on the availability of intuitive tools that can be configured for a variety of tasks. We propose a new method for supporting curators by means of document categorization, and describe the architecture of a curator-oriented tool implementing this method using techniques that require no computational linguistic or programming expertise. To demonstrate the feasibility of this approach, we prototyped an application of this method to support a real curation task: identifying PubMed abstracts that contain allergen cross-reactivity information. We tested the performance of two different classifier algorithms (CART and ANN), applied to both composite and single-word features, using several feature scoring functions. Both classifiers exceeded our performance targets, the ANN classifier yielding the best results. These results show that the method we propose can deliver the level of performance needed to assist database curation.
Allergens↗
The Molecular Biology Database Collection: 2006 update.
The NAR Molecular Biology Database Collection is a public online resource that contains links to all databases described in this issue of Nucleic Acids Research. In addition, this collection lists databases that have been featured in previous issues of NAR, as well as selected other databases that are freely available to the public and may be useful to the molecular biologist. The 2006 update includes 858 databases, 139 more than the previous one. The databases come with brief summaries, many of which have been updated recently. Each database is assigned a stable accession number that does not change if the database moves to a new location and its URL, authors' names or the contact person address are updated. The complete database list and summaries are available online at the Nucleic Acids Research website http://nar.oxfordjournals.org/.
Databases, Genetic↗
Semantic search among heterogeneous biological databases based on gene ontology.
Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.
Database Management Systems↗
A new network-based biologic database system.
Bioinformatics is playing an increasingly important role in the processing and analysis of biomedical data. The collection, storage and analysis of biologic information are key components of bioinformatics. In the genome era, with the explosion of sequence and structural information available to researchers, the structure of biologic databases is becoming more complicated, the contents is becoming larger, and the management and development is also becoming more difficult. A network-based biologic database has been developed. This database system integrates administration, development and analysis of bioinformatics with common and friendly interface. For the life scientists without much computer programming expertise, the system is easy to master.
Computational Biology↗
Using meta computing tools to facilitate large-scale analyses of biological databases.
Given the high rate at which biological data are being collected and made public, it is essential that computational tools be developed that are capable of efficiently accessing and analyzing these data. High-performance distributed computing resources can play a key role in enabling large-scale analyses of biological databases. We use a distributed computing environment, Legion, to enable large-scale computations on the Protein Data Bank (PDB). In particular, we employ the Feature program to scan all protein structures in the PDB in search for unrecognized potential cation binding sites. We evaluate the efficiency of Legion's parallel execution capabilities and analyze the initial biological implications that result from having a site annotation scan of the entire PDB. We discuss four interesting proteins with unannotated, high-scoring candidate cation binding sites.
Algorithms↗
DBcat: a catalog of 500 biological databases.
The DBcat (http://www.infobiogen.fr/services/dbcat ) is a comprehensive catalog of biological databases, maintained and curated at Infobiogen. It contains 500 databases classified by application domains. The DBcat is a structured flat-file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for download from Infobiogen anonymous ftp server.
Biology↗
CSB.DB: a comprehensive systems-biology database.
SUMMARY: The open access comprehensive systems-biology database (CSB.DB) presents the results of bio-statistical analyses on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life's complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The central part of CSB.DB, which we describe in this applications note, is a set of co-response databases that currently focus on the three key model organisms, Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana. CSB.DB gives easy access to the results of large-scale co-response analyses, which are currently based exclusively on the publicly available compendia of transcript profiles. By scanning for the best co-responses among changing transcript levels, CSB.DB allows to infer hypotheses on the functional interaction of genes. These hypotheses are novel and not accessible through analysis of sequence homology. The database enables the search for pairs of genes and larger units of genes, which are under common transcriptional control. In addition, statistical tools are offered to the user, which allow validation and comparison of those co-responses that were discovered by gene queries performed on the currently available set of pre-selectable datasets. AVAILABILITY: All co-response databases can be accessed through the CSB.DB Web server (http://csbdb.mpimp-golm.mpg.de/).
Database Management Systems↗
Restructuring the genome data base: a model for a federation of biological databases.
The creation of a federation of public biological databases has been proposed. Formerly independent systems will need to be modified to interoperate better within this federation. This will enable the federated system to provide biologists with an integrated view of biological data. The GDB Human Genome Data Base is being restructured to participate in the proposed federation. GDB itself will be organized into a collection of related data sets in support of human gene mapping. The techniques that will be used to link these data sets will be applicable to the federation as a whole. Links will be based on stable accession numbers that have no inherent information content and are guaranteed always to be recognized. Improvements will be made in the links between GDB and the nucleotide sequence databases to test this approach further.
Amino Acid Sequence↗
The Molecular Biology Database Collection: 2005 update.
The Nucleic Acids Research Molecular Biology Database Collection is a public online resource that lists the databases described in this and previous issues of Nucleic Acids Research together with other databases of value to the biologist and available throughout the world. All databases included in this Collection are freely available to the public. The 2005 update includes 719 databases, 171 more than the 2004 one. The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task. The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories. The database summaries provide brief descriptions of the databases, contact details, appropriate references and acknowledgements. The online summaries also serve as a venue for the maintainers of each database to introduce database updates and other improvements in the scope and tools. These updates are particularly important for those databases that have not been described in print in the recent past. The database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oupjournals.org/.
Allergy and Immunology↗
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
Animals↗
DBcat: a catalog of biological databases.
The DBcat (http://www.infobiogen.fr/services/dbcat) is a comprehensive catalog of biological databases, maintained and curated on a daily basis at GIS Infobiogen. It contains more than 400 databases classified by application domains. The DBcat is a structured flat file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for downloading from Infobiogen anonymous ftp server.
Biology↗
Integrating biological databases.
Recent years have seen an explosion in the amount of available biological data. More and more genomes are being sequenced and annotated, and protein and gene interaction data are accumulating. Biological databases have been invaluable for managing these data and for making them accessible. Depending on the data that they contain, the databases fulfil different functions. But, although they are architecturally similar, so far their integration has proved problematic.
Animals↗
From biological databases to platforms for biomedical discovery.
The use of high-throughput DNA sequencing and proteomic methods has led to an unprecedented increase in the amount of genomic and proteomic data. Application of computing technologies and development of computational tools to analyze and present these data has not kept pace with the accumulation of information. Here, we discuss the use of different database systems to store biological information and mention some of the key emerging computing technologies that are likely to have a key role in the future of bioinformatics.
Algorithms↗
Electronic access to mouse tumor data: the Mouse Tumor Biology Database (MTB) project.
The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary and induced cancers by providing electronic access to: (i) tumor names and classifications, (ii) tumor incidence and latency data in different strains of mice, (iii) tumor pathology reports and images, (iv) information on genetic factors associated with tumors and tumor development, and (v) references (published and unpublished data). This resource has been designed to aid researchers in such areas as choosing experimental models, reviewing patterns of mutations in specific cancers, and identifying genes that are commonly mutated across a spectrum of cancers. MTB also provides hypertext links to related on-line resources and databases. MTB is accessible via the World Wide Web at http://tumor.informatics.jax.org. User support is available for MTB by Email at mgi-help@informatics.jax.org
Age of Onset↗