PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 12807806

Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances.

Luis Marenco·Nicholas Tosches·Chiquito Crasto·Gordon Shepherd·Perry L Miller·Prakash M Nadkarni
View original source ↗Export metadata ↓

Abstract

The EAV/CR framework, designed for database support of rapidly evolving scientific domains, utilizes metadata to facilitate schema maintenance and automatic generation of Web-enabled browsing interfaces to the data. EAV/CR is used in SenseLab, a neuroscience database that is part of the national Human Brain Project. This report describes various enhancements to the framework. These include (1) the ability to create "portals" that present different subsets of the schema to users with a particular research focus, (2) a generic XML-based protocol to assist data extraction and population of the database by external agents, (3) a limited form of ad hoc data query, and (4) semantic descriptors for interclass relationships and links to controlled vocabularies such as the UMLS.

Explore related subjects

Database Management SystemsDatabases as TopicInternetProgramming LanguagesSemanticsSoftwareVocabulary, ControlledJournal ArticleResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Luis Marenco, Nicholas Tosches, Chiquito Crasto, Gordon Shepherd, Perry L Miller, Prakash M Nadkarni. 2003-06-04. Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances.. https://doi.org/10.1197/jamia.m1303

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2003

The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD).

BACKGROUND: The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. DESCRIPTION: The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at http://www.longhornarraydatabase.org CONCLUSIONS: Our development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data.

Database Management Systems↗
PubMed2003

Digital extractor: analysis of digital differential display output.

Digital Extractor is a program for the high-throughput processing of data sets derived from digital differential display-based comparisons of EST libraries. These comparisons can be utilized to identify discrete subsets of genes whose expression is restricted to distinct tissue types. The program facilitates these investigations by permitting parallel annotation of genes identified as being differentially expressed.

Database Management Systems↗
PubMed2003

Pathways database system: an integrated system for biological pathways.

MOTIVATION: During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. RESULTS: In this paper we present an integrated system, called Pathways Database System, with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (a) genomic information integrated with other biological data and presented from a pathway, rather than from the DNA sequence, perspective; (b) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (c) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels, and to pose predetermined queries; and (d) an implementation that allows for web(XML)-based dissemination of query outputs (i.e. pathways data) to researchers in the community, giving them control on the use of pathways data. AVAILABILITY: Available on request from the authors.

Database Management Systems↗