GeneCards

GeneCards aggregates and integrates genomic, transcriptomic, proteomic, genetic, and functional data for over 7,000 human genes with approved symbols from the HUGO/GDB nomenclature committee to support functional analysis and genomic research.

Key Features:

• Gene-centric coverage: Comprehensive entries for over 7,000 human genes with approved HUGO/GDB symbols.
• Multi-source integration: Aggregates information from approximately 150 web sources, including SWISS-PROT, OMIM, Genatlas, and GDB.
• Data types: Provides genomic sequences, genomic locations, cDNA assemblies, orthologies, 3D protein structures, gene expression profiles, medical/clinical information, and focused SNP summaries.
• Regular updates: Gene entries are periodically updated and enhanced to incorporate new sequence and annotation data.
• Automated extraction: Uses Perl scripts to automatically extract and compile relevant data from external databases.
• Software architecture: Built using object-oriented Perl and a schema-driven XML format for data representation.
• Novel and predicted gene support: Generates detailed gene "cards" for known, novel, and predicted genes.
• Algorithmic query support: Implements algorithms for query reformulation to support automated information retrieval.

Scientific Applications:

• Functional analysis: Supports annotation and interpretation of gene function across multiple data modalities.
• Genomic research: Facilitates integrative analyses in genomic studies using assembled sequence and annotation data.
• Expression studies: Enables large-scale expression analyses, including DNA chip (microarray) and two-dimensional protein electrophoresis studies.
• Clinical and genetic association: Assists analysis of medical and genetic information related to health and disease.
• Novel gene characterization: Provides integrated evidence to support analysis of novel and predicted genes.

Methodology:

Data are compiled via object-oriented Perl and automated Perl scripts that extract and integrate information from ~150 web sources and databases (including SWISS-PROT, OMIM, Genatlas, and GDB); the system uses a schema-driven XML format and implements algorithms for query reformulation.