International Mammalian Genome Society

logo18th International Mouse Genome Conference

17-22 October 2004, Seattle, USA


POSTER 98 - SEQUENCES MEET BIOLOGY: INTEGRATION OF SEQUENCES AS

DATABASE OBJECTS IN MOUSE GENOME INFORMATICS

Corbani LE, Baldarelli RM, King BL, Cousins S, Beal JS, Lewis J, Meiers DB, Walker MB, Kadin JA, Richardson JE, Blake JA, Ringwald M, Eppig JT, Bult CJ

The Jackson Laboratory, Bar Harbor, United States

The Mouse Genome Informatics (MGI) Database is a public resource that provides curated and integrated information on the biology and genetics of the laboratory mouse. With the recent 3.0 release, MGI has radically improved support for sequence data. Nucleotide and protein sequences are represented as distinct database objects, rather than accession ID attributes of other objects.  The full power of relational integration now connects sequence information to the existing MGI integrated platform of curated biological domains such as: genes, gene expression, gene function, phenotypes, strains, mammalian orthology, and chromosomal positioning, and soon to come, SNPs. MGI now stores information for all mouse sequences from GenBank, SWISS-PROT, LocusLink, RefSeq, Ensembl and NCBI gene models, TIGR and NIA Mouse Gene Indices, and DoTS. Information for each sequence includes source attributes such as library, strain, tissue, gender, etc. mapped to MGI controlled vocabularies whenever possible and sequence attributes such as type, description, provider, length, genome assembly coordinates (for gene models), etc. Users can query for sequences using any or all of the biological domains mentioned above and get results back in a variety of formats (HTML, tab delimited, FASTA). An additional aspect of this implementation is a robust and uniform system for loading sequence data, clone data, sequence-to-gene associations, and sequence-to-clone associations from a variety of sources, all within the context of MGI's commitment to high quality data.  Storing and integrating sequences as objects in MGI is a first step toward a much more precise representation of sequence features and attributes through the development of sequence feature maps.  The details and challenges of our implementation of sequences as objects and the benefits this brings to our user community will be presented. The MGI database can be accessed at http://www.informatics.jax.org.

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