Query the SIMO Database
about samples, clones, 16S gene sequences, and other SIMO research products
is organized in a relational database management system. The database
model was designed to reflect the natural hierarchy that exists among
samples and information and materials derived from them, and to maintain
the complete research context for data stored in the system (view
database diagram). Referential integrity constraints, data dictionaries,
and list-based data entry applications are used to ensure the integrity
and quality of all information stored in the database.
database is primarily designed for archival, synthesis, and distribution
of data from SIMO research to the microbial ecology community. However,
information derived from analysis of 16S sequences using standard bioinformatics
tools, such as the Ribosomal
Database Project's Sequence Match program and sequence alignment
tools in the FASTA package,
is stored in the database to provide taxonomic context. Additional information
about SIMO taxonomic methodology and RDPquery,
an end-user Java program for classifying 16S rRNA sequences, are available
on the Bacterial Taxonomy page.
Various sequence formatting options are also provided to facilitate use
of SIMO data with other databases and applications.
can access the full database for data entry, querying, and administration
using a combination of private web applications and custom database interface
programs. Other researchers can access portions of the database to look
up specific 16S rRNA sequences or search for sequences by taxonomic characteristics
or ecological characteristics of the original sample.
and structure of the SIMO 16S rRNA database are described in more detail
in the following publication:
W.M., M.A. Moran and J.T. Hollibaugh. 2002. Efforts to link ecological
metadata with bacterial gene sequences at the Sapelo Island Microbial
Observatory. Proceedings of the 6th World Multiconference on Systemics,
Cybernetics, and Informatics -- Information Systems Development II. VII:402-407.
Acrobat® version, PowerPoint® presentation).