Mouse-related websites (A comparative review)
The Jackson Laboratory (JAX mice) http://jaxmice.jax.org/index.html
Mouse Genome Informatics (MGI) http://www.informatics.jax.org/
BioMedNet mouse knockout database http://research.bmn.com/mkmd
TBASE http://tbase.jax.org/
Nagy Lab http://www.mshri.on.ca/nagy/
No longer
available on the web:
SEBI http://molgen.biologie.uni-mainz.de/mouse/SEBI.html
Lexicon Genetics
mining the genome http://www.lexgen.com/omnibank/omnibank.htm
The Jackson Laboratory (JAX mice)
This is a comprehensive site containing tools for biological research using the mouse as a model. It provides information on a wide range of mouse strains, background literature, protocols, and ordering information,
Mouse Genome Informatics (MGI)
This site is maintained by the Jackson Laboratory, and provides information on different aspects of the mouse genome, including markers, alleles, phenotypes, and polymorphisms. It also provides tools for comparative studies with genomes of other organisms.
BioMedNet mouse knockout database
This is a site containing information related to phenotypes of knockouts and information on gene insertion mutations and classical mutants. It also has links to literature databases such as MEDLINE and BioMedNet.
TBASE
TBASE
is another site that is connected to the Jackson Laboratory. This site attempts
to organize all of the information on
transgenic animals and targeted mutations that is generated and analyzed
worldwide. There is a specific emphasis on gathering information on mouse
knockouts.
Nagy Lab
This
is a site from a lab from the Samuel Lunenfeld Research Institute. It houses
the Cre transgenic and floxed genes databases, as well as literature references
connected to these mice. The databases include information on entries that are
currently being tested, as well as those in the process of being produced.
The sites
managed by the Jackson laboratory (JAX mice, MGI and TBASE) contain
overwhelming amounts of information on mouse strains covering a wide variety of
biological areas, including cancer, immunology, neurobiology, diabetes and
obesity. The categories of mice are clear, making it easy to locate your strain
of interest. There are a great number of research tools listed for the study of
mouse genomics. These sites also have links to a number of useful databases
such as a gene expression database, the mouse genome sequence project, and the
mouse tumor biology database. The MGI and TBASE sites are a bit more manageable
because they are scaled down from the JAX mice site. Taken together, you can
retrieve most of the information you need just by visiting these three sites.
By signing into the BioMedNet mouse knockout database, you can have a number of resources emailed to you periodically, including information of research tools associated with BioMedNet partners (registration is free, quick and easy). This site contains a lot of relevant information on phenotypes related to the many genotypes represented in the database. It contains over 8,000 entries and over 3,000 unique genes to browse. It also has simple and advanced search features, allowing you to narrow down your searches in the mouse database (if youšre a subscriber).
The Cre and
floxed genes databases on the Nagy lab site are pretty easy to navigate. The
entries are directly linked to literature references and have information about
the specificity of the promoters as well as links to the email addresses of
individuals to contact for more information. Also included are lists of entries
that have yet to be tested as well as those that are currently being made,
showing their attempts to keep these databases up-to-date.
There arenšt many weaknesses for the Jackson laboratory sites. There is an overwhelming amount of information stored, which does make it difficult to locate desired information. And often times you need to be pretty specific in the search fields to effectively weed out information you donšt need.
A weakness of the BioMedNet site is that you have to be a subscriber in order to access the Mouse
Knockout And Mutation Database, and this database is no longer available to new
subscribers. You can use the browse option, but thatšs not as easy to navigate
through.
The information
on the Nagy lab site could be more detailed and comprehensive. Currently, you
need to access background literature to get more information on the Cre
promoters and floxed genes, and sometimes these articles arenšt readily
accessible.
The Jackson laboratory sites are very comprehensive concerning strain information, background literature, and research protocols. The current collection consists of 2 million JAX mice and over 2,800 strains, 97% of which are available only from the Jackson laboratory. Taken together, the three sites cover most, if not all, of the information you would need on mouse strains.
It seems like the BioMedNet site is comprehensive with respect to abstract concerning the phenotypes and genotypes of the databasešs knockout and mutant mice. It includes mice that may be useful for a variety of biological fieldsie. knockouts for studying neurology, immunology and physiology. The database contains over 8,000 entries and over 3000 unique genes to browse.
The
database on the JAX mice site is updated daily at 1:30 AM (eastern standard
time).
The
TBASE arm of the Jackson laboratory sites is normally updated weekly. However, as
of January 1, 2004, TBASE was no longer being updated. There are current
efforts to merge the TBASE contents with the MGI database, which also seems to
be updated weekly.
The
BioMedNet mouse database seems to be updated weekly, given that the last update
occurred on May 19, 2004.
The
databases on the Nagy lab site arenšt updated frequently. The last update for
the Cre transgenic database was on March 15, 2003.
All of the sites
were easy to use, although BioMedNet did pose some difficulty. Initially, you
need to log in and provide a password, but that didnšt take a great amount of
time. However, in order to access the mouse database, you need to be a
subscriber, and the site is no longer taking new subscribers.
All of the five
sites Išve reviewed loaded up very quickly. However, this may be due to the
timing of when I visited. I would imagine that there would be delay in
accessing the sites during periods of high internet traffic.
Oak Ridge
National Laboratory Mutant Mouse Database http://lsd.ornl.gov/mouse/
Charles River
laboratories http://www.criver.com/
Taconic http://www.taconic.com/
JAX mice 4
stars
MGI 4
stars
BioMedNet 3
stars (neutral, because I didnšt
have access to the database)
TBASE 3
stars
Nagy Lab 2
stars