Mouse-related websites (A comparative review)

 

URLs

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

 

 

DESCRIPTIONS

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.

 

STRENGTHS

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.

 

WEAKNESSES

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.

 

COMPREHENSIVENESS

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 fields‹ie. knockouts for studying neurology, immunology and physiology. The database contains over 8,000 entries and over 3000 unique genes to browse.

 

The databases on the Nagy lab site are not as comprehensive, due to the limited knowledge of Cre and floxed genes as compared to the types of entries covered in the other sites reviewed.

 

TIMELINESS

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.

 

EASE OF USE

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.

 

RESPONSIVENESS

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.

 

SIMILAR/RELATED SITES

Oak Ridge National Laboratory Mutant Mouse Database http://lsd.ornl.gov/mouse/

Charles River laboratories http://www.criver.com/

Taconic http://www.taconic.com/

 

OVERALL EVALUATION

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

 

 

Reviewer: Bonnie Cheung