Bioinformatics at The Jackson Laboratory
JAX® NOTES Issue 462, Summer 1995
Marge May, User Support
Mouse Genome Informatics
The goals of the Mouse Genome Informatics Project at The Jackson Laboratory are to develop and maintain information resources to support scientific research.
The Mouse Genome Informatics Project produces the Mouse Genome Database, a comprehensive database of mouse genetic information, and the Encyclopedia of the Mouse Genome, a graphical tool for the display of mouse genetic maps. In addition, we maintain electronic bulletin boards to facilitate communication among researchers.
The purpose of this article is to briefly describe the major features of these resources and provide information needed to access them. For additional information or assistance, please contact:
Mouse Genome Informatics User Support
E-mail: mgi-help@informatics.jax.org
Phone: 207-288-6445
Fax: 207-288-2516
The Mouse Genome Database (MGD) contains the following kinds of information:
Mouse Genome Database
Genetic Markers
Information on markers includes symbol, name, chromosomal assignment, position assignment, EC number, alleles, nomenclature change history.
Mapping Data
Data is captured in the form of experimental types including haplotype data from crosses and recombinant inbred strains, in situ experiments, somatic cell hybrid concordance values, pulse field gel and various physical mapping analyses. In addition, some records include information regarding deletion mapping and chromosomal aberrations.
Mammalian Homology Data
Information on homologies between mouse and human and over 50 other mammalian species. For each gene homologous to mouse, data include the species, symbol, and chromosomal location.
Probes and PCR Primers
Characteristics of the molecular reagent such as species, type, size, insert site, vector and sequence are provided along with RFLPs or PCR-generated variants between inbred strains. The Genbank number and ATCC number are given if available.
Gene Descriptions
Descriptions include function and general expression information. For mutants, strain where they arose, inheritance, differences in phenotype among alleles, general classification of effect, disease model data (similar to human OMIM).
Characteristics of Inbred Strains
Characteristics of mouse strains such as longevity, fecundity, and drug sensitivity.
Citations
Medline formal citations comprising a master bibliography for MGD. Most of the data in MGD are extracted from scientific journal articles.
Accessing MGD
MGD is available on the Internet via the World Wide Web (WWW). To access MGD, you need a WWW "browser" running on your machine to connect to the Internet. WWW browsers are available for all hardware platforms. Popular browsers include NCSA Mosaic and Netscape. For educational and other non-profit institutions, browsers can be obtained free-of-charge via anonymous ftp. We recommend using the most current versions available for your machine. Ftp addresses for some of the most popular browsers include:
Netscape: ftp2.mcom.com
Mosaic: ftp.ncsa.uiunc.edu
Einet:ftp.einet.net
A browser provides access to resources on the WWW. Each resource has an address sometimes called a "location" or "URL". The WWW address for MGD is: http://www.informatics.jax.org
This address opens the Jackson Laboratory Bioinformatics WWW Home Page which provides links to MGD, the Encyclopedia of the Mouse Genome Home Page, Mouse Genome Informatics news and announcements, and other Bioinformatics servers on the WWW (Figure 1).
Searching MGD
MGD provides query forms for searching. To build a query, you enter or select values for one or more fields on the form and click on the "Do Query" button to start the search. If you are unsure about how a form or a particular field is used, you can access online help documentation from each form.
There are six query forms available in MGD: Mouse Genetic Marker Information, Mammalian Homology Data, Probes and Clones Data, PCR Primer Data, Mapping Data and Citation.
For example, the Mouse Genetic Marker Information query form includes fields that enable you to search by symbol, chromosome, locus name, centimorgan position, phenotypic classification, among other options (Figure 2).
When you enter information in one or more fields and run the query, MGD processes the query and presents a summarized list of records that match the search criteria (Figure 3).
Each item in the list is "linked" to a detailed record. When you click on the link (a highlighted word or phrase), the related information is then displayed (Figure 4).
Each detailed record provides links to other related data in the database and sometimes, to data in another database such as GDB or Genbank. Each subsequent view of data presents its own links to other data, enabling you to "browse" through a database or set of databases.
Handling Query Results
Query results are displayed in hypertext files. Each browser provides options to work with files such as saving to a text file, printing a file, and sending a file via E-mail. In addition, you can copy text from a browser window to a word processing file.
Encyclopedia of the Mouse Genome
The Encyclopedia of the Mouse Genome (encyclopedia) displays linkage maps of mouse chromosomes showing relative centimorgan positions of mouse loci and mammalian gene homologies. The Encyclopedia is a software application that runs on your Macintosh or UNIX machine. You can run the Encyclopedia "standalone" and view data files downloaded from our ftp server, or run it interactively with MDG. Interaction of the Encyclopedia with MGD provides options to build maps using "live" MGD data, view selected regions of mouse chromosomes, and select one from a list of over 50 mammalian species for viewing homologies.
The Encyclopedia presents information in a "window" divided into "panes". Each time you open a data file, you open an Encyclopedia window and multiple windows can be open at one time (Figure 5).
Window panes can be re-sized horizontally and vertically as can the whole window. The resolution of the map can be changed by using Zoom In/Out menu options or special key sequences. When you select a locus on the map or on the locus list in the lower right pane, notes, and references will automatically display in the middle and upper right panes respectively. If you select a symbol from the locus list in the lower right pane, the map will automatically adjust to highlight and display the selected locus.
The Encyclopedia provides options to modify the way a locus is displayed on a map, save a map to a PICT file, print a map, copy text information from the notes and references panes and paste to a text file.
Viewing data files
If you load the Encyclopedia application and data files onto your Macintosh or UNIX workstation, you can run the Encyclopedia in "standalone" mode and display those files with no connection to a network.
Viewing maps with MGD information
There are two ways in which the Encyclopedia and MGD can interact. First, from the MGD home page, you can choose to Build an Encyclopedia linkage map using MGD information. A query form will then be displayed which provides options to select a chromosome, specify a region of a chromosome, or include homologous loci from one of 53 mammalian species (Figure 6).
Secondly, you can "link" the Encyclopedia to your browser and initiate an MGD search of locus information by selecting a locus displayed on an Encyclopedia map. Currently, this option is supported only by the Mosaic browser. When the Encyclopedia and Mosaic are linked, then, when you open an Encyclopedia map, Mosaic will automatically start up. Each time you click on a locus displayed on the map, MGD will retrieve the detailed locus information for the selected locus.
Downloading the Encyclopedia application and data files
The current versions of the Encyclopedia application are 1.0a13 for the Macintosh and 3.0a2 for UNIX. The supported UNIX machines are SunSPARC and DEC Alpha workstations.
The current data files for the Encyclopedia are the 1994 Chromosome Committee Reports and the July 1995 MIT Release #11 files. These files can be downloaded from the WWW or our ftp server.
To download from WWW, use the Encyclopedia Home Page (accessible from the MGD Home Page). The Encyclopedia Home Page provides options to download the application and data files and instructions for configuring your browser to enable interaction of MGD with the Encyclopedia.
To download using an ftp program, connect to our anonymous ftp server: ftp.informatics.jax.org
After logging in as user "anonymous", change to the directory pub/informatics/encyclo/3.0. The subdirectories "mac" and "unix" contain the application files, and the subdirectory "data/3.0" contains the data files.
Electron Bulletin Board Service
The electronic bulletin boards provide a forum for researchers to discuss various topics. MGI-LIST is the most widely subscribed list and is intended for discussions of general interest to the research community. News and announcements related to Mouse Genome Informatics databases and services are sent to this list.
The way a bulletin board works is that a subscriber sends a message to the list and all subscribers to that list receive a copy. Replies are automatically sent to the list as well.
Additional lists include MGD-LIST, ENCYCLO-LIST, NOMEN-LIST, CHR1-LIST, CHR2-LIST (and so on for each chromosome).
If you wish to subscribe, send a message from the E-mail address you will use for this correspondence to: listserver@informatics.jax.org
The text of the message must read: subscribe<listname><your name>
To get general information about the bulletin boards, send the message "help" to the address given above.
Supporting the User Community
A primary goal is to support resesarchers in their search for scientific information. Two full-time User Support personnel are available to answer questions regarding our software and data. We also encourage users to contact User Support to let us know how we can improve our databases and services.
Online User Feedback
The researchers who use databases can have direct input into new developments by letting us know what features or data they would like to see. We encourage use of the online User Feedback form as a means to send questions, comments, ideas, and bug reports. The User Feedback form is also available from the MGD Home Page.
