Meta-Database Catalog of 2D gel images found in Web databases - 2DWG

http://www-lecb.ncifcrf.gov/2dwgDB/2DWG.html

cp 2DWGnaming.html /home/ips2/www-lmmb/htdocs/2dwgDB/ This is a catalog of some of the 2D gel images found in a search of 2D gel databases on the web. We will be refering to this catalog as the "2DWG" meta-database. A meta-database contains information about data in other databases. Data for the 2DWG is acquired by a conbination of review of results from web searching as well as submissions by web database authors. The image files are generally in GIF, JPEG or TIFF file formats which are suitable for Web browsers. The table is organized by tissue type to make it easier to find data on the same tissue from different web sources. Note, you can search 2DWG by keywords to generate specific subtables. This is much faster than scrolling the entire 2DWG catalog.

The table is organized as a spreadsheet with column headings at the top. Each row corresponds to a gel image with the fields in the row describing the gel. The fields are defined in the Glossary of fields.

Hint: because the table is very wide, you might want to increase the width of your browser (it looks best with Netscape). Note also that the Miscellaneous column has information in a smaller font. This is hard to read with 72 dots-per-inch displays, but when printed on a 300DPI or better printer it is quite readable.

Each table entry is defined with a database name in the Image URL (eg. a plasma gel image), DB URL which indicates where the image came from in the web server (eg. the page describing the plasma gel), a link to the related web organization server URL, (eg. "ExPASy") where more information might be found on the sample, the methods, etc. In addition, some of the servers have maps identifying the proteins in these gel images, so the Map URL is also put into a table entry if it exists. Otherwise, it is defined to be a raw gel image. These may be passive or active, with the latter leading back into protein identification databases residing on these other servers. While most gel images have pI oriented acid to basic, some gels are reversed. We indicate this where possible by specifying the pIe range as increasing (acid to basic, eg. 4-8) or decreasing (basic to acid, eg. 8-4). Since many of these databases are being improved, you can expect these entries to change with some images being deleted and new ones added or replaced.

This catalog will be continuously revised and edited. If you have corrections or additions to this table, or know of published 2D Web gels you think should be included, or have other suggestions to make the table easier to use or more relevant, contact Peter Lemkin (Ed), NCI/FCRDC by E-mail at lemkin@ncifcrf.gov. You will notice that some of the fields in the table are empty. In many of the web databases, this information is missing or not apparent. We will be working to resolve as much of this missing data as possible.

Flicker comparison of 2D gel images

The NCI Flicker program is a Java application running on your web browser for visually comparing images over the Internet. In the future, you will be able to flicker compare a gel image residing on your computer with one of the images in this table.

NOTE: In addition, you can more easily select gels to 2DWG gels to flicker. However, you must go to a separate web page to pick two gels from separate lists of gels or arbitrary URLs.

In these databases, some images are reversed in the horizontal pI direction and others may be reversed in Mr in the vertical direction. Flicker will let you transform an image with the Flip Horiz and Flip Vert operations to flip an image in the horizontal and vertical dimensions. Because some images are on a larger scale (either through the way they were run or because of the scanner resolution), you might consider using the Affine Transform option to make the regions being compared have similar scale.

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Gel image file naming conflicts - feedback requested

There are potential naming conflicts in naming 2D gel image files for Web published databases. The 2DWG naming convetions discusses a suggested convention. We are soliciting comments on a Web-publishing policy for naming 2D gel image files.