SWISS-2DPAGE is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and SDS-PAGE tool established in 1993. Until March 2011, SWISS-2DPAGE has been maintained, collaboratively, by the Biomedical Proteomics Research Group (BPRG) of the Geneva University and the Proteome Informatics Group of the Swiss Institute of Bioinformatics (SIB). Since April 2011, SWISS-2DPAGE is being maintained by the Swiss-Prot and the Vital-IT of the Swiss Institute of Bioinformatics.
The SWISS-2DPAGE database assembles data on proteins identified on certain 2-D PAGE and SDS-PAGE maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition, peptide masses) and bibliographical references. In addition to this textual data, SWISS-2DPAGE gives several 2-D PAGE and SDS-PAGE images showing the experimentally determined location of the protein, as well as a theoretical region computed from the sequence protein, indicating where the protein might be found in the gel.
Cross-references are provided to Medline and many other federated 2-DE databases, e.g. ( World-2DPAGE Repository, UCD-2DPAGE, Plasmo2Dbase, COMPLUYEAST 2D-PAGE DATABASE, REPRODUCTION-2DPAGE, 2DBase, Cornea-2DPAGE, OGP-WWW, PHCI-2DPAGE, Siena-2DPAGE, YEPD, and many other 2D-PAGE databases ) and to UniProtKB/Swiss-Prot, which provides many links to other databases (EMBL, Genbank, PROSITE, OMIM, etc).
The entries in the SWISS-2DPAGE are text files structured to be readable by human as well as by computer programs. However, symbols familiar to biochemists, chemists and molecular biologists are also used. Each entry corresponds to one protein and is composed of lines. Different types of lines, each with their own format, are used to record the various data which make up the entry.
Each line begins with a two-character line code, which indicates the type of data contained in the line.
The ID (IDentification) line is always the first line of an entry.
The AC (ACcession number) line lists the accession number(s) associated with an entry.
The DT (DaTe) lines show the date of creation and last modification of the database entry.
The DE (DEscription) lines contain general descriptive information about the protein stored. This information is generally sufficient to identify the protein precisely.
The GN (Gene Name) line contains the name(s) of the gene(s) that code for the stored protein sequence.
The OS (Organism Species) line specifies the organism(s) which was the source of the stored protein.
The OC (Organism Classification) lines contain the taxonomic classification of the source organism. The taxonomic classification used is that maintained at the NCBI and used by the nucleotide sequence databases (EMBL/GenBank/DDBJ).
The OX (Organism taXonomy cross-reference) line is used to indicate the identifier assigned to a specific source organism in a taxonomic database.
The MT (MasTer) lines are specific to SWISS-2DPAGE. These lines indicate on what types of maps the protein has been identified (such as PLASMA, LIVER, etc.).
The IM (IMages) lines list the 2-D PAGE and SDS-PAGE images which are associated to the entry.
Several two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) databases have been established and updated for more than 15 years. Only recently have developments of computer networks and high-speed transfer protocols provided the required tools for sharing comprehensive and hypermedia 2-D PAGE databases. Proteins present in samples of human tissue, cells, cell lines and body fluids are assembled and described in an accessible uniform format. SWISS-2DPAGE can be freely accessed through the World-Wide Web (WWW) network on the ExPASy molecular biology server.
