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DBGET Overview
1. Web of Molecular Biology Databases
DBGET is the backbone retrieval system for all GenomeNet databases including a number of molecular biology databases that are mirrored at the GenomeNet.
DBGET is based on a flat-file view of molecular biology databases, where the database is considered as a collection of entries.
Because each entry is given a unique entry name (or an accession number) within a database, the molecular biology databases in the world can be retrieved uniformly by the combination of the database name and the entry name:
database:entry
In KEGG an organism is a collection of genes, which may also be considered as a flat-file database.
Any gene or gene product (protein or RNA) in KEGG can thus be specified by the combination of the organism name and the gene name:
organism:gene
When two data entries are related in any way, it is customary to incorporate cross-reference information in the molecular biology databases.
Examples include links between sequence data and literature data or between amino acid sequence data and nucleotide sequence data.
The link information between two entries is a binary relation represented by:
database1:entry1 --> database2:entry2
LinkDB is a collection of all such direct links in the GenomeNet databases as well as indirect links that are computationally obtained by combining multiple links and/or using links in reverse directions.
2. Database Categories
The DBGET/LinkDB system integrates different databases in different ways depending on the availability of mirroring, keyword indexing, and linking.
The databases are thus classified into five categories.
| Category | Main commands | Remark |
|---|
| bget | bfind | blink |
| 1. KEGG databases | yes | yes | yes | Mirrored at GenomeNet |
| 2. Other DBGET databases | yes | yes | yes |
| 3. Searchable databases on the Web | no | yes | yes | Used as Web resources |
| 4. Link-only databases on the Web | no | no | yes |
| 5. PubMed database | yes | no | yes |
3. KEGG Databases (Category 1 Databases)
The KEGG databases at GenomeNet are the following. Most of them are daily updated.
4. Other DBGET Databases (Category 2 Databases)
Other databases mirrored at GenomeNet are the following.
5. Searchable Databases on the Web (Category 3 Databases)
The following databases are search-only databases. The actual contents are retrieved from the original sites.
References
- Kanehisa, M.; Linking databases and organisms: GenomeNet resources in Japan. Trends Biochem Sci. 22, 442-444 (1997).
[pubmed]
- Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an integrated database retrieval system. Pacific Symp. Biocomputing 1998, 683-694 (1997).
[pubmed]
(DBGET has a root in the IDEAS package originally developed for GenBank in the early 1980s)
- Kanehisa, M., Klein, P., Greif, P., and DeLisi, C.; Computer analysis and structure prediction of nucleic acids and proteins. Nucleic Acids Res. 12, 417-428 (1984).
[pubmed]
[pdf]
- Kanehisa, M.I.; Los Alamos sequence analysis package for nucleic acids and proteins. Nucleic Acids Res. 10, 183-196 (1982).
[pubmed]
[pdf]
Last updated: June 27, 2019
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