FlyBase:Reference Manual F. Links to and from FlyBase
FlyBase provides stable links to FlyBase for use by other databases, and links to other databases from FlyBase. Links to FlyBase data items, and links between data items in FlyBase and other databases are described in the sections that follow. Drosophila Resources includes a linked list of additional databases likely to be of interest to users of FlyBase.
F.1. FlyBase Identifier Numbers
FlyBase assigns unique identifier numbers to several classes of object within the database. One reason for this is to allow unambiguous cross-references both within FlyBase and between FlyBase and other databases.
FlyBase identifier numbers have the general form FBxxnnnnnnn where xx is an alphabetical code for the identifier class and nnnnnnn is a 7 digit number, padded with leading zeros.
The following classes of object are now publicly available in FlyBase data:
FBab - aberration FBal - allele FBba - balancer/genotype variant FBcl - clone FBgn - gene FBim - image FBmc - molecular construct FBms - molecular segment FBpp - polypeptide FBrf - reference FBst - stock FBti - transposable element insertion FBtp - transgenic construct or natural transposon FBtr - transcript Each object has a single Primary identifier number that is used to uniquely identify it in the database.
An object may also have any number of Secondary identifier numbers. If an object has a secondary identifier number, it generally indicates that at some point an entry has been merged with or split from other entries in the database. This may have occured due to more data becoming available in the literature or due to correction of previous errors in the database.
The rules for when primary identifier numbers become secondary are complex. Some examples are included below:
A merge: If two entries A and B are found to refer to the same object, then a new primary identifier number will be given to the merged entry, and the old identifier numbers of entries A and B will be listed under this merged entry as secondary identifier numbers.
A split (case 1): If one entry is found to correspond to two (or more) objects, e.g., entry A does, in fact, refer to objects X and Y, then X and Y, as new objects, each get new primary identifier numbers and the old primary identifier number of the suppressed entry A is listed as a secondary identifier number under both X and Y.
A split (case 2): If one entry is found to correspond to two (or more) objects, e.g. entry A refers to objects A and X, then the existing entry for A and the new entry for X each get a new primary identifier number and the old primary identifier number of A is listed as a secondary identifier number under both A and X.
If an object is simply renamed, i.e. its valid symbol in FlyBase is changed without there being a merge or a split, its primary identifier number does not change.
The following classes of identifier were previously used in FlyBase, but are no longer in current use as identifier numbers in the database.
FBan - annotation
F.2. Links to Drosophila data outside of FlyBase
FlyBase includes "pointers" to data kept by other databases in two different ways.
These are accession numbers that are incorporated into the FlyBase database, for sequence and certain other molecular data, and for reference data.
These links derive from linking tables that are maintained and provided to FlyBase by the external database. Linkouts are combined with FlyBase data for reporting on FlyBase web pages.
Accession numbers from the following databases are currently incorporated into FlyBase records as FlyBase-curated links:
DDBJ/EMBL/GenBank - the nucleic acid sequence databases of Japan, the U.S., and Europe EPD - Eukaryotic Promoter Database (Bucher) GPCRDB - The G protein-coupled receptor database InterPro - a database of protein families, domains and functional sites MEROPS - Protease database miRBase - microRNA data MitoDrome - A database of annotated Dmel nuclear genes encoding mitochondrial proteins. PDB - Protein Data Bank (Brookhaven) PubMed - biomedical literature citations and abstracts Rfam - RNA families database of alignments and CMs TRANSFAC - A database of transcription factors and their binding sites UniProtKB/Swiss-Prot - UniProt Knowledgebase, Swiss-Prot section UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section