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.
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 unique identifiers 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 are now publicly available in FlyBase data:
Rules followed in assigning ID values include:
If an entry's name is changed its
ID does not, except under the following circumstances:
If two entries a and b are found to refer to the same object,
then a new ID will be given to the merged entry. The IDs of entries a
and b will be listed under this merged entry as secondary Ids.
If one entry is found to be two (or more), e.g., entry a does, in fact,
refer to objects x and y, then x and y,
as new entries, get new IDs and that of the suppressed entry a is listed
as a secondary ID to both x and y.
If one entry is found to be two (or more) e.g. entry a refers to entries
a and x then the existing entry for a gets a new
ID and a's old ID is listed as a secondary ID; the new entry x
gets a new ID with a's old ID as a secondary ID.
These IDs will enable those that use this database to cross-reference others
to automatically ensure consistency in the names of genes, alleles and aberrations
and other FlyBase objects. Those referring to Drosophila gene, allele
or aberration names or symbols in other databases are recommended to use FlyBase
IDs. Please contact FlyBase for further information and help.
This Internet link is a public access entity that will return FlyBase data reports when queried with a FlyBase ID value. It is a suggested network link for other databases:
http://flybase.org/.bin/fbidq.html
Example usage:
http://flybase.net/.bin/fbidq.html -- for interactive use
http://flybase.net/.bin/fbidq.html?FBgn0012345
http://flybase.net/.bin/fbidq.html?FBgn0032145+fbgn0023415+ FBGN0044312
Similar links are available at FlyBase mirror sites for quicker service to various regions. The link format for any mirror site is
http://hostname:port/.bin/fbidq.html
This ID search is case-insensitive, and supports multiple values in a query as well as the '*' wild card at the end (e.g., FBgn000123*).
There are additional URLs that should be useful to those who wish to establish hypertext links to FlyBase from their own servers. The first is a link to the script that returns fully hyperlinked FlyBase gene reports:
http://flybase.net/.bin/fbgenq.html?
You can link to this script with either a correctly capitalized FlyBase gene symbol or FBgn ID for that gene. For example the Drosophila gene that currently has the symbol Adf1 has been assigned the FlyBase gene number FBgn0000054, so you can link to it using the URL:
http://flybase.net/.bin/fbgenq.html?FBgn0000054
We do not encourage you to use the gene symbol to link to the gene, since gene symbols are subject to change for a variety of reasons, such as when two or more groups of alleles are discovered to be alleles of one and the same gene. If you wish to do so anyway, these are the recommended URLs:
http://flybase.net/.bin/fbgenq.html?symbol=Symbol-Here
for valid symbols
http://flybase.net/.bin/fbgenq.html?synonym=Symbol-Here
for synonyms
For example,
http://flybase.net/.bin/fbgenq.html?symbol=His3.3B
http://flybase.net/.bin/fbgenq.html?synonym=CG8989
The following links to FlyBase query items at the Indiana server are designed to be stable. A general query is of the form:
http://flybase.org/.bin/fbxxxq.html?keywords
where 'xxx' in 'fbxxxq' is replaced
by an indicator of the data section:
fbabsq aberrations query
fbgenq genes query
fbpeoq people query
fbrefq reference query
fbstoq stocks query
For example, this looks up all gene records with 'esterase' in them:
http://flybase.net/.bin/fbgenq.html?esterase
The ".html" suffix provides results in html format. With no suffix the result is a list of records in gopher format. Complex queries are possible using the SRS query syntax at this server.
If you would like assistance in setting up links to these sorts of URL's for FlyBase, please e-mail FlyBase at flybase-help at morgan.harvard.edu. If you would like to use types of links not described here, send e-mail to FlyBase; there are many other sorts of public links that could be provided if there are database and Web page maintainers who would make use of them.
FlyBase includes "pointers" to data kept by other databases in one of two ways. One category is FlyBase-curated links. These are accession numbers that are incorporated into the FlyBase database, for sequence and certain other molecular data. The other category is FlyBase linkouts. These links derive from linking tables that are maintained by the external database and provided to FlyBase. Linkouts are combined with FlyBase data for reporting on FlyBase web pages.
Accession numbers from the following databases are incorporated into FlyBase records:
The file external-databases.txt contains a list of the accession numbers from these databases and the records in FlyBase to which they refer. Note that in this file SGML is used to represent Greek font, [] enclose superscipts and [[]] enclose subscripts. The data are sorted alpha-numerically by AC number or prefix, where AC is the primary accession number of the external database (FlyBase does not support secondary accession numbers of external databases). The format of records in external-databases.txt is as follows:
FlyBase currently supports linkouts from Genes reports to external databases. For example, see the Linkouts section of the Synopsis Gene Report for tim. Databases suitable for this kind of linking to FlyBase are those with mature data structures whose data are expressed in terms of FlyBase genetic objects that carry stable identifiers or as sequences that can be mapped to the reference sequence of a Drosophila species. FlyBase currently accepts linkout data for genes in a simple spreadsheet table (tab-delimited, 4 columns), plus a summary record for the external database with link information and name. We are happy to consider additional linkout databases, and will support linkouts for dataclasses other than Genes in the future. Please contact us if you would like to contribute links to your database. Information for linkout providers is available here. The databases that currently provide linkouts from FlyBase are:
Information on non-Drosophila orthologs is available in FlyBase as linkouts to Inparanoid. These are included in the 'Closest relatives' section of Gene and Annotation reports. For an example, see the Synopsis report for eag.