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FlyBase Reference Manual F. Links to and from FlyBase
Last Updated: 26 November 2003

• Reference Manual F. Links to and from FlyBase
• F.1. FlyBase Identifier Numbers
• F.2. Other links to FlyBase
• F.3. Links to other molecular databases
• F.4. Links to databases of other genomes

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 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:

• gn - genes, e.g., FBgn0012345
• an - genomic sequence annotations, e.g., FBan0004717
• al - alleles, e.g., FBal0001234
• ab - aberrations, e.g., FBab0123456
• ba - balancer chromosomes, e.g., FBba0000021
• rf - references, e.g., FBrf0987654
• tp - transposons, e.g, FBtp0001234
• mc - molecular constructs, e.g., FBmc0001234
• ms - molecular component, e.g., FBms0001234
• sp - species, e.g., FBsp0098765
• pp - polypeptides, e.g, FBpp0001234
• ti - transposon insertion, e.g., FBti0001234
• tr - transcripts, e.g, FBtr0001234
• cl - clones, e.g., FBcl0000123

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*).

F.2. Other links to FlyBase

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.

F.3. Links to other molecular databases

The External Databases section of FlyBase includes information on the links between FlyBase and other molecular databases. FlyBase includes "pointers" to data kept by other databases by including their unique accession numbers, rather than duplicating the data within FlyBase. The file external-databases.txt contains a list of the accession numbers from external databases and the records in FlyBase to which they refer.

In external-databases.txt,

• if the external database record refers to a gene then the syntax is:
  AC|FBgn_ID|FlyBase_gene_symbol|FlyBase_gene_full_name|genetic_map_position|cytogenetic_map_position
  e.g.: D13825|FBgn0010114|hig|hikaru genki|2-[59]|45C
  
• If the external database record refers to a particular allele then the syntax is:
  AC|FBgn_ID[FBal_ID]|FlyBase_gene_symbol[Flybase_allele_symbol]|FlyBase_full_gene_name[FlyBase_allele_name]|genetic_map_position|cytogenetic_map_position
  e.g.: M14954|FBgn0003996[FBal0018259]|w[IR1]|white[Inducer Reactive-1]|1-1.5|3C2
  The FlyBase_allele_name domain will be a duplicate of the FlyBase_allele_symbol if the allele does not have a full name.
  e.g.: K03136|FBgn0001077[FBal0004822]|ftz[Rpl]|fushi tarazu[Rpl]|3-47.5|84B1-84B2
  
• If the external database refers to a particular chromosome aberration then the syntax is:
  AC|FBab_ID|FlyBase_aberration_symbol
  e.g.: L32746|FBab0004197|In(1)sc[8]
  where AC is the primary accession number of the external database (FlyBase does not support secondary accession numbers of external databases).
  
• For the nucleic sequence databases (EMBL, NCBI, DDBJ) accession numbers may be followed by PID numbers, i.e.:
  AC;<PID_number>|FBgn_ID[FBal_ID]|FlyBase_gene_symbol[Flybase_allele_symbol]|FlyBase_full_gene_name[FlyBase_allele_name]|genetic_map_position|cytogenetic_map_position

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.

• DDBJ/GENBANK/EMBL: the nucleic acid sequence databases of Japan, the U.S., and Europe.
• EPD: - Eukaryotic Promoter Database (Bucher).
• GCR: - The G protein-coupled receptor database.
• MEROPS: - Protease database.
• NRL_3D: - NRL_3D database.
• PDB: - Protein Data Bank (Brookhaven).
• PIR: - PIR International.
• SWP: - SWISS-PROT.
• TF: - The TRANSFAC database of transcription factors and their binding sites.
• TREMBL: - EBI TREMBL (Translated EMBL)
• dbSTS: - NCBI STS database (dbSTS).
• dbEST: - NCBI EST database (dbEST).

F.4. Links to databases of other genomes

FlyBase establishes, by curation of the literature and from other sources (other databases, nucleic acid sequence records), links between Drosophila genes and those of other organisms. These links appear in the relevant gene reports. For convenience a table of links, sorted by foreign database, is also made available in the External Databanks section of FlyBase.

In the file genetic-links.txt, the syntax of the cross-links is:
foreign_database_abbreviation:identifier_number|foreign_database_gene_symbol [(synonym_symbol)]|FBgn_ID|FlyBase_gene_symbol
e.g.: MRK-12119|Mash1|FBgn0000022|ac

Abbreviations for 'foreign' databases are:

• DICTDB: Dictyostelium Database
• ECOGENE: Encyclopedia of E. coli genes
• EMBL: International Nucleotide Sequence Database Collaboration (GenBank, DDBJ, EMBL)
• GDB: Genome DataBase (Human)
• gi: Entrez Protein (NCBI)
• MAIZEDB: Maize Database
• MGI: Mouse Genome Informatics (Jackson Labs.)
• OMIM: Online Mendelian Inheritance in Man (NCBI)
• PDB: Protein DataBank
• PIR: Protein Information Resource Database
• protien_id: Entrez Protein (NCBI)
• SGDID: Saccharomyces cerevisiae Database (Stanford)
• STYGENE: Salmonella typhimurium Database
• SUBTILIST: B. subtilis Database
• SWP: Swiss-Prot (EBI)
• WP: Worm Pep (via Swiss-Prot)
• ZFIN: Zebra fish Database

Cross-links to databases that do not assign identifier numbers to genes, e.g., ACeDB (C. elegans) and the S. pombe database are not included in this list, although links to them are made in the genes file.