FlyBase database

In the biosciences, a database is a curated repository of raw data containing annotations, further analysis, and links to other databases. Examples of databases are the SWISSPROT database for annotated protein sequences or the FlyBase database of genetic and molecular data for Drosophila melanogaster. 

FlyBase (1999) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Research 27, 85-88. 

We expect that there may be a natural inclination for those initiating arrayer construction or array experiments to contact the authors of this article with further questions or problems. The section on arrayer construction was written by K.B. and that on preparation of arrays by K.W. Readers are encouraged to communicate with the relevant author (our addresses are listed in the FlyBase database) if they have further questions pertinent to these topics. Up-to-date protocols that we are following while working with Drosophila arrays are posted at K.W s Web Site ... 

The FlyBase Consortium 1999. The FlyBase Database of the Drosophila Genome Projects and Community Literature. Nucleic Acids Res. 27 85-88. 

PIR provides also some degree of crossreferencing to other biomolecu-lar databases by linking to the DDBJ/EMBL/GenBank nucleotide sequence databases, PDB, GDB, FlyBase, OMIM, SGD, and MGD. 

The ENZYME database (Bairoch, 1996) is also used to generate standardized description lines for enzyme entries and to allow information such as catalytic activity, cofactors, and relevant keywords to be taken from ENZYME and to be added automatically to TrEMBL entries. Additionally, specialized databases such as FlyBase (FlyBase Consortium, 1999) and MGD (Blake et al., 1999) are used to transfer information such as the correct gene nomenclature and cross references to these databases into TrEMBL entries. The automatic analysis and annotation of TrEMBL entries are redone and updated every TrEMBL release. 

Two hundred and twenty-nine desatl ESTs have been described in Flybase, EMBL or GENBANK databases (May 2003) 221 ESTs have a complete 5 -end, allowing grouping into five different categories of transcripts which only differ in their first exon (Tables 9.1 and 9.2). As shown in Table 9.2, desaturase transcripts have been found with a low abundance in all the tissues tested, except in the head, where they represent a high proportion of the total ESTs (0.2%). The five types of transcripts are not equivalently represented, in particular categories 3 and 5 contain only one EST each. The other three categories of transcripts represent 12 to 73 percent of the ESTs. 

Eukaryotic polymerase II promoter server Exlnt database ExPASy, tools FlyBase GDB GenBank,... 

Drysdale, R. A., M. A. Crosby, W. Gelbart, K. Campbell, D. Emmert, B. Matthews, S. Russo, et al. 2005. FlyBase Genes and gene models. Nucleic Acids Res 33, Database Issue D390-5. 

NCBI RefSeq http //www.ncbi.nIm.nih.gov/RefSeq Curated NR sequences genomes, transcripts and proteins derived from GenBank, EBI, DDBJ and model organism databases (e.g. TIGR, MGI, SGD, FlyBase) with wide taxonomic diversity. 

Gene sequence database. More than 20 other databases including SWISS-PROT, ACeDB, FlyBase, Eukaryotic Promoter Database, Restriction Enzyme Database, Transcription Factor Database, and CarbBank/CCSD. Databases and software development tools for sequence data available for anonymous ftp ncbi.nlm.nih.gov (130.14.25.1). 

We thank Sophia Kossida, Jason Comander, and Yonatan Grad for their helpful suggestions and discussion of the computational screen design and ScanACE and BLAST analysis. The databases used in this work are Flybase (http // www.flybase.org), WormBase (http //www.wormbase.org), and WormPD (http // www.proteome.com/databases/index.hlml). 

Drysdale R (2008) FlyBase a database for the Drosophila research community. Methods Mol Biol 420 45-59. doi 10.1007/978-l-59745-583-l 3... 

By nature, databases and their query interfaces change constantly. Although the particulars of a display may change periodically, the underlying data structure in FlyBase is... 

The most efficient way to access FlyBase, BDGP, and EDGP is via the WWW, which requires a computer, a connection to the Internet, and browser software, such as Netscape or Internet Explorer. The addresses (or uniform resource locators, URLs) on the Web to access the databases are shown in Table 28.1. 

The FlyBase home page includes a link to the Reference Manual. This manual describes the searches, content, and format for each data section, with an explanation of the crosslinks within FlyBase and between FlyBase and external databases. The Reference Manual is extensively hyperlinked within itself, to the files it describes, and to external resources. Each FlyBase data class provides a link, under Documents, back to the relevant section of the reference manual. 

FlyBase makes extensive use of a controlled vocabulary of terms and qualifiers, to allow users to search the database more easily and retrieve data sets with particular properties. The terms are stored in a file, controlled-vocabularies.txt, in the Documents section of FlyBase. Because the term must match the controlled vocabulary entry exactly, the easiest way to perform these searches is by using the pull-down menus in FlyBase complex query forms, which provide all possible search terms for a field. 

It is very good practice for any fly laboratory to maintain a database of all stocks (e.g., in Filemaker Pro). This database should include (1) the genotype of the full stock (2) notes about particular stocks that will aid in their maintenance and use and (3) a note of the origin of each stock, and to whom and when it was sent (this helps to recover a stock if one is unfortunate enough to lose it). If an investigator wishes to make the stock list available to a wider public, then it can be posted on FlyBase (E-mail to flybase-help mor-gan.harvard.edu). 

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