FlyBase
FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, "Drosophila melanogaster", a wide range of data are presented in different formats. Information in FlyBase originates from a variety of sources ranging from large-scale genome projects to the primary research literature. These data types include mutant phenotypes; molecular characterization of mutant alleles; and other deviations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models, and molecular classification of gene product functions. Query  tools allow navigation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from the several ontologies used to capture functional, phenotypic, and anatomical data. The database offers several different query tools in order to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Links between FlyBase and external databases, such as BDGP or modENCODE, provide opportunities for further exploration into other model organism databases and other resources of biological and molecular information. The FlyBase project is carried out by a consortium of "Drosophila" researchers and computer  scientists at Harvard University and Indiana University in the United States, and University of Cambridge in the United Kingdom. FlyBase is one of the organizations contributing to the Generic Model Organism Database (GMOD). Background. "Drosophila melanogaster" has been an experimental organism since the early 1900s, and has since been placed at the forefront of many areas of research. As this field of research spread and became global, researchers working on the same problems needed a way to communicate and monitor progress in the field. This niche was initially filled by community newsletters such as the Drosophila Information Service (DIS), which  dates back to 1934 when the field was starting to spread from Thomas Hunt Morgan's lab. Material in these pages presented regular 'catalogs' of mutations, and bibliographies of the Drosophila literature. As computer infrastructure developed in the '80s and '90s, these newsletters gave way and merged with internet mailing lists, and these eventually became online resources and data. In 1992, data on the genetics and genomics of "D. melanogaster" and related species were electronically available over the Internet through the funded FlyBase, BDGP (Berkeley Drosophila Genome Project) and EDGP (European Drosophila Genome Project) informatics groups. These groups recognized that  most genome project and community data types overlapped. They decided it would be of value to present the scientific community with an integrated view of the data. In October 1992, the National Center for Human Genome Research of the NIH funded the FlyBase project with the objective of designing, building and releasing a database of genetic and molecular information concerning "Drosophila melanogaster". FlyBase also receives support from the Medical Research Council, London. In 1998, the FlyBase consortium integrated the information into a single Drosophila genomics server. the FlyBase project was carried out by a consortium of Drosophila researchers and computer  scientists at Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico. Contents. FlyBase contains a complete annotation of the "Drosophila melanogaster" genome that is updated several times per year. It also included a searchable bibliography of research on "Drosophila" genetics in the last century. Information on current researchers, and a partial pedigree of relationships between current researchers, was searchable, based on registration of the participating scientist. The site also provides a large database of images illustrating the full genome, and several movies detailing embryogenesis (ImageBrowser). The two major tributaries to the database are the large  multispecies data sets deposited by the Drosophila 12 Genomes Consortium (Clark et al 2007) and Crosby et al 2007. Search Strategies—Gene reports for genes from all twelve sequenced Drosophila genomes are available in FlyBase. There are four main ways this data can be browsed: Precomputed Files BLAST, Gbrowse, and Gene Report Pages. Gbrowse and precomputed files are for genome-wide analysis, bioinformatics, and comparative genomics. BLAST and gene report pages are for a specific gene, protein, or region across the species. When looking for cytology there are two main tools available. Use Cytosearch when looking for cytologically-mapped genes  or deficiencies, that have not been molecularly mapped to the sequence. Use Gbrowse when looking for molecularly mapped sequences, insertions, or Affymetrix probes. There are two main query tools in FlyBase. The first main query tool is called Jump to Gene (J2G). This is found in the top right of the blue navigation bar on every page of FlyBase. This tool is useful when you know exactly what you are looking for and want to go to the report page with that data. The second main query tool is called QuickSearch. This is located on the FlyBase homepage. This  tool is most useful when you want to look up something quickly that you may only know a little about. Searching can be performed within D. melanogaster only or within all species. Data other than genes can be searched using the ‘data class’ menu. Related research. The following provides two examples of research that is related to or uses FlyBase: