FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. [1] 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. [2] 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. [3] Links between FlyBase and external databases, such as BDGP [4] or modENCODE, [5] provide opportunities for further exploration into other model organism databases and other resources of biological and molecular information. [6] 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). [7]
As of 2022 [update] the FlyBase home page requested a website access fee of US$150.00 per person per year, stating that "The NHGRI has reduced the funding of FlyBase by 50%". [8]
Drosophila melanogaster has been an experimental organism since the early 1900s, and has since been placed at the forefront of many areas of research. [9] 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. [10] In 1998, the FlyBase consortium integrated the information into a single Drosophila genomics server. As of 2022 [update] 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. [11]
FlyBase contains a complete annotation of the Drosophila melanogaster genome that is updated several times per year. [12] 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. [13] The site also provides a large database of images illustrating the full genome, and several movies detailing embryogenesis (ImageBrowser Archived 2007-03-24 at the Wayback Machine ). 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. [14]
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 [15] BLAST, [16] Gbrowse, [17] 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 [18] 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.
The following provides two examples of research that is related to or uses FlyBase:
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
Michael Ashburner was an English biologist and Professor in the Department of Genetics at University of Cambridge. He was also the former joint-head and co-founder of the European Bioinformatics Institute (EBI) of the European Molecular Biology Laboratory (EMBL) and a Fellow of Churchill College, Cambridge.
Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.
The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.
The Rat Genome Database (RGD) is a database of rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse, human, and five other species.
The Saccharomyces Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. Further information is located at the Yeastract curated repository.
The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service.
The Open Regulatory Annotation Database is designed to promote community-based curation of regulatory information. Specifically, the database contains information about regulatory regions, transcription factor binding sites, regulatory variants, and haplotypes.
SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.
In molecular biology and genetics, DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome, by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in which they participate. Among other things, it identifies the locations of genes and all the coding regions in a genome and determines what those genes do.
Suzanna (Suzi) E. Lewis was a scientist and Principal investigator at the Berkeley Bioinformatics Open-source Project based at Lawrence Berkeley National Laboratory until her retirement in 2019. Lewis led the development of open standards and software for genome annotation and ontologies.
Blast2GO, first published in 2005, is a bioinformatics software tool for the automatic, high-throughput functional annotation of novel sequence data. It makes use of the BLAST algorithm to identify similar sequences to then transfers existing functional annotation from yet characterised sequences to the novel one. The functional information is represented via the Gene Ontology (GO), a controlled vocabulary of functional attributes. The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species.
In bioinformatics, the PANTHER classification system is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products. PANTHER is part of the Gene Ontology Reference Genome Project designed to classify proteins and their genes for high-throughput analysis.
Gene Ontology (GO) term enrichment is a technique for interpreting sets of genes making use of the Gene Ontology system of classification, in which genes are assigned to a set of predefined bins depending on their functional characteristics. For example, the gene FasR is categorized as being a receptor, involved in apoptosis and located on the plasma membrane.
Proboscipedia (pb) is a protein coding gene in Drosophila melanogaster.
Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.
SoyBase is a database created by the United States Department of Agriculture. It contains genetic information about soybeans. It includes genetic maps, information about Mendelian genetics and molecular data regarding genes and sequences. It was started in 1990 and is freely available to individuals and organizations worldwide.
Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.
