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FlyBase: enhancing Drosophila Gene Ontology annotations

S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi-Sutherland, A. Schroeder, R. Seal, H. Zhang
2009 Nucleic Acids Research  
FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information.  ...  Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location.  ...  S.T. would like to thank the members of the Gene Ontology Consortium and particularly the GO Reference Genome Annotation Group for support with all aspects of GO annotation and ontology development.  ... 
doi:10.1093/nar/gkn788 pmid:18948289 pmcid:PMC2686450 fatcat:ce6tuo7gxbdfzo3sfgtxshlloy

FlyBase 102—advanced approaches to interrogating FlyBase

Susan E. St. Pierre, Laura Ponting, Raymund Stefancsik, Peter McQuilton
2013 Nucleic Acids Research  
FlyBase (http://flybase.org) is the leading website and database of Drosophila genes and genomes.  ...  The first section explores gene function in FlyBase, using our TermLink tool to search with Controlled Vocabulary terms and our new RNA-Seq Search tool to search gene expression.  ...  ACKNOWLEDGEMENTS We would like to thank the PIs, curators and developers of FlyBase for their comments on the manuscript.  ... 
doi:10.1093/nar/gkt1092 pmid:24234449 pmcid:PMC3964969 fatcat:mwzvr4w5ajhn7phzqly6iwjari

FlyBase: genes and gene models

R. A. Drysdale
2004 Nucleic Acids Research  
For the most extensively studied species, Drosophila melanogaster, a wide range of data  ...  FlyBase (http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae.  ...  ACKNOWLEDGEMENTS FlyBase is supported by grant P41 HG00739 from the National Human Genome Research Institute, National Institutes of Health, with additional support from the Medical Research Council (London  ... 
doi:10.1093/nar/gki046 pmid:15608223 pmcid:PMC540000 fatcat:2eyap3qjijbkjpsng5wiihwkbi

FlyBase 2.0: the next generation

Jim Thurmond, Joshua L Goodman, Victor B Strelets, Helen Attrill, L Sian Gramates, Steven J Marygold, Beverley B Matthews, Gillian Millburn, Giulia Antonazzo, Vitor Trovisco, Thomas C Kaufman, Brian R Calvi (+34 others)
2018 Nucleic Acids Research  
An important new data class called 'experimental tools' consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila  ...  The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila.  ...  ACKNOWLEDGEMENTS We would like to thanks the other PIs, curators, and developers of FlyBase for their comments on the manuscript. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gky1003 pmid:30364959 fatcat:edyizmh3fjcuhkbwrq7fdsyooe

The FlyBase database of the Drosophila genome projects and community literature

The FlyBase Consortium
2002 Nucleic Acids Research  
There are many points of entry to the genome within FlyBase, most notably through maps, gene ontologies, structured phenotypic and gene expression data, and anatomy.  ...  Following on the success of the Drosophila genome project, FlyBase has primary responsibility for the continual reannotation of the D.melanogaster genome.  ...  Requests for help and questions about FlyBase should be addressed to flybase-help@morgan.harvard.edu.  ... 
doi:10.1093/nar/30.1.106 pmid:11752267 pmcid:PMC99082 fatcat:y3h4q6igdbfbhjmunnki7gnrsm

FlyBase at 25: looking to the future

L. Sian Gramates, Steven J. Marygold, Gilberto dos Santos, Jose-Maria Urbano, Giulia Antonazzo, Beverley B. Matthews, Alix J. Rey, Christopher J. Tabone, Madeline A. Crosby, David B. Emmert, Kathleen Falls, Joshua L. Goodman (+6 others)
2016 Nucleic Acids Research  
Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions  ...  Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community.  ...  ACKNOWLEDGEMENTS We would like to thanks the PIs, curators, and developers of FlyBase for their comments on the manuscript.  ... 
doi:10.1093/nar/gkw1016 pmid:27799470 pmcid:PMC5210523 fatcat:nw3to6susnfplnfpo54pxqw27a

FlyBase: A guided tour of highlighted features

L Sian Gramates, Julie Agapite, Helen Attrill, Brian R Calvi, Madeline A Crosby, Gilberto dos Santos, Joshua L Goodman, Damien Goutte-Gattat, Victoria K Jenkins, Thomas Kaufman, Aoife Larkin, Beverley B Matthews (+2 others)
2022 Genetics  
FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster.  ...  We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase.  ...  Acknowledgments The authors would like to thank the PIs, curators, and developers of FlyBase for their comments on the manuscript. Discussions with Alder M.  ... 
doi:10.1093/genetics/iyac035 pmid:35266522 pmcid:PMC8982030 fatcat:bvoxngtcxzcrhhl7prxhf7uxxy

Using FlyBase, a Database of Drosophila Genes and Genomes [chapter]

Steven J. Marygold, Madeline A. Crosby, Joshua L. Goodman
2016 Msphere  
In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback.  ...  For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster.  ...  Gene model annotations in FlyBase For D. melanogaster, FlyBase has produced manually annotated gene models for over a decade (34) .  ... 
doi:10.1007/978-1-4939-6371-3_1 pmid:27730573 pmcid:PMC5107610 fatcat:gbtsjk6xj5esbp6wt6ttdswhp4

The FlyBase database of the Drosophila genome projects and community literature

2003 Nucleic Acids Research  
FlyBase (http://flybase.bio.indiana.edu/) provides an integrated view of the fundamental genomic and genetic data on the major genetic model Drosophila melanogaster and related species. FlyBase has  ...  ACKNOWLEDGEMENTS FlyBase is supported by grants from the National Institutes of Health (National Human Genome Research Institute) to W. M. Gelbart and the Medical Research Council, London to M.  ...  The Berkeley Drosophila Genome Project is supported by grants from the Department of Energy and from the National Institutes of Health (National Human Genome Research Institute) to G. M. Rubin.  ... 
doi:10.1093/nar/gkg094 pmid:12519974 pmcid:PMC165541 fatcat:hf2ejbytzve4fe7w4ozlbqpxg4

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

Helen Attrill, Kathleen Falls, Joshua L. Goodman, Gillian H. Millburn, Giulia Antonazzo, Alix J. Rey, Steven J. Marygold
2015 Nucleic Acids Research  
To this end, FlyBase (flybase.org), the MOD for Drosophila melanogaster, has established a 'Gene Group' resource: high-quality sets of genes derived from the published literature and organized into individual  ...  Many publications describe sets of genes or gene products that share a common biology.  ...  Gene Ontology (GO) annotations can be used to search for gene products that are related by common biological attributes, but annotation is not exhaustive and expressing features that pertain to sequence  ... 
doi:10.1093/nar/gkv1046 pmid:26467478 pmcid:PMC4702782 fatcat:2ljorlbf4jgkrilfxniusk6pcy

Opportunities for text mining in the FlyBase genetic literature curation workflow

P. McQuilton
2012 Database: The Journal of Biological Databases and Curation  
He also thanks colleagues at FlyBase, particularly Steven Marygold, David Osumi-Sutherland and Gillian Millburn, for critical reading of the article, and members of FlyBase Cambridge for their work in  ...  Acknowledgements The author thanks the BioCreative group for the invitation to give a talk at the BioCreative Workshop 2012 on the FlyBase genetic literature curation workflow, from which this article  ...  For example, we use Sequence Ontology (SO) (3) terms to denote the type of gene and GO terms (4) to annotate these genes for molecular function, cellular component and biological process.  ... 
doi:10.1093/database/bas039 pmid:23160412 pmcid:PMC3500518 fatcat:6yptxqk7x5hcfpedsyjju2jixe

FlyTED: the Drosophila Testis Gene Expression Database

Jun Zhao, Graham Klyne, Elizabeth Benson, Elin Gudmannsdottir, Helen White-Cooper, David Shotton
2009 Nucleic Acids Research  
FlyTED, the Drosophila Testis Gene Expression Database, is a biological research database for gene expression images from the testis of the fruit fly Drosophila melanogaster.  ...  It currently contains 2762 mRNA in situ hybridization images and ancillary metadata revealing the patterns of gene expression of 817 Drosophila genes in testes of wild type flies and of seven meiotic arrest  ...  In addition to the gene name, each image is also annotated with the FlyBase identification number (gene id) that uniquely identifies each gene, which is linked to the corresponding FlyBase gene report  ... 
doi:10.1093/nar/gkp1006 pmid:19934263 pmcid:PMC2808924 fatcat:h6ecgitkkzbath5py75f6idk4m

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

M. S. Halfon, S. M. Gallo, C. M. Bergman
2007 Nucleic Acids Research  
containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites.  ...  The identification and study of the cis-regulatory elements that control gene expression are important areas of biological research, but few resources exist to facilitate large-scale bioinformatics studies  ...  Likewise, fewer than 1% of Drosophila genes currently have annotated TFBS data (5) .  ... 
doi:10.1093/nar/gkm876 pmid:18039705 pmcid:PMC2238825 fatcat:vyryxdivxvbltkms4qcmupxsoa

OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster

Alistair Miles, Jun Zhao, Graham Klyne, Helen White-Cooper, David Shotton
2010 Journal of Biomedical Informatics  
These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers  ...  Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com.  ...  For the same reason, we have not yet attempted to map the data onto existing biomedical ontologies such as the Sequence Ontology (SO), 26 the Gene Ontology (GO), 27 or the Drosophila Anatomy Ontology  ... 
doi:10.1016/j.jbi.2010.04.004 pmid:20382263 fatcat:axpgbbkw3zauzkajc3h3jogiga

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database

Ulrike Pfreundt, Daniel P. James, Susan Tweedie, Derek Wilson, Sarah A. Teichmann, Boris Adryan
2009 Nucleic Acids Research  
Furthermore, experimental evidence from the literature was classified into a defined vocabulary, and in collaboration with FlyBase, translated into Gene Ontology (GO) annotation.  ...  While our GO annotations will also be available through FlyBase as they will be incorporated into the genes' official GO annotation in the future, the entire evidence used for classification including  ...  ACKNOWLEDGEMENTS The authors thank Nick Brown and Steven Marygold at FlyBase for enabling UP to participate in this collaboration and for comments on the manuscript.  ... 
doi:10.1093/nar/gkp910 pmid:19884132 pmcid:PMC2808907 fatcat:mpgt6a2cuzfq3agikptnae6q6y
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