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FlyBase: integration and improvements to query tools

R. J. Wilson, J. L. Goodman, V. B. Strelets
2007 Nucleic Acids Research  
Recently, FlyBase has developed Interactions Browser and enhanced GBrowse, which are graphical query tools, and made improvements to the search tools QuickSearch and QueryBuilder.  ...  The database serves researchers of diverse backgrounds and interests, and offers several different query tools to provide efficient access to the data available and facilitate the discovery of significant  ...  Funding to pay the Open Access publication charges for this article was provided from the NIH grant (P41 HG00739) to FlyBase. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm930 pmid:18160408 pmcid:PMC2238994 fatcat:ioblhziscnactksgzsbe4lidri

FlyBase 102—advanced approaches to interrogating FlyBase

Susan E. St. Pierre, Laura Ponting, Raymund Stefancsik, Peter McQuilton
2013 Nucleic Acids Research  
Finally, we move on to discuss our most powerful search tool, QueryBuilder, before describing pre-computed cuts of the data and how to query the database programmatically.  ...  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: a Drosophila database. Flybase Consortium

1998 Nucleic Acids Research  
FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase  ...  FlyBase (http://flybase.bio.indiana.edu/ ) is a comprehensive database of genetic and molecular data concerning Drosophila.  ...  ACKNOWLEDGEMENTS FlyBase is supported by grants from the National Institutes of Health (National Human Genome Research Institute) and the Medical Research Council, London.  ... 
doi:10.1093/nar/26.1.85 pmid:9399806 pmcid:PMC147222 fatcat:5fe67mmgqbf5falyxzgw3z4nki

FlyBase 101 - the basics of navigating FlyBase

P. McQuilton, S. E. St. Pierre, J. Thurmond
2011 Nucleic Acids Research  
The next section introduces some of the search tools available on FlyBase, in particular, our heavily used and recently redesigned search tool QuickSearch, found on the FlyBase homepage.  ...  Whether you use the fruit fly as an experimental system or want to apply Drosophila biological knowledge to another field of study, FlyBase can help you successfully navigate the wealth of available Drosophila  ...  ACKNOWLEDGEMENTS We would like to thank the PIs, curators and developers of FlyBase for their comments on the manuscript. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr1030 pmid:22127867 pmcid:PMC3245098 fatcat:wxamunskpzg7zprvy5pmh23hdm

FlyBase: improvements to the bibliography

Steven J. Marygold, Paul C. Leyland, Ruth L. Seal, Joshua L. Goodman, Jim Thurmond, Victor B. Strelets, Robert J. Wilson
2012 Nucleic Acids Research  
Although this article is focused on bibliographic data, many of the features and tools described are applicable to browsing and querying other datasets in FlyBase.  ...  We highlight recent improvements in these areas and describe the advantages of using the FlyBase bibliography over alternative literature resources.  ...  In either case, the easiest and fastest way to query bibliographic data is to use the QuickSearch tool on the FlyBase homepage (6) .  ... 
doi:10.1093/nar/gks1024 pmid:23125371 pmcid:PMC3531214 fatcat:hibhwutfvbashm6jsnxgadwpku

FlyBase: genes and gene models

R. A. Drysdale
2004 Nucleic Acids Research  
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  ...  This tool allows the user to query the genes dataset for many records at once, by valid symbol or by FlyBase identification number.  ... 
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  
At the beginning of 2018, 'FlyBase 2.0' was released with a significantly improved user interface and new tools.  ...  researcher to design and carry out experiments.  ...  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

Exploring FlyBase Data Using QuickSearch

Steven J. Marygold, Giulia Antonazzo, Helen Attrill, Marta Costa, Madeline A. Crosby, Gilberto dos Santos, Joshua L. Goodman, L. Sian Gramates, Beverley B. Matthews, Alix J. Rey, Jim Thurmond
2016 Current Protocols in Bioinformatics  
Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs.  ...  With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research.  ...  Acknowledgments FlyBase is funded by the National Human Genome Research Institute at the U.S. National Institutes of Health (#U41HG000739, PI N. Perrimon) and the U.K.  ... 
doi:10.1002/cpbi.19 pmid:27930807 pmcid:PMC5152691 fatcat:gak43qcvjndcphz774srcxvzkq

The FlyBase database of the Drosophila genome projects and community literature

The FlyBase Consortium
2002 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.  ...  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.  ...  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: 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  
In this paper, we emphasize the dedicated reports and tools we've constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities.  ...  As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities  ...  Yu, Wilson Leung, Martha Bhattacharya, and Brian Dempsey were invaluable to the "FlyBase in the Classroom" section, and we thank them for their contributions.  ... 
doi:10.1093/genetics/iyac035 pmid:35266522 pmcid:PMC8982030 fatcat:bvoxngtcxzcrhhl7prxhf7uxxy

FlyBase portals to human disease research usingDrosophilamodels

Gillian H. Millburn, Madeline A. Crosby, L. Sian Gramates, Susan Tweedie
2016 Disease Models & Mechanisms  
Finally, we discuss search strategies and new query tools that are available to access the disease model data in FlyBase.  ...  To facilitate this, FlyBase has developed a dedicated tool for querying and navigating relevant data, which include mutations that model a disease and any associated interacting modifiers.  ...  Acknowledgements We would like to acknowledge the team that maintain the Disease Ontology; in particular we thank Lynn Schriml and Elvira Mitraka for their rapid response to our suggested changes to DO  ... 
doi:10.1242/dmm.023317 pmid:26935103 pmcid:PMC4826978 fatcat:yhhupuyp4zgptd7vyw2edmzedq

FlyBase: anatomical data, images and queries

G. Grumbling
2006 Nucleic Acids Research  
The FlyBase Consortium curates, annotates, integrates and maintains a wide variety of data within this domain.  ...  Access to the data is provided through graphical and textual user interfaces tailored to particular types of data.  ...  Additional support for FlyBase is provided by the Medical Research Council (UK), grant G9535792MB. Funding to pay the Open Access publication charges for this article was provided by NHGRI.  ... 
doi:10.1093/nar/gkj068 pmid:16381917 pmcid:PMC1347431 fatcat:b7f7zxzr65f5jhq375slrtfpma

Inside FlyBase: Biocuration as a career

Susan St. Pierre, Peter McQuilton
2009 Fly  
As research in the biological sciences continues to advance at a rapid pace, it is increasingly important that the data be captured, standardized, organized and made accessible to the scientific community  ...  Here we describe the process of biocuration from our perspective as FlyBase curators.  ...  Acknowledgments We would like to thank all of the FlyBase members for their critical reading of this manuscript. FlyBase is supported by the U.S.  ... 
doi:10.4161/fly.3.1.7769 pmid:19182544 pmcid:PMC2837272 fatcat:qxixus4knvf6xeazth2zm2kyba

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  
Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its focus to serve a broader scientific community.  ...  and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.  ...  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

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

Steven J. Marygold, Madeline A. Crosby, Joshua L. Goodman
2016 Msphere  
This chapter provides an overview of the data content, organization and available tools within FlyBase, focusing on recent improvements.  ...  data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability  ...  New or improved tools have also been developed in order to effectively search and analyze these novel data.  ... 
doi:10.1007/978-1-4939-6371-3_1 pmid:27730573 pmcid:PMC5107610 fatcat:gbtsjk6xj5esbp6wt6ttdswhp4
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