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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  
We highlight recent improvements in these areas and describe the advantages of using the FlyBase bibliography over alternative literature resources.  ...  Here, we describe the organization and main features of the bibliography in FlyBase (flybase.org), the MOD for Drosophila melanogaster.  ...  Questions about or suggested improvements to the bibliography, or any other area of FlyBase, are encouraged and can be submitted via the 'Contact FlyBase' link at the foot of any FlyBase webpage.  ... 
doi:10.1093/nar/gks1024 pmid:23125371 pmcid:PMC3531214 fatcat:hibhwutfvbashm6jsnxgadwpku

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  
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  ...  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.  ...  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

Phenotypic data in FlyBase

R. Drysdale
2001 Briefings in Bioinformatics  
This paper discusses the mechanisms FlyBase has implemented to systematise published phenotypic data about Drosophila, and provides an introduction to the query tools available for the mining of the data  ...  data to maximise the potential of genomic analysis.  ...  Acknowledgements The phenotypic data in FlyBase is curated at FlyBase-Cambridge by Gillian Millburn, Chihiro Yamada and the author.  ... 
doi:10.1093/bib/2.1.68 pmid:11465064 fatcat:rof5miilfreyndoxfaoac6iu3m

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.  ...  The ultimate goal of the reannotation effort is to decorate the euchromatic sequence of the genome with as much biological information as is available from the community and from the major genome project  ...  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

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  
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.  ...  Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs.  ...  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

Inside FlyBase: Biocuration as a career

Susan St. Pierre, Peter McQuilton
2009 Fly  
This is the job of a biocurator. Here we describe the process of biocuration from our perspective as FlyBase curators.  ...  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  ...  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: 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  
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  ...  FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster.  ...  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

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.  ...  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

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

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

Steven J. Marygold, Madeline A. Crosby, Joshua L. Goodman
2016 Msphere  
FlyBase has taken several approaches to respond to these changes in the research landscape.  ...  This chapter provides an overview of the data content, organization and available tools within FlyBase, focusing on recent improvements.  ...  improvements can be brought to the attention of users.  ... 
doi:10.1007/978-1-4939-6371-3_1 pmid:27730573 pmcid:PMC5107610 fatcat:gbtsjk6xj5esbp6wt6ttdswhp4

Opportunities for text mining in the FlyBase genetic literature curation workflow

P. McQuilton
2012 Database: The Journal of Biological Databases and Curation  
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  ...  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  ...  Another improvement we are exploring is the addition of text mining to the FlyBase curation pipeline.  ... 
doi:10.1093/database/bas039 pmid:23160412 pmcid:PMC3500518 fatcat:6yptxqk7x5hcfpedsyjju2jixe

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 (+3 others)
2022
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  ...  FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster.  ...  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:10.17863/cam.84528 fatcat:qhgkd6rpz5ekbkefhn5a2wazhy

Directly e-mailing authors of newly published papers encourages community curation

Stephanie M. Bunt, Gary B. Grumbling, Helen I. Field, Steven J. Marygold, Nicholas H. Brown, Gillian H. Millburn
2012 Database: The Journal of Biological Databases and Curation  
Here, we report recent improvements to the triaging process used by FlyBase.  ...  These authors contributed equally to this work. z The members of the FlyBase Consortium are listed in the Acknowledgements.  ...  We would also like to thank members of FlyBase and three anonymous reviewers for critical comments on the manuscript, members of the FlyBase community curation subcommittee for helping to improve the design  ... 
doi:10.1093/database/bas024 pmid:22554788 pmcid:PMC3342516 fatcat:l7onb4nia5aefozvio7lqe6c3e

BOOTSTRAPPING THE RECOGNITION AND ANAPHORIC LINKING OF NAMED ENTITIES IN DROSOPHILA ARTICLES

ANDREAS VLACHOS, CAROLINE GASPERIN, IAN LEWIN, TED BRISCOE
2005 Biocomputing 2006  
We also present guidelines for annotation of gene mentions in texts and outline how the resulting system is used to aid FlyBase curation.  ...  This paper demonstrates how Drosophila gene name recognition and anaphoric linking of gene names and their products can be achieved using existing information in FlyBase and the Sequence Ontology.  ...  We would like to thank Alexander Morgan for making the annotated test data available to us and for advice on replication of the experiment reported in Morgan et al. 5 , Chihiro Yamada for his expert  ... 
doi:10.1142/9789812701626_0010 fatcat:zopw5gnzobanllledtov36usum
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