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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 ( 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

Mouse Genome Informatics (MGI): reflecting on 25 years

Janan T. Eppig, Joel E. Richardson, James A. Kadin, Martin Ringwald, Judith A. Blake, Carol J. Bult
2015 Mammalian Genome  
This mission is ever more feasible as the revolution in genetics knowledge, the ability to sequence genomes, and the ability to specifically manipulate mammalian genomes are now at our fingertips.  ...  From its inception in 1989, the mission of the Mouse Genome Informatics (MGI) resource remains to integrate genetic, genomic, and biological data about the laboratory mouse to facilitate the study of human  ...  Acknowledgments We take this opportunity to thank all 168 individuals who are or were part of the MGI team during the first 25 years. Current and former MGI staff are listed in Fig. 6 .  ... 
doi:10.1007/s00335-015-9589-4 pmid:26238262 pmcid:PMC4534491 fatcat:uevvmlmyobagjowk5fuggyflze

How stock centres end: a history of living Drosophila collections

2019 BJHS Themes  
All of the stock centres in this story faced challenges of how to pay for care and curation, engaging with a problem that has been discussed by biologists and their funders since the 1940s: what are the  ...  to biologists.  ...  are crucial to biology. 25 The third section looks in detail at how these relationships have worked (or not) in practice, and howin the case of Drosophilathey resulted in the flourishing of one stock  ... 
doi:10.1017/bjt.2019.14 pmid:32133157 pmcid:PMC7056353 fatcat:w6urqdilvng5fe3vmaiqo6tcim

GIF-DB, a WWW database on gene interactions involved in Drosophila melanogaster development

B. Jacq, F. Horn, F. Janody, N. Gompel, O. Serralbo, E. Mohr, C. Leroy, B. Bellon, L. Fasano, P. Laurenti, L. Roder
1997 Nucleic Acids Research  
The original concept of interaction databases examplified by GIF-DB could be extended to other biological subjects and organisms so as to study gene regulatory networks in an evolutionary perspective.  ...  GIF-DB achieves a high level of integration with other databases such as FlyBase, EMBL and SWISS-PROT through numerous hyperlinks.  ...  ACKNOWLEDGEMENTS We would like to thank C. Vermenot and S. Daloiseau for help in literature analysis, B. Mahé for a prototype version of the query search program, C. Chemla and V.  ... 
doi:10.1093/nar/25.1.67 pmid:9016506 pmcid:PMC146365 fatcat:obxesvsbtrdn5goggdyqn2agye

The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes

A C Spradling, D Stern, A Beaton, E J Rhem, T Laverty, N Mozden, S Misra, G M Rubin
1999 Genetics  
We now report that the primary collection has grown to contain 1045 strains that disrupt more than 25% of the estimated 3600 Drosophila genes that are essential for adult viability.  ...  Sequences flanking >920 insertions have been determined to exactly position them in the genome and to identify 376 potentially affected transcripts from collections of EST sequences.  ...  fail to disrupt any gene, increasing the total number of Wasserman, and L. Yue. We are also grateful to many workers who lines that will need to be analyzed.  ... 
pmid:10471706 pmcid:PMC1460730 fatcat:bybmbqwzb5gz5f5xl4ub5xccku

Comparing citation numbers between articles at two stages of a Model Organism Database curation workflow

Michael P. Lauruhn, Gillian Millburn
2017 Proceedings of the 6th International Workshop on Mining Scientific Publications - WOSP 2017  
This paper follows previous research (Beradini, et al. 2016) that attempted to use quantitative data to determine if and how literature curated by a MOD makes a difference to the access and reuse of the  ...  The research addresses whether articles that have been through the detailed curation process of a MOD are more likely to be cited when compared to 'similar' articles that are not curated.  ...  Acknowledgments We would also like to thank members of Elsevier Labs and the Elsevier Scopus team for technical assistance.  ... 
doi:10.1145/3127526.3127536 dblp:conf/jcdl/LauruhnM17 fatcat:hcqipmoocfasbbvpm7gwgeakni

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.  ...  With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase  ...  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

Revisiting Web Server Workload Invariants in the Context of Scientific Web Sites

Anne Faber, Minaxi Gupta, Camilo Viecco
2006 ACM/IEEE SC 2006 Conference (SC'06)  
The Web has evolved much from when Arlitt and Williamson proposed the ten Web workload invariants more than a decade ago. Many diverse communities now depend on the Web in their day-to-day lives.  ...  We investigate appropriate revisions to the invariants that do not hold and also propose three new invariants for scientific Web servers.  ...  Acknowledgments We would like to acknowledge the help of the following colleagues in acquiring various data sets: Don Gilbert for Flybase logs, John Bollinger and Randy Bramley for ReciprocalNet logs,  ... 
doi:10.1109/sc.2006.52 fatcat:tjcd2lxs75ck3ot7me4hhdaoum

A UDP-GalNAc:PolypeptideN-Acetylgalactosaminyltransferase Is Essential for Viability inDrosophila melanogaster

Kelly G. Ten Hagen, Duy T. Tran
2002 Journal of Biological Chemistry  
The third mutant contains an arginine to tryptophan amino acid change, which, when expressed in COS7 cells, resulted in a dramatic reduction of transferase activity in vitro.  ...  Here, we have determined the molecular nature of the mutations in three independent mutant alleles. Two of the mutant alleles contain premature stop codons within the coding region of pgant35A.  ...  The GFP bal-ancer chromosomes allow one to then visualize the chromosomal composition of D. melanogaster embryos and larvae by looking for GFP fluorescence; only embryos or larvae having at least one copy  ... 
doi:10.1074/jbc.m201807200 pmid:11925446 fatcat:gfjubeine5f7ljiwrudxpjfife

Gene name identification and normalization using a model organism database

Alexander A. Morgan, Lynette Hirschman, Marc Colosimo, Alexander S. Yeh, Jeff B. Colombe
2004 Journal of Biomedical Informatics  
We report here on a series of experiments related to the application of natural language processing to aid in the curation process for FlyBase.  ...  These experiments indicate that the lexical resources provided by FlyBase are complete enough to achieve high recall on the gene list task, and that normalization requires accurate disambiguation; different  ...  Previously, we had looked at different matching schemes to reproduce the gene list associated with paper references in FlyBase on both abstracts and the available full text articles [19] .  ... 
doi:10.1016/j.jbi.2004.08.010 pmid:15542014 fatcat:f2r63l3ecfhrtjxm2eo2omfxvq

FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development

Stefan A. Koestler, Begum Alaybeyoglu, Christian X. Weichenberger, Arzu Celik
2015 F1000Research  
Especially the latter information is however to a large extent scattered throughout the literature. FlyOde is an online platform for the systematic assembly of data on Results: D. eye development.  ...  It consists of data on eye development obtained from the m. literature, and a web interface for users to interactively display these data as a gene regulatory network.  ...  Click here to access the data. Analysis and characterization of the FlyOde network. Includes Supplementary Figures 2, 3, 4 . Click here to access the data.  ... 
doi:10.12688/f1000research.7556.1 pmid:26998229 pmcid:PMC4786896 fatcat:3mwario25bgy3jpnk23ipklzy4

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

Sandra N Loevenich, Erich Brunner, Nichole L King, Eric W Deutsch, Stephen E Stein, The FlyBase Consortium, Ruedi Aebersold, Ernst Hafen
2009 BMC Bioinformatics  
Acknowledgements The FlyBase Consortium comprises: FlyBase-Harvard: W.  ...  Such identification is not intended to imply recommendation or endorsement by the NIST, nor it is intended to imply that the materials or equipment identified are necessarily the best available for this  ...  They will be the subject of future reassessment by FlyBase annotators.  ... 
doi:10.1186/1471-2105-10-59 pmid:19210778 pmcid:PMC2648944 fatcat:rg3tbhynp5g67jobpaigyd3w4e—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update

Yanhui Hu, Aram Comjean, Charles Roesel, Arunachalam Vinayagam, Ian Flockhart, Jonathan Zirin, Lizabeth Perkins, Norbert Perrimon, Stephanie E. Mohr
2016 Nucleic Acids Research  
The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (  ...  ) serve as a reagent production tracking system, screen data repository, and portal to the community.  ...  The authors also extend our thanks to the members of the Perrimon lab and to the FlyBase consortium for helpful discussions regarding our online tools and website.  ... 
doi:10.1093/nar/gkw977 pmid:27924039 pmcid:PMC5210654 fatcat:zfht7ymfxrcydhtm7u4h646nse

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy (+18 others)
2002 Genome Biology  
genes, afforded FlyBase the opportunity to significantly improve genomic annotations.  ...  At present, experimental data and human curation remain essential to generate high-quality genome annotations.  ...  Identification of other snoRNAs should be possible in the future with the use of algorithms like Snoscan, which looks for 2-O-ribose methylation guide snoRNAs [35] ; however, the program will have to  ... 
pmid:12537572 pmcid:PMC151185 fatcat:p4il6giudzgfjmv3zlhucle3va

A novel family of single VWC-domain proteins in invertebrates

T.J. Sheldon, I. Miguel-Aliaga, A.P. Gould, W.R. Taylor, D. Conklin
2007 FEBS Letters  
SVCs are predicted to be secreted and a structural model for the family is proposed, using a known von Willebrand factor C-domain (VWC) structure as template.  ...  All SVCs possess eight cysteines, consistent with the loss of one bonded pair from the 10-cysteine canonical pattern of most VWC domains.  ...  ., A.G. and W.T. were funded by the Medical Research Council. I.M.-A. was funded by a Marie Curie Intra-European Fellowship.  ... 
doi:10.1016/j.febslet.2007.10.016 pmid:18028914 fatcat:zx7jgt5oy5fy5j4c7zrjgn34ha
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