Exploring FlyBase Data Using QuickSearch

Steven J. Marygold1, Giulia Antonazzo1, Helen Attrill1, Marta Costa1, Madeline A. Crosby2, Gilberto dos Santos2, Joshua L. Goodman3, L. Sian Gramates2, Beverley B. Matthews2, Alix J. Rey1, Jim Thurmond3, null null4

1 Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, 2 The Biological Laboratories, Harvard University, Cambridge, Massachusetts, 3 Department of Biology, Indiana University, Bloomington, Indiana, 4 null
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.31
DOI:  10.1002/cpbi.19
Online Posting Date:  December, 2016
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Abstract

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic‐scale and high‐throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This unit describes the functionality of all aspects of the QuickSearch tool. 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. © 2016 by John Wiley & Sons, Inc.

Keywords: FlyBase; Drosophila melanogaster ; biological database; query tools; QuickSearch

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Using the Simple Tab of QuickSearch
  • Basic Protocol 2: Using the Data Class Tab of QuickSearch
  • Basic Protocol 3: Using the References Tab of QuickSearch
  • Basic Protocol 4: Using the Gene Groups Tab of QuickSearch
  • Basic Protocol 5: Using the Human Disease Tab of QuickSearch
  • Basic Protocol 6: Using the Gene Ontology (GO) Tab of QuickSearch
  • Basic Protocol 7: Using the Expression Tab of QuickSearch
  • Basic Protocol 8: Using the Phenotype Tab of QuickSearch
  • Basic Protocol 9: Using the Protein Domains Tab of QuickSearch
  • Basic Protocol 10: Using the Orthologs Tab of QuickSearch
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

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Literature Cited

Literature Cited
   Amberger, J.S. , Bocchini, C.A. , Schiettecatte, F. , Scott, A.F. , and Hamosh, A. 2015. OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 43:D789‐798. doi: 10.1093/nar/gku1205.
   Attrill, H. , Falls, K. , Goodman, J.L. , Millburn, G.H. , Antonazzo, G. , Rey, A.J. , Marygold, S.J. , and the FlyBase Consortium. 2016. FlyBase: Establishing a Gene Group resource for Drosophila melanogaster . Nucleic Acids Res. 44:D786‐792. doi: 10.1093/nar/gkv1046.
   Binns, D. , Dimmer, E. , Huntley, R. , Barrell, D. , O'Donovan, C. , and Apweiler, R. 2009. QuickGO: A web‐based tool for Gene Ontology searching. Bioinformatics 25:3045‐3046. doi: 10.1093/bioinformatics/btp536.
   Carbon, S. , Ireland, A. , Mungall, C.J. , Shu, S. , Marshall, B. , Lewis, S. , the AmiGO Hub, and the Web Presence Working Group. 2009. AmiGO: Online access to ontology and annotation data. Bioinformatics 25:288‐289. doi: 10.1093/bioinformatics/btn615.
   Costa, M. , Reeve, S. , Grumbling, G. , and Osumi‐Sutherland, D. 2013. The Drosophila anatomy ontology. J. Biomed. Semantics 4:32. doi: 10.1186/2041‐1480‐4‐32.
   Drysdale, R. 2001. Phenotypic data in FlyBase. Brief. Bioinform. 2:68‐80. doi: 10.1093/bib/2.1.68.
   Gray, K.A. , Yates, B. , Seal, R.L. , Wright, M.W. , and Bruford, E.A. 2015. Genenames.org: The HGNC resources in 2015. Nucleic Acids Res. 43:D1079‐1085. doi: 10.1093/nar/gku1071.
   Gray, K.A. , Seal, R.L. , Tweedie, S. , Wright, M.W. , and Bruford, E.A. 2016. A review of the new HGNC gene family resource. Hum. Genomics 10:6. doi: 10.1186/s40246‐016‐0062‐6.
   Hu, Y. , Flockhart, I. , Vinayagam, A. , Bergwitz, C. , Berger, B. , Perrimon, N. , and Mohr, S.E. 2011. An integrative approach to ortholog prediction for disease‐focused and other functional studies. BMC Bioinformatics 12:357. doi: 10.1186/1471‐2105‐12‐357.
   Kibbe, W.A. , Arze, C. , Felix, V. , Mitraka, E. , Bolton, E. , Fu, G. , Mungall, C.J. , Binder, J.X. , Malone, J. , Vasant, D. , Parkinson, H. , and Schriml, L.M. 2015. Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 43:D1071‐1078. doi: 10.1093/nar/gku1011.
   Kriventseva, E.V. , Tegenfeldt, F. , Petty, T.J. , Waterhouse, R.M. , Simao, F.A. , Pozdnyakov, I.A. , Ioannidis, P. , and Zdobnov, E.M. 2015. OrthoDB v8: Update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res. 43:D250‐256. doi: 10.1093/nar/gku1220.
   Marygold, S.J. , Crosby, M.A. , Goodman, J.L. , and the FlyBase Consortium. 2016. Using FlyBase, a Database of Drosophila Genes and Genomes. In Drosophila: Methods and Protocols, 2nd ed., vol. 1478 ( C. Dahmann , ed.) p. 372. Springer, New York.
   Marygold, S.J. , Leyland, P.C. , Seal, R.L. , Goodman, J.L. , Thurmond, J. , Strelets, V.B. , Wilson, R.J. , and the FlyBase Consortium. 2013. FlyBase: Improvements to the bibliography. Nucleic Acids Res. 41:D751‐757. doi: 10.1093/nar/gks1024.
   McQuilton, P. , St Pierre, S.E. , Thurmond, J. , and the FlyBase Consortium. 2012. FlyBase 101—the basics of navigating FlyBase. Nucleic Acids Res. 40:D706‐714. doi: 10.1093/nar/gkr1030.
   Millburn, G.H. , Crosby, M.A. , Gramates, L.S. , Tweedie, S. , and the FlyBase Consortium. 2016. FlyBase portals to human disease research using Drosophila models. Dis. Model Mech. 9:245‐252. doi: 10.1242/dmm.023317.
   Mitchell, A. , Chang, H.Y. , Daugherty, L. , Fraser, M. , Hunter, S. , Lopez, R. , McAnulla, C. , McMenamin, C. , Nuka, G. , Pesseat, S. , Sangrador‐Vegas, A. , Scheremetjew, M. , Rato, C. , Yong, S.Y. , Bateman, A. , Punta, M. , Attwood, T.K. , Sigrist, C.J. , Redaschi, N. , Rivoire, C. , Xenarios, I. , Kahn, D. , Guyot, D. , Bork, P. , Letunic, I. , Gough, J. , Oates, M. , Haft, D. , Huang, H. , Natale, D.A. , Wu, C.H. , Orengo, C. , Sillitoe, I. , Mi, H. , Thomas, P.D. , and Finn, R.D. 2015. The InterPro protein families database: The classification resource after 15 years. Nucleic Acids Res. 43:D213‐221. doi: 10.1093/nar/gku1243.
   Osumi‐Sutherland, D. , Marygold, S.J. , Millburn, G.H. , McQuilton, P.A. , Ponting, L. , Stefancsik, R. , Falls, K. , Brown, N.H. , and Gkoutos, G.V. 2013. The Drosophila phenotype ontology. J. Biomed. Semantics 4:30. doi: 10.1186/2041‐1480‐4‐30.
   St Pierre, S.E. , Ponting, L. , Stefancsik, R. , McQuilton, P. , and the FlyBase Consortium. 2014. FlyBase 102–advanced approaches to interrogating FlyBase. Nucleic Acids Res. 42:D780‐788. doi: 10.1093/nar/gkt1092.
   The Gene Ontology Consortium. 2015. Gene Ontology Consortium: Going forward. Nucleic Acids Res. 43:D1049‐1056. doi: 10.1093/nar/gku1179.
   The UniProt Consortium. 2015. UniProt: A hub for protein information. Nucleic Acids Res. 43:D204‐212. doi: 10.1093/nar/gku989.
   Tweedie, S. , Ashburner, M. , Falls, K. , Leyland, P. , McQuilton, P. , Marygold, S. , Millburn, G. , Osumi‐Sutherland, D. , Schroeder, A. , Seal, R. , Zhang, H. , and the FlyBase Consortium. 2009. FlyBase: Enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 37:D555‐559. doi: 10.1093/nar/gkn788.
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