Copyright 1993 by The Genetics Society of America.
All Rights Reserved.
FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <ftp://flybase.org/flybase>.
This publication may be copied for non-commercial, scientific uses by individuals or organizations (including for-profit organizations). FlyBase is freely distributed to the scientific community on the understanding that it will not be used for commercial gain by any organization. Any commercial use of this publication, or any parts thereof, is expressly prohibited without permission in writing from the FlyBase consortium.
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase. The files containing the text of Lindsley and Zimm (1992) The Genome of Drosophila melanogaster are the copyright of Academic Press and are redistributed in FlyBase by their agreement. These files cannot be redistributed by users without the explicit permission of Academic Press. Reference records taken from the BIOSIS database are the copyright of BIOSIS.
We suggest FlyBase be referenced
in publications in the following manner:
I.3. Publications about FlyBase
The following publications about FlyBase have appeared:
The e-mail addresses belowed are modified to reduce spam to these addresses; combine the two components with an ampersand in the standard form of an e-mail address.
FlyBase has established two central e-mail addresses to which communications and questions about FlyBase should be sent. Do not use these mailing addresses for commercial purposes! For help and general communications to FlyBase:
For corrections and updates of FlyBase data:
Community announcements are included on FlyBase. Announcements of upcoming Drosophila meetings and other notices and requests that individuals wish to promulgate to the community at large may be posted here. Send requests for postings to:
Technical communications or questions about the FlyBase server may be addressed to:
We very much welcome corrections and additions to the data in FlyBase, comments about the types of data that we now (or should) make available or about the structure of FlyBase. FlyBase is meant to serve the Drosophila community. Only if we receive some feedback from the community will we know how best to do this.
The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at Harvard University, University of Cambridge (UK), Indiana University, University of California, and the European Bioinformatics Institute. A complete list of consortium members is included below.
FlyBase is supported by the National Human Genome Research Institute (U.S.A.), grant P41-HG00739. Additional support for FlyBase is provided by the Medical Research Council (U.K.), grant G9535792MB.
FlyBase-Harvard
Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA. Telephone (1)-617-496-5667; fax: (1)-617-496-1354.To send e-mail to FlyBase-Harvard personnel, add the domain morgan.harvard.edu to the string indicated below (with the exception noted below).
FlyBase-Cambridge
Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. Telephone: (44)-(0)1223-333969 or -333963; fax: (44)-(0)1223-333992.To send e-mail to FlyBase-Cambridge personnel, add the domain gen.cam.ac.uk to the string indicated below.
FlyBase-Indiana
Department of Biology, Indiana University, 1001 E. 3rd St., Bloomington, Indiana 47405-3700, USA. Telephone (1)-812-855-3033 or -5782 or -0587; fax: (1)-812-855-2577.To send e-mail to FlyBase-Indiana personnel, add the domain bio.indiana.edu (exceptions as noted) to the string indicated below.
FlyBase-Berkeley
University of California at Berkeley, LSA Rm. 539, Berkeley, California 94720-3200, USA. Telephone (1)-510-486-6217; Fax (1)-510-486-6798.To send e-mail to FlyBase-Berkeley personnel, add the domain fruitfly.org to the string indicated below.
Project Collaborator - National Center for Biotechnology Information
National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA. Telephone (1)-301-496-2475; fax: (1)-301-480-9241.FlyBase has an independent group of advisors with whom they meet periodically. Members of the group change from time to time depending on availability and interest, but both Drosophila workers and computer scientists are always included. Contact FlyBase if you would like the names of the current FlyBase advisors.
FlyBase is supported by grant P41 HG00739 from the NIH (National Human Genome Research Institute) with additional support from the HGMP Programme of the MRC (London).
We acknowledge the help of Dr. Phyllis Moses (Academic Press) and Dr. D.L. Lindsley and Dr. G. Zimm in making the Redbook data available to FlyBase, and for considerable help and encouragement.
We thank Dr. D.J. Lipman and his staff at the NCBI in Washington for their help in getting FlyBase launched. We are very grateful to Rainer Fuchs at EMBL, Amos Bairoch in Geneva, Alan Bleasby at Daresbury, Scott Federhen at the NCBI, Yoshihiro Ugawa and Takashi Gojobori at the DDBJ, Martin Bishop at the MRC Rosalind Franklin Center for Genomics Research and Reinhard Doelz at the Biozentrum for helping to make this database available. Thanks too to John Garavelli (PIR), Rainer Fuchs (EMBL) and Amos Bairoch (Geneva) for help in cross-checking between FlyBase and the Nucleic Acid/Protein databases, to Chris Brown and colleagues (Otago) for making their TransTerm database available through FlyBase and Philip Bucher for cross-references to the Eukaryotic Promoter Database.
FlyBase thanks the authors and publishers of the sources of the published bibliographies for their permission to incorporate these into FlyBase. In particular, we thank Jane Rosov of Medline, Diane Hoffman of BIOSIS and Gerhard Baechli for their enormous help, the administrators of the International Nucleic Acid Sequence Data Libraries for extracting all of the Drosophila records for us (and in keeping us up-to-date), Beth Owens of the Environmental Mutagen Information Center, Oak Ridge for a download of all of their Drosophila data, Doreen Simpson of the University of Cambridge Computing Service for her help in machine reading the printed bibliographies, Jane Snaith for typing many records that were impossible to machine read and, above all, Irwin Herskowitz, without whose long term commitment the bibliography would have been impossible to assemble. Many members of the Drosophila community have been very helpful in tracking down obscure publications or in checking references. We are very grateful for this help.
We thank Dr. Richard Skaer and the Company of Biologists for providing the content lists of their journals on disk and for past donations of subscriptions to Development, Journal of Cell Science and Journal of Experimental Biology.
John Merriam was a member of the FlyBase consortium for its first two years and we thank him and his colleagues for their invaluable efforts. Work in John Merriam's group was supported by NIH grant LM04896 from the National Library of Medicine.
We thank C. Savakis and Inga Sidén-Kiamos for their collaboration in integrating the European Drosophila Mapping Project data with FlyBase.
FlyBase is a complex database, both in terms of its structure and data. In addition, FlyBase is still in a stage of very rapid development and change. Rather than withhold data from the community until we are confident that everything is 'right' we will be releasing data and files which are not 'perfect'. We will be aware of some of the problems and will indicate these in this section of Reference Manual I: The FlyBase Project. If users find others, will they please let us know, and we can then at least attempt to correct them.
1. We have not yet systematically checked the text of either the genes or the aberrations files for consistency of cross-referencing gene, allele and aberration names. Some of these cross-references remain to names that FlyBase regards as synonyms.
2. There remain a few titles of journals and other publications that have proven very difficult to trace. They are identified in the table of abbreviations as having no full title. Any help in tracing these would be much appreciated.
The bibliography has been automatically screened for duplicate entries. This is not a perfect process and some duplicates may well remain. A second problem with the bibliography is that some of our sources were either all in upper case or all in lower case. Some errors of capitalization remain. Any instances of such errors, or duplicates, should be brought to our attention. Finally, both Medline and BIOSIS keyword index publications in a manner which includes many of little relevance to FlyBase (an example are all papers on the in vitro culture of Leishmania, since this is done in Schneider's Drosophila tissue-culture medium). We may have been less than perfect in spotting such publications and eliminating them.
3. There remain problems, especially in aberrations with the attribution of data to some of the fields. For example, some phenotypic data remains in the 'genetics' field.
4. Map positions are not yet included in the external-databases.txt file.