Documents of various types are placed in the Documents section of FlyBase. Included are both versions of the Redbook, personal communications to FlyBase, FlyBase documentation, including this Reference Manual, and controlled-vocabulary lists, documents related to Drosophila genetic nomenclature, postings to the network newsgroup bionet.drosophila, copies of the announcements that appear on FlyBase, subject indices from DIS, and more.
G.1. Genetic nomenclature of Drosophila
The Nomenclature section of Documents is directory is for documents that are concerned with the problems of gene, allele, aberration and transposon names and symbols and their representation in both the database and text.
The file nomenclature.html is a rather complete document produced by FlyBase that includes both a statement of the practice of FlyBase and recommendations to the community (other file formats are also posted). In addition, this directory includes a file of the abbreviations for species names, species-abbreviations.txt. These are used by FlyBase for the description of genes and aberrations from species other than D. melanogaster and for the description of transposons carrying 'foreign' genes.
FlyBase is happy to advise members of the community, and editors, who have questions on the naming of specific genes, etc.
G.2. Controlled vocabularies used by FlyBase
For many reasons several of the fields in FlyBase use controlled vocabularies. This makes it much easier (and more robust) to make links within the database, as well as making it much easier to search the database for information. The controlled vocabularies are only implemented in certain fields in FlyBase. These are indicated by [cv] in the appropriate place in this documentation.
controlled-vocabularies.txt includes the terms used by FlyBase as controlled vocabularies. Comment lines begin with the ! character. Lines with only this character have only been inserted for readability.
Sections of the controlled vocabulary are introduced by a line with the syntax:
!VOCABULARY: <TEXT>
e.g.
!VOCABULARY: PHENOTYPIC CLASS
!CURATION-ONLY VOCABULARY: <text>
The second example indicates a vocabulary used only by FlyBase curators.
A major section of controlled-vocabularies.txt is a list of terms used to describe the parts of a fly. The chief objective of this catalog is to help FlyBase curators in establishing a controlled vocabulary for use when describing phenotypes. It may, however, also be of wider interest to the community. The objective of this catalog is to have as complete a list (with synonyms) of recognizable 'objects' as possible.
The syntax of a controlled-vocabulary term line is:
[%|<|$]<term> ; FBbt:<########> ; synonym:<synonym> ; abbrev:<valid-abbrev> ; maybe:<possible-synonym> ; FBrf:<#######> ; comment:<comment> [ % | < | ~ <term>]
At this time FBbt numbers have only been assigned to the $whole organism domain.
Within sections these lists have a roughly hierarchical structure, but some vocabularies are not simple hierarchies, they are directed acyclic graphs, where a child term may have more than one parent term. Within some vocabularies three classes of relationship between a term and its parent term(s) are indicated by the characters % < and ~. These symbols may either precede or follow a term. When preceding a term there is no space between the relationship symbol and the term. When following a term the in-line relationships are placed after all other attributes of a term and the symbols are both preceded and followed by a space.
The symbol % means that a term 'is an instance of' its parent term; thus 'endoderm' is an instance of 'germ layer'.
The symbol < means that a term is 'a part of' its parent term; thus 'adult brain' is a part of the 'adult central nervous system'.
The symbol ~ means 'derived from'; it is used to indicate developmental relationships between structures in the body parts hierarchy. Thus the 'eye' develops from the 'eye disc'. It is, of course, impossible accurately to represent the complexity of development in a table such as this, and the relationships indicated by the ~ symbol are inevitably oversimplified.
An example of in-line relationships:
%1-1I ; FBbt:00001458 % interneuron
%1-1I, thoracic ; FBbt:00001459 ~ neuroblast NB1-1, thoracic < embryonic
thorax
This means that '1-1I, thoracic' is an instance of its parent '1-1I', is a part of its parent 'embryonic thorax' and develops from its parent 'neuroblast NB1-1, thoracic'.
The symbol $ indicates the root term of a domain.
Comments, additions and corrections are sought.
Acknowledgments: FlyBase thanks many colleagues for their help with the whole organism and subcellular domains.
A variety of information related to the development and maintenance of FlyBase are combined in the Working Papers folder. Genome-related documents of historical interest are included, along with more specialized FlyBase documents.
G.4.1. Lindsley and Zimm (1992) - The New Redbook
The Genome of Drosophila melanogaster
Dan L. Lindsley & Georgianna G. Zimm
Copyright 1992 By Academic Press, Inc.
All Rights Reserved.
No part of this publication may be reproduced or retransmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher.
ISBN 0-12-450990-8
Academic Press, Inc.
1250 Sixth Avenue, San Diego, California 92101-4311
FlyBase includes the complete text of Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992) in the Redbook directory of Documents. This is by a specific contract with Academic Press and users of these files must not reproduce or redistribute these files without permission from Academic Press. We thank Dr. Phyllis Moses of Academic Press, and Dan Lindsley for their help in making it possible for the Redbook text to be made available to FlyBase.
All the data in the GENES section of the Redbook are included in Genes.
Because of its complexity this text is split into a number of subdirectories.
Miscellany is a directory of files with the "text" of the special sections of Lindsley and Zimm. File names are intuitive in most cases, but some abbreviations may not be obvious. These are the file names and the book sections they include:
Rich-text is a directory of Redbook text in 'rich text' format.
errors.txt is a list of corrections to the published text of Lindsley and Zimm. It is not an update of Lindsley and Zimm, but simply a list of the errors of commission and omission that have been spotted. Having said this, some new material has inevitably crept in. Many of the corrections are minor typos, but some are more important. Georgianna Zimm and Dan Lindsley contributed many of the corrections and others have been contributed by the community. Most have been found in the process of converting the text of Lindsley and Zimm into a database format, since this has allowed us to write programs to identify inconsistencies in the text that would otherwise be very difficult to find.
If you find further errors please send an e-mail message to flybase-updates at morgan.harvard.edu (reformat to standard e-mail address). and we will add them to this table.
This table is sorted by page and column, corresponding to the published text. Should anybody want it sorted in any other way please send e-mail to FlyBase.
The structure of the file is that each correction begins with a page number in column 1. This is followed by the column (i.e., L, Left or R, Right) and, if helpful, a line number or indication that the correction refers to a table or figure. New lines are indicated by the line number above which the new text is to be inserted, e.g. as 4+, if to be inserted before line 4. When the 'entry' field is filled in, then the line numbers refer to within that entry, else they refer to the page or table. [Blank lines are not counted.] Then, on successive lines starting in field 6 are (a) the name of the entry to which the correction applies (if the entry name itself is corrected then it is given in its original Lindsley and Zimm form), (b) the old text to be deleted, between double quotes (") (note that if the correction is simply an addition of text then this field is empty), (c) the new text, between double quotes (note that if the old text is simply to be deleted this field will be empty), (d) any comment on the correction (this field includes font errors) and (e) the person who identified the error, followed by the date. The date field will allow you to spot new or changed entries in successive versions of this table.
The symbol ;; is used to separate columns in tabular text. Square brackets, [], enclose superscripts. Changes to font are noted within {}. Greek letters are written out, e.g., alpha, beta. Text omitted from these annotations is indicated by a double period ..
The Redbook files have not (and will not) be corrected. They will be preserved as a copy of the text of Lindsley and Zimm as published in 1992. However, the changes have been made in Genes which incorporates the text of Lindsley and Zimm (1992).
G.4.3. Lindsley and Grell (1968) - The Old Redbook
The text of the Genetic variations of Drosophila melanogaster by Dan L. Lindsley and Ed H. Grell (1968, Carnegie Institution of Washington, Washington, DC) is now available as a series of text files on FlyBase. The files are in LandG1968, within the Red Book folder, and each file bears the name of a section of the book, e.g., preface.txt, mutations.txt, special-chromosomes.txt, etc.
A copy of this book on magnetic tape was provided to FlyBase by Dan Lindsley. This copy was in Unix troff format and has been parsed into something more readable for the files in LandG1968. The parsing is less than perfect, and these files differ from the book in the following ways:
The material from Lindsley and Grell (1968) that had been omitted from Lindsley and Zimm (1992) has now been incorporated into FlyBase Genes and Aberrations.
G.5. Greybook Errors - Ashburner (1989)
The Greybook folder contains a file of errors that have been found in Ashburner's Drosophila: A Laboratory Manual and Drosophila: A Laboratory Handbook (Cold Spring Harbor Press, 1989). The purpose of this file is only to bring notice of typographical or obvious errors, it is not to update the text. The only additions made are (a) adding references to literature originally given as being 'in press' and (b) changes to the text where matters of laboratory safety are concerned. The format is similar to that of the Redbook errors file.
The structure of the file is that each correction begins with a page number in column 1. This is followed by the column (i.e. L, Left or R, Right, M, Middle) and, if helpful, a line number or indication that the correction refers to a table or figure. Then, on successive lines starting in field 6 are (a) the old text to be deleted, between double quotes (") (note, that if the correction is simply an addition of text then this field is empty), (b) the new text, between double quotes (note, that if the old text is simply to be deleted this field will be empty), (c) any comment on the correction and (d) the person who identified the error, followed by the date.
The symbol ;; is used to separate columns in tabular text. Square brackets, [], enclose superscripts. Changes to font are noted within {}. Greek letters are written out, e.g. alpha, beta. Text omitted from these annotations is indicated by a double period ..
In this file line numbers are indicated as being +, i.e. from the top of the page, or -, i.e. from the bottom of the page (blank lines are not counted; for tables horizontal rules are not counted as lines). Page numbers without a prefix refer to the Handbook, page numbers with the prefix M refer to the Manual.
Please bring any further errors to our attention, either by e-mail to flybase-updates at morgan.harvard.edu (reformat to standard e-mail address). or by contacting Michael Ashburner (m.ashburner at gen.cam.ac.uk, reformat to standard e-mail address) directly.
G.6. Personal communications to FlyBase
The policy of FlyBase with respect to the incorporation of unpublished data into the database is as follows. Data will only be considered for curation if available to FlyBase in written or electronic form. FlyBase will not capture data from oral presentations at meetings or seminars, from posters or by word of mouth (we will, however, curate published abstracts). If colleagues wish unpublished data to be considered for incorporation into FlyBase then those data must be submitted to FlyBase in writing or by e-mail (e-mail submissions to flybase-updates at morgan.harvard.edu (reformat to standard e-mail address) are strongly preferred). Each personal communication will be assigned a FlyBase reference (FBrf) identifier number, and the data will be tied to this citation in the database. These references will appear in the FlyBase bibliographic files, and become citeable publications upon entry into the public FlyBase database. The author(s) of the communications will be informed of these reference numbers soon after receipt of the data. Personal communications received in written form (i.e., not electronically) will be archived by FlyBase. The FlyBase record will then contain only the statement that a copy of the communication may be obtained from FlyBase. We encourage the citation of these personal communications in the literature in the form:
Gelbart, W.M. (1994). Personal communication to FlyBase.< http://flybase.org/.bin/fbpcq.html?FBrf0075300>
Personal communications are incorporated into the FlyBase bibliography and can be searched with the References query form. Select 'Personal Communication to FlyBase' from the Publication Type menu to limit your search to personal communications.
The News section of FlyBase contains announcements that appear on FlyBase, Drosophila Information Service subject indices prepared by J. Thompson, Jr., a link to archived bionet.drosophila messages, and archived issues of the now defunct Drosophila Information Newsletter.
These are announcements from the community, or from FlyBase, to users of FlyBase. They remain on FlyBase only as long as they are timely. Announcements are placed in one of four categories:
G.7.2. Newsgroup bionet.drosophila
bionet.drosophila is a moderated electronic newsgroup ("bulletin board") devoted to Drosophila. This is for all Drosophila workers and can be used to exchange information, request stocks or other reagents, give notices about meetings or for any other information that will interest fly workers. FlyBase will use this news group as a way of letting the community know about updates and changes to FlyBase. FlyBase provides a search option for archived bionet.drosophila postings in the News directory.
Messages posted to bionet.drosophila can be read from the BIONET Drosophila web page, through USENET feed (bionet.drosophila), or by e-mail. To receive it by e-mail, send the message "subscribe dros" (without the quotation marks) to one of the following two sites:
Messages can be posted to bionet.drosophila from the BIONET Drosophila web page, from local USENET sites, or by e-mail to one of the following addresses:
G.7.3. Drosophila Information Service (D. I. S.) subject indices
Subject indices of Drosophila Information Service (D. I. S.), from volume 1 to volume 71, have been prepared by James Thompson Jr. These have been made available by Dr. Thompson to FlyBase.
These files are essentially those published in D. I. S. 75, the major difference is that in the D. I. S text species belonging to genera of drosophilids other than Drosophila are included in the main alphabetical index. In these files they are includes in the species index.
G.7.4. Drosophila Information Newsletter archive
Drosophila Information Newsletter (D.I.N) was an electronic newsletter for the Drosophila community. D.I.N ceased publication with volume 20, after bionet.drosophila was established. The 20 issues of D.I.N. are archived in the DIN folder under Other Documents. The filenames are of the type dinvol2.txt, the number indicating the volume. The Tables of Contents of all 20 issues of D.I.N. are listed in the file dinTablesofContents.html, with links to each D.I.N. file.