Connecting to FlyBase with a Gopher client
To reach FlyBase directly with a Gopher client that points to another server, type the following command:
The link to add to your Gopher server to tunnel to Indiana is:
Name=IUBio Biology Archive, Indiana University
Type=1
Port=72
Path=
Host=flybase.bio.indiana.edu
A full mirror of FlyBase Gopher services is available at:
Partial mirrors of FlyBase (everything except the Redbook files) are available to Gopher users at:
Other biology archives may provide Gopher access to FlyBase files. These include ftp.ebi.ac.uk (the European Bioinformatics Institute) and bioinformatics.weizmann.ac.il (132.76.55.12) at the Weizmann Institute. Please note that these sites may not maintain a complete or up-to-date copy of FlyBase, and may not provide the facility to search FlyBase files.
Note that direct Telnet access into FlyBase at IUBio is not possible, you must use FTP. If you attempt to logon to FlyBase at IUBio via telnet in any other way than FTP, then you will be frustrated.
The FlyBase Gopher Interface
Gopher, Gopher+, and WAIS clients have a text-based user interface. Examples used in the following explanation are generalized Gopher sample pages. Details of the display differ among clients. At this writing, the top level menu of the FlyBase server looks like this:
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Root gopher server: flybase.bio.indiana.edu
1. Getting Started with FlyBase - A Brief Introduction
2. Genes/
3. Aberrations/
4. Transposons/
5. Clones/
6. Maps/
7. People/
8. Stocks/
9. References/
10. Searches/
11. Images/
12. Genome Projects/
13. Allied Data & External Databanks/
14. Documents, Nomenclature & News/
15. Alternative Views of FlyBase/
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Items followed by / are subdirectories, or folders; selecting these will display the contents of that directory. Items with an extension, such as .txt, followed by a date and size, are files; selecting these will display the contents of the file on your screen. Once displayed, files can be saved to disk, printed, or e-mailed to an address you provide. What you need to type to accomplish a particular task depends on your browser; read the documentation for your browser, or try typing your browser's help command.
Selection of the Genes folder, for example, returns this menu:
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Genes
1. Search FlyBase Genes <?>
2. Search FlyBase Genes with options/ <??>
3. Search FlyBase Alleles/ <??>
4. Expression Pattern Search <HTML>
5. SymbolSearch <HTML>
6. All-genes-by-map-location/
7. All-genes-by-gene-symbol/
8. Map of Genes <HTML>
9. Gene order maps/
10. Interactive Fly hierarchy: cross-index to FlyBase genes <HTML>
11. Function and Structure/
12. Wild Stocks/
13. Genes Documentation (html) <HTML>
14. Genes Documentation (text)
15. Genes-search-help [15Aug96, 3kb]
16. cytosearch.hform [9Oct97, 4kb] <HTML>
17. cytosearch_global.hform [27Aug97, 1kb] <HTML>
18. fbalquery.hform [20Nov97, 16kb] <HTML>
19. fbgquery.hform [20Nov97, 69kb] <HTML>
20. gene-synonyms.txt [20Nov97, 941kb]
21. genes-data-updated-9603 [20Nov97, 1kb]
22. genes.txt [20Nov97, 50498kb]
23. synonyms.doc [18Jul97, 2kb]
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Items marked <HTML> are not viewable with your browser. Items marked <?> are simple queries available to all clients in this category. Those marked <??> are interactive forms that are accessible only to Gopher+ users.
Gopher Search Queries
The search engine behind FlyBase searches is now SRS. FlyBase files that have been indexed to allow searching include Genes, Aberrations, Clones, People, Stock lists, FlyBase documentation, News archives, and References. Searches are accessible through either the Searches menu item in the top directory, or from the relevant subdirectory.
Selection of a simple query such as item 1 in the menu above returns a screen onto which you type one or more keywords. The keyword(s) you provide will be compared to an index of all words that appear in the relevant file. A list of records that contain your keyword(s) will be returned. Select an item from the list to see the complete record.
Keyword options
When more than one keyword is provided without logical operators FlyBase returns records that contain all of the keywords. To find records that contain any of your keywords use 'or' between each pair of words. To find records that have one keyword but not another, use 'not' between pairs of words ('or' and 'not' operations cannot be combined). The wild card character * (asterisk) can be used for leading or trailing characters (e.g., a search of Stocks for *bxd* will find stocks that have either aberrations or alleles that include bxd in the symbol).
When multiple records are found the page returned to your screen contains a list of record titles followed by the 'Select items to return as one document <??>' option. Select a title to view a single record, or choose the 'Select items' option. This option allows you produce a single file containing some or all of the identified records. To create a file with a subset of the records found, note the record numbers you wish to include (this is the number in parentheses to the left of the record title), select this item, and then fill in the numbers of the items to include in the file. Typing 1..4, leaving all other options on the default setting, will produce a text file with records 1 through 4, and display this file on your screen. You can then print, copy, or e-mail the file using the commands appropriate to your browser.
The ability of Gopher+ clients to process forms allows more specific search queries to be constructed using the query with options form. In this way simple searches can be made more specific by limiting the search for keywords to specific fields. Complex questions can be asked by providing multiple field-specific search criteria with appropriate logical operators.
The options form - a Genes example
As with other Gopher forms, move the cursor from field to field with the tab key; press ENTER only when you have completed the form. The interactive fields in the Genes dialog, and the actions taken on a keyword(s) placed in each field are:
As with the simple searches, the default logical operator for multiple keywords in a single field, or single keywords in multiple fields, is 'and'. Records that meet all of the criteria will be returned. Use * as a wild card.
Example 1: The keyword Ubx in the Search for? field will produce a long list of records (currently 101 items) that contain this gene symbol somewhere in the text. Placing the same keyword in the Gene field of the dialog form finds only the Ubx record (note: to see fusion genes involving Ubx, use wild cards, *Ubx*).
Example 2: The keyword lethal in the Phenotype field plus the keyword 20F in the Max. Cyto. Location field, with the Class set to 'all' or 'genes', finds all of the genes on the X chromosome for which lethal alleles are known.
The query results and options are the same as those described above for the simple search.