IUBio Archive biology data searches via WAIS and Gopher

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Wed Nov 4 16:03:33 EST 1992

This is a summary of new biology data searching and retrieval offerings
at the IUBio Archive (Internet host ftp.bio.indiana.edu).  These
data are now available via a Wide Area Information Server, WAIS, as
well as via Internet Gopher.

General WAIS source to
IUBio Archive of Biology software and data

   :version  3 
   :ip-address ""
   :ip-name "ftp.bio.indiana.edu"
   :tcp-port 210
   :database-name "INFO"
   :cost 0.00 
   :cost-unit :free 
   :maintainer "archive at bio.indiana.edu"
   :description "
This WAIS service includes several indexed Biology information sources,
including Genbank nucleic acid gene sequence databank, Drosophila genetics
BioSci/Bionet network news, and others. 

     = = = = = = = = = = = = = = = = = = = = = = = =

This WAIS service sports several zippy modifications.  These include
boolean operators 'and' and 'not', partial word matches,
literal phrase matches, and extended number of results.

Boolean searches: The terms 'and' and 'not' are effective 
    in modifying the query.   For example,
    Query: red and green not blue
    Result: just those records with both the words 'red' and 'green',
            excluding all records with the word 'blue'.
Partial words:  The asterisk (*) applied at the end of
    a partial word will match all documents with words that 
    start with the partial word.  For example,
    Query: hum*
    Result: all records with 'hum', 'hummingbird', 'human',
            'humbug', etc.
Literal phrases:  If quotes (') or double quotes (\") surrounding
     a phrase, it will match that phrase exactly.  For example,
     Query: 'red rooster-39'
     Result:  only those records with the the full string
            'red rooster-39' will be matched.
These features can generally be mixed in a query, for example:
     Query:  'Df(32)-[34]red' and hum* not Brown

Results limit (Gopher only):  The maximum number of results that 
     are returned for a query is by default up to 100. 
     But you may set a higher, or lower, maximum by appending
     the greater than (>) symbol immediately followed by the
     number you wish at the end of your query.  For example,
     Query:  brown and cow* or "red rooster" >300
     Result:  up to 300 matches will be returned.
The program source to these modifications will be available via
Internet Gopher or anonymous ftp to ftp.bio.indiana.edu, in
folder IUBio Software+Data/util/wais/ as iubio-wais-8b5.tar.Z
(full source) or iubio-wais-8b5.tar.patches  for a difference or
patch file.  (This is not ready as of 4Nov92).

Short list of current IUBio Archive WAIS sources
(Note: These searches are also available via Internet Gopher
to ftp.bio.indiana.edu)

   :database-name "arcdocs"
   :description "
This is an index of abstracts, readme, help and related information
on the IUBio Archive of Biology Software and Data.  It is updated
approximately monthly.  Files described in these documents are
generally available via ftp or gopher to ftp.bio.indiana.edu.

   :database-name "fly-address"
   :description "
This is an index of the addresses for Drosophila researchers

   :database-name "fly-amero"
   :description "
Cytological features database.
This is a database of polytene chromosome sites that have been found to
bind antibodies to particular Drosophila proteins.

   :database-name "fly-clones"
   :description "

   :database-name "fly-din"
   :description "
This is an index of the electronic Drosophila Information Newsletter.

   :database-name "flybase"
   :description "
This is an index of the Drosophila database, FlyBase, as maintained
by Micheal Ashburner.

   :database-name "flystock-bg"
   :description "
This is an index of the Drosophila fruitfly stocks maintained
by the stock center at Bowling Green USA.

   :database-name "flystock-bl"
   :description "
This is an index of the Drosophila fruitfly stocks maintained
by the stock center at Bloomington USA.

   :database-name "flystock-um"
   :description "
This is an index of the Drosophila fruitfly stocks maintained
by the stock center at Umea Sweden.

   :database-name "genbank"
   :description "
This is an index of the Genbank databank of gene sequences:
Genetic Sequence Data Bank, NCBI-GenBank Flat File Release 73.1
86626 loci, 110208764 bases, from 86626 reported sequences

   :database-name "gbnew"
   :description "
This is an index of updates sinces the latest full release of Genbank,
the databank of all known gene sequences. It is updated weekly 
from the update files maintained by NCBI at ncbi.nlm.nih.gov.  

   :database-name "journals"
   :description "
This is an index of the table of contents of several biology

   :database-name "methods"
   :description "
This is an index of a collection of materials and methods recipes
for molecular biologists.  

   :database-name "netnews"
   :description "
This is an index of news articles from the BioSci/Bionet newsgroups,
as well as the Sci.Bio Usenet group and the bitnet.listserv.info-gcg

   :database-name "prosite"
   :description "
This is an index of the PROSITE dictionary of protein sites and 
patterns, as produced by Amos Bairoch.

   :database-name "redbook"
   :cost 0.00 
   :cost-unit :free 
   :maintainer "archive at bio.indiana.edu"
   :description "
This is an index of the book 'The Genome of Drosophila melanogaster'
by Dan Lindsley and Georgina Zimm.

Don Gilbert                                     gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405

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