From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: No more interactive logins -> try Gopher
Summary: Internet Gopher
Organization: Biology, Indiana University - Bloomington
Date: Tue, 31 Mar 92 23:20:49 GMT

In article <INFO-GCG%92033114395679@UTORONTO.BITNET> GGUTMAN@UCIVMSC.BITNET writes:
>
>     The most recent "New From Genbank" newsletter (Vol. 5, No. 1) announces the
>impending end of the GenBank contract to Intelligenetics, and its assumption by
...
>     There is at least one important service which under current plans will be
>dropped, namely the ability to search the databases interactively through either
>NCBI (National Center for Biotechnology Information) as of October of this year.
>Most of the same services, and many new ones, will still be available to the
>scientific community following this changeover, including the mail-servers
>allowing searching and retrieval of sequences in the databases.
>
>     Expanding the capabilities of the mail-servers is fine, but at least for me
>this would not replace the value of interactive logins, brief though they are,
>for the kind of searching I often need to do.  I would encourage anyone

There is now another, perhaps better, alternative to IRX at genbank.bio.net.
This is searching Genbank and several other biology databases thru Internet Gopher,
for those of you with internet access (UCI.EDU is an internet address).
You need to pick up Internet Gopher software and install / have it installed
on your favorite computer.  Then you can search current Genbank, PIR, EMBL
and smaller databases for keywords, authors, subject matter, species, etc.
It isn't the same as IRX, but it is very fast, free, and easily accessible
with Gopher software & internet connections. 

Gopher software is available thru anonymous ftp to boombox.micro.umn.edu,
folder pub/gopher/ for several computer systems, or from ftp.bio.indiana.edu,
folder util/gopher.  Since the notice below about 5+ BioGophers have sprung
up around the world, including an indexed PIR protein database at Univ. Houston
(Dan Davison) and and indexed EMBL database at Biozentrum der Universitaet (Reinhard
Doelz).

Here is the full notice from bionet software a while back:

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Newsgroups: bionet.software
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Genbank key search & fetch thru IUBio Gopher hole (long)
Organization: Biology, Indiana University - Bloomington
Date: Mon, 17 Feb 92 02:33:13 GMT


This rather long note is in response to questions about what to make
of Internet Gopher, WAIS and other Internet information searching
methods, and specifically how does this relate to Genbank keyword
searching and entry fetching, as compared with the IRX service at
genbank.bio.net, and perhaps to e-mail services.

I see Gopher as potentially the best of the lot, though it doesn't 
exclude the usefulness of any of the others.  But I don't want to 
debate merits now, rather to let you know there is now a Gopher server 
for Genbank that you can try and compare with the others.

Internet gopher is pretty easy to learn to use.  Gopher and WAIS provide 
somewhat different protocols for serving information out to clients over the
Internet.  Gopher is strong on browsing -- you can find new things just by
pointing at lists.  WAIS is strong on linking together many dispersed
servers to answer a given question.  I think they both are good, but I
think Gopher is an order of magnitude easier to learn, and install, and 
consequently will be more useful to more people.  

They both provide simple client and server programs, including
a way to index text files and to query that index for key word searches. 
Gopher in fact relies on the WAIS indexing and searching routines.  However,
both of these protocols encourage customization of the searching service
as needed.  

I've done some of that with the Gopher server at IUBio archive.  Over the
weekend, I installed the complete NCBI/GenBank FlatFile release, indexed
it with a modified waisindex, and put up questions in the gopher hole
to use this.

You can, for instance, fetch a single sequence entry by providing
its accession number or locus name as the question:
   Genbank fetch by accession number <?>
   X51902
   -- will fetch the sequence "Alcaligenes eutrophus gene for 10Sa RNA"

Or you can provide key words:
  Genbank search by def/key/source/author <?>
  Acanthamoeba castellanii
  -- will list all sequences of that species of amoeba.

The boolean operator NOT can be used to restrict your selection keys:
  Genbank search by def/key/source/author <?>
  Acanthamoeba castellanii and not RNA
  -- will list/fetch all of that species excluding RNA sequences

The boolean operators AND and OR are not recognized as operators.
However, this search software will weight an entry by the number
of word matches, so that in a search with two or more words, those
entries which match the most words will appear at the top of the list
(the equivalent of an AND search), and those entries which match
only one word will be at the bottom (the remains of an OR search).

The currently installed Genbank is release 0.01 (January 1992) from
NCBI, which has some 62,807 sequence entries (nearly 200 megabytes
of sequence and descriptive data).  This is based on release 70 of
Genbank plus many entries from Medline added at NCBI.  It was
obtained by anonymous ftp to ncbi.nlm.nih.gov, cd ncbi-genbank.

The fields that are indexed from the Genbank Flatfile format are:
  Locus, Accession, Description, Keywords, Source, Organism, Authors,
  and Title.

The index files take up about 40 megabytes, compared to 190 megabytes
for the sequence files.  It takes about 15-20 minutes on a Sparcstation2
to index the sequences.  A search for a unique keyword like locus name
or accession number takes no perceptible time.  A typical keyword query 
with a handful of matches will take a few seconds, a bit longer if you request
hundreds or more matches.  This compares to about 4 hours for the GCG 
program stringsearch running on the same machine with the same query.

This software may be of interest to anyone with a Genbank flatfile 
on disk, and a few spare megabytes for indexing, to give thought to 
installing Gopher with this indexing software.   

The indexing/search software for the Gopher server has been modified from
the wais index/search release 8 b3 by Brewster Kahle, which was obtained
via ftp to think.com.   The modifications involve indexing for the
Genbank flatfile format, restricting indexing weights to one hit per
entry for any word, adding NOT boolean searching, and adding output
of long hit lists to a file for user's retrieval.  The max number of
hits to list and display can be selected be ending the question
with ">100.10" for instance to list to file the 100 best, and display 
on the gopher screen the 10 best matches.

As a reminder, Internet Gopher client and server software is available
via ftp to boombox.micro.umn.edu, in directory pub/gopher/

I've installed Gopher on the IUBio archive because it was easy to
install.  I probably won't be installing a WAIS server here, because to
be useful to WAIS, you must index files, and many of the files at this
archive don't lend easily themselves to that.

These genbank searching modifications will be available to others.

                         -- Don Gilbert
												 

Example using the gopher text terminal client:

% gopher ftp.bio.indiana.edu

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	Internet Gopher Information Client v0.7

                 Root Directory

          1.   About IUBio Gopher.
          2.  About IUBio Biology Archive.
          3.  Drosophila Archive/
          4.  Genbank  Readme.
          5.  Genbank fetch by accession number <?>
   -->    6.  Genbank search by def/key/source/author <?>
          7.  IUBio Software+Data/
          8.  Network News archive/
          9.  Other Gophers/

Index word(s) to search for: protozoa and not cdna 

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      Genbank search by def/key/source/author: protozoa and not cdna

          1.  V00002 Acanthamoeba castelani gene encoding actin I..
          2.  Y00624 A.castellanii non-muscle myosin heavy chain gene, partia.
          3.  J02974 Myosin IB heavy chain gene, complete cds..
          4.  M30780 A.castellanii myosin I heavy chain (MIL) gene, complete .
          5.  M60954 Acanthamoeba castellanii myosin heavy chain (HMWMI) gene.
          6.  K03053 Amoeba (A.castellanii) ribosomal RNA gene..
          7.  M34003 A.castellanii 5S RNA..
          8.  M13435 A.castellanii mature small subunit rRNA gene, complete..
          9.  M60878 B.bigemina merozoite surface protein (p58) gene, complet.
          10. K02834 Babesia bovis rearranging (BabR) locus, second repeated .
          11. X59604 B.bigemina gene A small subunit rRNA.
          12. X59605 B.bigemina gene B small subunit rRNA.
          13. X59607 B.bigemina gene C small subunit rRNA.
          14. M35557 C.campylum 5.8S ribosomal RNA..
          15. M35558 C.colpoda 5.8S ribosomal RNA..
   -->    16. Long list of matching items, count=100.  {max defaults to 100}

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Long list of matching items:

#  List of entries, and [match score], for search string:
#    'protozoa and not cdna'
#  The max number of entries in this list, and on display, can be
#  indicated at the end of your search string as, for example
#    'red and not blue >200'    to list up to 200, or
#    'red and not blue >500.50' to list up to 500, and show up to 50.
#
V00002 Acanthamoeba castelani gene encoding actin I.     [  5]
Y00624 A.castellanii non-muscle myosin heavy chain gene, partial cds.    [  5]
J02974 Myosin IB heavy chain gene, complete cds.         [  5]
M30780 A.castellanii myosin I heavy chain (MIL) gene, complete cds.      [  5]
M60954 Acanthamoeba castellanii myosin heavy chain (HMWMI) gene, complete
...
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Comparison of search strategies with the waisindex/search program and 
with the IRX program.

example data file:
------------------
blue flower sequence
blue, green flower sequence
blue, green, red flower sequence
black flower sequence
blue dog sequence
								
                 irx matches       	modified-wais matches
query            (unweigthed)  	       	(weighted, best at top)
-----      	-----------		----------------
blue    	blue flower		blue flower [10]
		blue, green fl.		blue, green fl.[10]
		blue, green, red fl. 	blue, green, red fl[10]
		blue dog		blue dog [10]

blue and green	blue, green fl		blue, green fl. [20]
		blue, green, red fl	blue, green, red fl [20]
					blue flower [10]
					blue dog [10]

blue or red	blue flower		blue, green, red fl [20]
		blue, green fl		blue flower [10]
		blue, green, red fl	blue, green flower [10]
		blue dog		blue dog [10]
						
blue and not green  blue flower		blue flower [10]
		blue dog		blue dog [10]

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

 

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