From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Newsgroups: bionet.molbio.genbank
Subject: Re: Easy access to GenBank updates.
Date: 23 Jan 93 08:34:23 GMT
Reply-To: doelz@urz.unibas.ch
Distribution: bionet
Organization: EMBnet Switzerland [BASEL]

In article <1993Jan22.215415.16856@welchgate.welch.jhu.edu>, danj@welchgate.welch.jhu.edu (Dan Jacobson) writes:
|> In article <1993Jan22.180612.29502@comp.bioz.unibas.ch> doelz@urz.unibas.ch writes:
|> >My experience with GOPHER is that the retrieval of database information is 
|> >insufficient for particular aspects due to the weakness of the underlying
|> >WAIS engine. As we receive hundreds of GOPHER requests for EMBL , I checked
|> >the logs and found that many people try furiously to narrow the result list
|> >without actually achieving much. Its actually a good start but much is left 
|> >to be desired wrt queries. 
|> >
|> 
|> I'll just add that the searches at IUBio, Harvard (AAtDB, ACEDB), and those
|> searches here at Hopkins support booleans (and, or, not), wildcards (*), 
|> and phrase searches ("  ").  These are using Wais code which Don Gilbert 
|> (and the usgs) modified.  The Searches at NIH support "and" but not wildcards
|> or phrase definitions.  These allow the user to narrow the search down 
|> significantly.
|> 

Agreed - with the small BUT that these queries are no longer asked in an 
intuitive fashion so that the 'rare' user "Joe Biologist" might well be 
unable to remember what the syntax is. I was more referring to the fact 
that you can neither search specific fields (unless they are particularly 
indexed), nor specific combinations of search sets. Further, I would like to 
have repetitive questions on a once evaluated set. That is what I called 
insufficient in GOPHER/WAIS searches - you need to be a boolean expert 
and know about the restrictions quite well before you achieve this with 
a Gopher type WAIS query. Also remember that the Z39.50 protocol had booleans
in it but the WAIS implementation we all use (from Thinking machines) has this 
one castrated so that hacks outside of the protocol at the receiving side 
are necessary to reintroduce booleans (that's at least the status where I 
looked at the code last time - it might have changed since). 

As a general matter of criticismi towards GOPHER/WAIS, a FULL-TEXT search 
(and this is what WAIS does) is restricted to the siginficance of the 
text, and the redundancy contained therein. This is the wrong approach for 
factual data but excellent for journals and references. 

As I said, GOPHER/WAIS is an excellent start, and might nne to be improved 
in the future. 
  
Thure Etzold (at EMBL) has written a Sequence Retrieval System (called SRS) 
which is currently released as Version 3.0; it permits most of the search 
types mentioned before. The only current restrictions are VAX/VMS and non-
networked operation, this is that you need to telnet to the site where the
anonymous SRS is installed. There is such a site in Europe, use GOPHER to 
figure out where ( :-) ) and this is a huge success for querying EMBL, 
PIR and SWISSPROT data. 

If you call it ancient to do such a  telnet session remember that with a 
GOPHER/WAIS engine the machine blamed most is the remote server. Network-
wise the solution might be ancient but trafficwise it is merely identical. 

Regads 
Reinhard 
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