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xembl wais source

David Steffen steffen at mbir.bcm.tmc.edu
Sat Feb 15 13:04:03 EST 1992

Rainer.Fuchs at EMBL-HEIDELBERG.DE writes:
>After playing with WAIS for a while I was not convinced that it is the
>optimal solution for the particular problem of finding an entry in a sequence
>database. Seems to be sort of overkill because in most cases you would like
>to limit your search to certain fields such as Authors, Keywords, Species,
>Accession#, etc. This is exactly what you *cannot* do with WAIS

I think this is an excellent description of a major limitation of
WAIS.  I agree 1000% with your analysis WRT using WAIS to search EMBL,
and have found this to be a limitation in other cases as well.  The
unique and powerful features of WAIS (e.g. "get me more articles like
this one") rarely work in my experience, and the absence of being able
to limit searches to fields and to do boolean searches are sorely
missed.  I find WAIS suboptimal but acceptable for searching the
bionet newsgroups, and very suboptimal for searching OMIM.  The best
thing I can say about WAIS is that since the introduction of WAIS,
many more databases have become available.  I would much rather have
the bionet newsgroups and OMIM and even EMBL available by WAIS than to
have them unavailable.  I had decided to accept and even encourage
WAIS because I saw it as becoming a standard, a standard which
appeared to encourage the making available of databases.  However,
this "standardization" seems to be coming apart recently; e.g. the
appearance of gopher.  That being the case, I think it would be VERY
worth while for those of us in the biological community to initiate a
discussion on the advantages and disadvantages of the various
potential standards, and the advantages and disadvantages of having
one standard vs. having multiple coexisting standards.  I would
propose we include the following potential standards in our
(I have used WAIS, GOPHER, and IRX, and like IRX best).

I have virtually no experience setting up databases for any of these,
so I would very much like to hear comments from those who do have such
experience; if users such as I were to succeed in pushing a standard
that made setting up the databases very hard, I suspect we would be
punished with a dearth of databases to use.

So, any interest in a discussion?

Questions to start the ball rolling:

What potential standards should be added to the above list?

Should we try to settle on a single standard, or should we have
multiple coexisting standards, each used where it is the most

Which of the above potential standards is easiest/most powerful for

Which of the above standards is easiest for the implementers of

David Steffen
Department of Cell Biology, Baylor College of Medicine, Houston TX 77030
Telephone = (713) 798-6655, FAX = (713) 790-0545
Internet = steffen at mbir.bcm.tmc.edu

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