Re: Any freely-available cancer pathology databases?

"Mike" <[EMAIL PROTECTED]> wrote in message news:<[EMAIL PROTECTED]>...
> Anyone know of any freely-available, searchable, cancer pathology databases
> (generic or, preferrably, breast cancer specific)?  I'd like to be able to
> perform queries
> based on certain characteristics, such as BRCA1 mutations, P53
> overexpression, etc.  Something like a database of pathology reports.
> 
> Thanks,
> 
> Mike

As Anita mentioned, PubMed (www.ncbi.nlm.nih.gov) is probably the
easiest tool to use for such searches. It is a huge database of
bibliographic references to over 11 million articles from 1966 to the
present. Most articles have abstracts and some have links to free
full-text versions. The articles can be textword-searched using
Boolean operators, and they have also been indexed by subject
according to a controlled thesaurus of over 35,000 terms qualified by
subheadings. There are also about 200,000 chemical terms to which
individual drugs and chemicals have been mapped (avoiding the need to
textword search all the chemical and trade names of a particular drug
or all the synonyms for a particular protein, for example). This is a
great advantage, since it quickly becomes tedious to AND-together all
the possible textwords for something like breast cancer (breast cancer
AND breast carcinoma AND breast neoplasms AND breast neoplasia AND
mammary cancer AND mammmary carcinoma AND mammary neoplasm AND all the
plurals of those, etc.). There are also handy headings for concepts
like "disease free interval," "treatment outcome," "survival
analysis," various types of clinical trial and epidemiologic study
design, etc., so if you only want disease-free survival rates for
multicenter, double-blind, randomized controlled trials with a
follow-up period for brachytherapy of prostate cancer versus
transurethral prostatectomy, for example, you can get that all in one
step instead of fussing with a zillion textwords and rooting through a
pile of false drops. If you select MEDLINE from the types of format
(default is called CITATION), you can see where an article has been
indexed and use some of those indexing terms for additional searches,
or you can hit the Related Articles link and let the system do it for
you. There are also features linking specific proteins and chemicals
to other databases, especially all the nucleotide and protein sequence
databanks, the LocusLink utility that links all articles about
individual gene products from humans and several other major species
to all the other databases in the system, etc. Depending on what you
are trying to do (check on progress in a particular disease? general
research on oncogenes?), you will be able to tailor your searches to
pick up the features of interest to you. If the article you want is
not available free through PubMed Central, you can usually get it
through a local medical library or ask your public library to order a
copy from the National Library of Medicine.  I can usually help out
with ideas for search strategies to find particular things of
interest, since I've worked for this database for 25 yrs.
Let me know if I can be of help.

Helen Stanbro 
P.S. If other readers are surprised to hear from me after a
several-month hiatus, my apologies! Our computer system was
overwhelmed by virus attacks and we have had to re-do the whole system
and drop our former our Earthlink e-mail service entirely. I'm only
just now figuring out how to access newsgroups through the new system,
but if this test-posting goes through, perhaps I'll be able to
participate again.