[Biophp-dev] Progress! Eutils ESearch and ESummary

S Clark biophp-dev@bioinformatics.org
Thu, 24 Apr 2003 13:55:20 -0600

They can use a little work to better abstract them, and they could stand some
more testing, but I've finally had time to sit down and work on
them.  I've just uploaded semi-official ESearch and ESummary
interface modules, along with a support modules (a simple class for
"POST"'ing queries and returning the "file"handle for the response, 
and a "generic" xml parser class designed to work off of filehandles), and a
simple example query program that uses them (pass the example program a search
query, e.g. 

php esearch_test.php "Cheese AND Chocolate" 

and it does a search, returns any ID's it gets back (up to the default of 25),
and then fetches summaries of each one and displays them.)

Unlike EFetch, it looks like ESearch and ESummary return the data in the same
general layout and same format regardless of which DB you are searching, so
it OUGHT to work with any of them (pubmed, OMIM, nucleotide, etc.)  I've given
it brief tests using pubmed, nucleotide, and taxonomy databases so far, and
it seems to work fine.  EFetch will be a bit more involved, since the "full"
information format varies between different databases - possibly we'll end up
with a "generic" EFetch class which will be "extended" to make separate 
EFetch_pubmed and EFetch_taxonomy (etc.) classes...

Nothing fancy, but it works.  No specific documentation for them yet, but
the ESearch and ESummary classes ought to be easy to figure out from the
example and source (some basic documentation will be forthcoming.)

As always, comments, suggestions, and huge cash prizes are welcome...