Has ENTREZ Changed?

Jonathan Epstein epstein at gold.nlm.nih.gov
Tue Nov 8 08:45:13 EST 1994

Craig Livingstone (cdl at bioch.ox.ac.uk) wrote:
> A colleague of mine noted this morning that a number of papers he
> previously knew to be included in the Medline subset of the Entrez
> database were no longer there.   A number of papers I would have
> previously expected to find in Entrez, I have recently only been 
> able to retrieve using either BIDS or Medline itself.   Is the subset
> of Medline in Entrez being trimmed?   If so this would be a great 
> pity as the link between the sequences in the protein/nucleic acid
> sections of Entrez and the literature which relate to them would 
> be being eroded - one of the most useful features of Entrez would be
> lost.

> Any more comments?

> Craig.

> ---------------------------------------------------------------------------------
> Craig D. Livingstone			        email:  cdl at bioch.ox.ac.uk
> Laboratory of Molecular Biophysics, 	    Telephone:  +44 865 275369 DAY
> University of Oxford,                             Fax:  +44 865 510454
> Rex Richards Building, 			       Mobile:  +44 850 003546
> South Parks Road, 
> Oxford OX1 3QU, U.K. 
>                                             WWW: http://geoff.biop.ox.ac.uk
> anonymous-ftp: geoff.biop.ox.ac.uk               http://sable.ox.ac.uk/~gliding
> ---------------------------------------------------------------------------------

Yes, Entrez has indeed changed; a message follows below which I sent last
week to the 800+ Network Entrez administrators.  In principle, your
Network Entrez administrator should have forwarded this information to
you, but I realize that sometimes this is impossible.  Note that (assuming
you're using Network Entrez), you still have as much MEDLINE available
as before, but you must configure to use "EntrezBigMed" to take advantage
of it.  Also note that "EntrezBigMed" is still considered to be somewhat
experimental, but it appears to be quite reliable.

Here's a more detailed recipe for switching back-and-forth between
the "Entrez" and "EntrezBigMed" services:
    Some of you are now using the EntrezBigMed server, which provides access
    to nearly six times as much MEDLINE data as the "Entrez" server.  While
    this is clearly a useful tool, please be aware that it is not yet in
    "final" release.  If you experience problems with the EntrezBigMed
    server being unavailable, please switch back to the Entrez server.  If
    you experience a reproducible problem, please report it to
    net-info at ncbi.nlm.nih.gov.  You can configure for EntrezBigMed and back
    again using the following procedure in the netentcf program:
      * Connect to the Dispatcher
      * Select Service-Specify
      * Select the Catalog button
      * Select "Entrez" or "EntrezBigMed"
      * Select the appropriate Resource from the bottom of the Catalog window
      * Accept this service/resource combination in the Service-Specify window
      * Attempt Service Request, and save the configuration
    You can also save copies of the NCBI configuration file (ncbi.ini,
    ncbi.cnf, ncbi.cfg or .ncbirc, depending upon your platform), and swapping
    them back-and-forth as necessary.

- Jonathan

------------------------- begin included message ----------------------------
Dear Network Entrez administrator:

Please pass the following information along to your Network Entrez users.

The data images for Entrez: Sequences 13.0 and Entrez: References 13.0
are now on line, and are available to Network Entrez users.  The CD-ROMs
containing these data will be received by most CD-ROM subscribers in
10-20 days.

The Entrez 13.0 CD-ROM release was more difficult than usual to produce
because it is the first Entrez release containing three CD-ROMs, resulting
in substantial software changes.  The expansion to three CD-ROMs was
necessary due to the continued rapid growth of molecular sequence data.

To avoid overflowing three CD-ROMs before October 1995, the MEDLINE subset
contained on Entrez 13.0 has been reduced from what appeared on Entrez
12.0 by 21%.  MEDLINE entries which are referenced within the sequence
databases are still included, as are MEDLINE entries which are closely
related to those entries.  "Closeness" in this case is determined using
Entrez's MEDLINE neighboring algorithm.

You can still obtain all of the Entrez 12.0 MEDLINE entries, and more,
using the EntrezBigMed service.  This service can be selected from
the 'netentcf' Catalog, which in turn can be accessed via the Service-Specify
button, after connecting to the Dispatcher.  Entrez 13.0 contains 168773
MEDLINE entries, but EntrezBigMed contains 1213424 entries.

The Entrez 13.0 dataset contains approximately 7% more sequence data than
the Entrez 12.0 dataset.

You can verify that you are using dataset 13.0 by selecting "About Entrez ...",
pressing the "More" button, and then reading the text window.

For a limited time, the Entrez 12.0 dataset will remain online.  Note
that if you have explicitly configured your computer to use version
Entrez 11.0 or earlier, then Network Entrez will not operate.  Please
review the configuration section of the Network Entrez README file if
you are in doubt.

No new Network Entrez client software will be distributed at this time.

The World Wide Web Entrez server (http://www.ncbi.nlm.nih.gov/Search/Entrez/)
also contains the Entrez 13.0 data.  A new paper which discusses and
compares the Entrez CD-ROM, Network Entrez and WWW Entrez is available at
URL http://atlas.nlm.nih.gov:5700/WWW2/WWW2_paper2.html.  This paper
contains a summary chart comparing these three types of Entrez; the chart
is likely to be of general interest.

As always, please let me know if you have any questions.

- Jonathan

Jonathan Epstein                                epstein at ncbi.nlm.nih.gov
National Center for Biotechnology Information   Phone: (301)496-2475
National Library of Medicine                    Building 38A, Room 8N805
National Institutes of Health                   8600 Rockville Pike
                                                Bethesda, MD 20894
------------------------- end included message ----------------------------

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