Clever 3.1 available (an Entrez access tool)

Pierre Rioux riouxp at megasun.BCH.UMontreal.CA
Thu Mar 28 14:48:03 EST 1996


CLEVER - COmmand Line Entrez VERsion available
----------------------------------------------

The latest version of the "clever" program for command line
access to the Entrez databases is now available to all.

What is it?
~~~~~~~~~~~

    clever is a character-based version of NCBI's Entrez program. It is an
    interactive tool that allows easy browsing of the Entrez database.
    It is also a batch tool that can be used as a search engine by
    other applications to retrieve records from the database automatically.
    A simple command-line interface allows users to write "scripts" that
    can search, retrieve and save information in many different formats.

Revision information (for the past year):
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Version 3.1 (still)
    January 1996
      - Added the AllowNull option
      - Fixed a bug in the SaveUIDS command (would not detect write errors).

Version 3.1
    September 20, 1995
      - Recompiled using the lastest NCBI toolkit.
      - Version number no longer follows NCBI releases... :-|
      - Changed the GenBank output routine in print.c, since
        the NCBI toolkit has added a more elegant way of doing it.
        BUG: The "showseq" option seems to be ignored for genbank output
        format (sequences are always shown).

Version 3.03
    February 3, 1995
      - Added the "Date" command, since Entrez now support this search field.

Version 3.02
    January 19, 1995
      - Worked around limitation in NCBI toolkit causing segmentation faults.

    December 20, 1994
      - Added the "all" keyword to the "pick", "not" and "union" commands.

Entrez is:
~~~~~~~~~~

       "a molecular sequence retrieval system developed at the
       National Center for Biotechnology Information (NCBI), a division of
       the National Library of Medicine (NLM).  Entrez provides an integrated
       approach for gaining access to nucleotide and protein sequence
       information, to the MEDLINE citations in which the sequences were
       published, and to a sequence-associated subset of MEDLINE.The sequence
       records are derived from a variety of database sources, including
       GenBank, EMBL, DDBJ, PIR, SWISS-PROT, PRF, and PDB.  With Entrez and a
       personal computer, you can rapidly search several hundred megabytes of
       sequence and literature data using techniques that are fast and
       intuitive."
               - Entrez User's Guide.

    The original Entrez program written by NCBI is a tool that uses
    windows, menus, and a pointing device; since not everyone
    has computers or terminals with graphics capabilities, clever was
    written to do the same work using only text input/output.

    In addition, the clever program permits BATCH access to the Entrez
    databases. Thus by use of script files, clever can be made to perform
    queries in batch mode.  In this way clever can be used as a "search
    engine" for any application which has as its input a set of database
    queries in clever format and can use as output any of the data in the
    Entrez databases (in any of the various formats supported by Entrez).

    clever comes in two flavors, "clever", which runs off local Entrez
    databases (e.g. on CD-ROM) and "nclever", which uses the network Entrez
    databases.


Platforms/Operating Systems
~~~~~~~~~~~~~~~~~~~~~~~~~~~

   clever will run on any hardware/operating system combination that
   are supported by the NCBI toolkit (for more information on the NCBI
   toolkit, send an email to toolbox at ncbi.nlm.nih.gov; for more information
   on Entrez, send mail to entrez at ncbi.nlm.nih.gov).  Presently this includes
   (from the README file supplied with the toolkit):

		* IBM 370
		* SUN (SunOS & Solaris)
		* DEC Alpha under OSF/1
		* DEC Alpha under AXP/OpenVMS
		* Macintosh A/UX
		* Microsoft Windows
		* DOS
		* CenterLine CodeCenter
		* Cray
		* Convex
		* Hewlett Packard
		* NeXT
		* IBM RS 6000
		* Silicon Graphics
		* ULTRIX
		* VAX/VMS

   Binaries for clever are supplied for some of these paltform/operating
   system combinations. See the relevant "Binaries" directory and
   "Obtaining Clever" below.

    
Obtaining Clever
~~~~~~~~~~~~~~~~

   clever can be obtained by gopher by pointing your gopher client at:

	megasun.bch.umontreal.ca

   and selecting:

	 -->  5.  Computational Molecular Biology- programs, documents, help/
 	  -->  9.  Entrez/
	   -->  1.  Clever- Interactive Command Line Entrez/

   or by anonymous ftp to:

	megasun.bch.umontreal.ca

   Files can be retrieved from the /pub/clever directory.


Installation Instructions
~~~~~~~~~~~~~~~~~~~~~~~~~

   There are two options for installing clever on your system.  The
   first is to obtain the code and compile it on your own system.
   obtain the cleverXXX.tar (where XXX is the current version number)
   from the Distribution directory in the repositories discribed above.
   Then read the INSTALLATION file in that directory.

   The second is to obtain a precompiled executable file.  Executables
   for some platforms are supplied in the Binaries directory located
   in the repositories described above.  Make sure you also have an
   appropriate ncbirc file available.  For unix systems, this will
   be a file called .ncbirc  and be located in your home directory.
   See the Entrez documentation for details on other computer platforms.
   A sample ncbirc file is provided in the Documentation directory.

   Note that to use clever you will need access to the entrez databases
   locally (e.g. on CDROM), and for nclever, you will need access granted 
   to your computer to read the Entrez databases at NCBI.  Send mail to
   entrez at ncbi.nlm.nih.gov for more information on obtaining the Entrez
   databases.


Further Information
~~~~~~~~~~~~~~~~~~~

   For more information about the clever project, send email to the
   Informatics Division of the Organelle Genome Megasequencing Unit
   at the Universite de Montreal:

	ogmp at bch.umontreal.ca

   All feedback welcome.


Credits
~~~~~~~

    This software was written by Pierre Rioux of the OGMP (Organelle
    Genome Megasequencing Project), Departement de Biochimie, Universite
    de Montreal (riouxp at bch.umontreal.ca) and William A. Gilbert, of
    the University of New Hampshire (gilbert at unh.edu) under the management of
    Tim Littlejohn, OGMP, Departement de Biochimie, Universite de Montreal
    (tim at bch.umontreal.ca).  Please send any comments/correspondence to
    ogmp at bch.umontreal.ca.  Thanks also to Jonathan Epstein at NCBI for
    providing some of the binary files of clever & nclever.
      
    The development of clever was supported by a grant from the Canadian
    Genome Analysis and Technology Program (CGAT).




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