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).
