From owner-bio-srs@hgmp.mrc.ac.uk Thu Apr 19 10:11:27 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7AC3C17AEB for ; Thu, 19 Apr 2001 10:11:26 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E06E617B5A for ; Thu, 19 Apr 2001 10:11:17 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 36B4A17AEB; Thu, 19 Apr 2001 10:07:59 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7C41617AC6 for ; Mon, 16 Apr 2001 12:14:50 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4C4FA17A8B for ; Mon, 16 Apr 2001 12:14:47 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA02248 for bionet-software-srs@net.bio.net; Mon, 16 Apr 2001 12:14:46 +0100 (BST) To: bionet-software-srs@net.bio.net From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: dbfetch - a CGI script for db entry retrieve Organization: EMBL - EBI Message-ID: <3ADAD425.68B652B8@ebi.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 987419686 2241 193.62.199.73 (16 Apr 2001 11:14:46 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: Mon, 16 Apr 2001 11:14:46 +0000 (UTC) X-Mailer: Mozilla 4.72C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en Date: Thu, 19 Apr 2001 10:07:59 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk ANNOUNCEMENT ================================================================ dbfetch ================================================================ a generic CGI program to retrieve biological database entries in various formats and styles (using SRS) ================================================================ by Heikki Lehvaslaiho ABSTRACT The program dbfetch is a perl CGI.pm-based script to serve database entries from up-to-date servers. It an extension of a interface used by the EBI script emblfetch. Serving raw sequence entries via http protocol makes it easy to create application programs accessing any sequences by their id, only. BACKGROUD I started to write this program with these specifications in mind: 1. Retrieve biological database entries over the Web based on unique entry IDs. 2. Offer consistent, platform and database engine independent interface. 3. Easy-to-write URL syntax where the ID is simply added to end. 4. Serve entries not only in HTML but also in raw, easy to parse text-only format. 5. Modular, expandable structure. Although the underlying database engine used in this script is SRS, the program can easily be modified to access other indexing systems (e.g. through the EMBOSS entret program). This script is NOT (at the moment) offering free text or keyword searches. Most importantly, this approach is not dependant on some heavy hard to maintain technology (CORBA). All it needs is a http connection and a parser for a database ASCII format. These parsers are now available in various open source projects (bioperl, biopython, biojava). USAGE Casual users need simple ways to access and browse database entries on the web. The HTML form-based interface caters for these users. Increasingly, users of bioinformatics services write small programs to analyze sequence and other database entries. However, it is difficult to maintain locally up-to-date databases and, in a larger environment, make those databases visible to all users. dbfetch makes it easy to access database entries from anywhere. As a first step, BioPerl modules Bio::DB::EMBL use dbfetch to retrieve data into Bio::Seq objects. The whole process is writable in three lines of BioPerl code: use Bio::DB::EMBL; $embl = new Bio::DB::EMBL; $seq = $embl->get_Seq_by_acc('J02231'); # do what needed to the entry print "seqid is ", $seq->id, "\n"; Currently Bio::DB::SwissProt accesses swissprot entries from the Expasy server and users can point their requests to its mirrors. This Expasy script has limitations (not serving TREMBL entries) and not it is not available to other databases. dbfetch tryies to overcome these problems. EXTENSIBILITY The dbfetch uses local SRS calls to retrieve entries. Each style (html or raw) is defined in its own subroutine. The details about each database (name, update database name, id field names, format) is kept in a global hash. An other hash stores a regular expression to retrieve a unique identifier from an entry. These two hashes and the subroutine building the web page are the only places that need to be touched when a new database is added. After modification it is advisable to run the dbfetch from command line to trigger a subroutine which check the two hashes for consistency. WHAT YOU COULD DO Please install dbfetch to your local server and let me know that it is available for inclusion into bioperl modules. Bioperl and related open source projects (e.g. biojava and biopython) have so far focused on sequence analysis. dbfetch makes it easier than ever to work with other data types, If you are willing to create or have suitable code for parsing and creating objects for other formats, please join in. To start with, the BioPerl project would welcome classes to store an manipulate literature reference (Medline) and protein structure (PDB) data which are database entries served by the current EBI dbfetch script. AVAILABILITY The dbfetch script is running at: http://www.ebi.ac.uk/cgi-bin/dbfetch It is available under Perl artistic license from the BioPerl (http://bioperl.org) CVS repository or directly from: http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/scripts/DB/dbfetch?cvsroot=bioperl and in due course in the next release (0.8) of BioPerl. From owner-bio-srs@hgmp.mrc.ac.uk Mon Apr 23 10:21:08 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 213DE17AC6 for ; Mon, 23 Apr 2001 10:21:05 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CA5F917ACE for ; Mon, 23 Apr 2001 10:21:02 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 381FD17AC6; Mon, 23 Apr 2001 10:20:54 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DA98117A70 for ; Fri, 20 Apr 2001 16:25:19 +0100 (BST) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9DF6D17A63 for ; Fri, 20 Apr 2001 16:25:13 +0100 (BST) Received: from guppy.vub.ac.be (guppy.vub.ac.be [134.184.129.2]) by sprettur.isnet.is (8.11.1/8.11.0/isnet) with ESMTP id f3KFP9T57994 for ; Fri, 20 Apr 2001 15:25:11 GMT (envelope-from news@vub.ac.be) Received: from snic.vub.ac.be (snic.vub.ac.be [134.184.129.20]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id RAA18653; Fri, 20 Apr 2001 17:24:28 +0200 (MET DST) for Received: (news@localhost) by snic.vub.ac.be (8.9.3/%I%.0.ap (snic.test)) id RAA26440; Fri, 20 Apr 2001 17:25:02 +0200 (MET DST) for bionet-software-srs@moderators.isc.org To: bionet-software-srs@moderators.isc.org From: Guy Bottu Newsgroups: bionet.software.srs Subject: what about transfac ? Organization: Belgian EMBnet Node Message-ID: <9bpkce$n20$1@snic.vub.ac.be> X-Trace: snic.vub.ac.be 987780302 23616 134.184.15.23 (20 Apr 2001 15:25:02 GMT) X-Complaints-To: usenet@snic.vub.ac.be NNTP-Posting-Date: 20 Apr 2001 15:25:02 GMT User-Agent: tin/1.4.3-20000502 ("Marian") (UNIX) (SunOS/5.7 (sun4u)) Date: Mon, 23 Apr 2001 10:20:54 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear colleagues, For the moment a number of public SRS servers have the TRANSFAC database version 4.0. As you might have noticed, there is now a version 5, but the copyright of TRANSFAC is owned by Biobase and it seems that not only must you pay to have a local copy, it is also forbidden to make it available to third parties. This will have a consequence for our SRS servers. Anyone a comment ? Dr. Guy Bottu