[BioRuby] Fwd: Changes to NCBI BLAST and E-utilities.

[Mauricio Herrera Cuadra]

Forwarding to the proper lists...

-------- Original Message --------
Subject: [O|B|F Helpdesk #889] Changes to NCBI BLAST and E-utilities.
Date: Fri, 5 Feb 2010 10:08:51 -0500
From: mcginnis via RT <support at helpdesk.open-bio.org>
Reply-To: support at helpdesk.open-bio.org
To: chris at bioteam.net, heikki at sanbi.ac.za, hlapp at gmx.net, 
jason at bioperl.org,        mauricio at open-bio.org


Fri Feb 05 10:08:51 2010: Request 889 was acted upon.
Transaction: Ticket created by mcginnis at ncbi.nlm.nih.gov
        Queue: support at open-bio.org
      Subject: Changes to NCBI BLAST and E-utilities.
        Owner: Nobody
   Requestors: mcginnis at ncbi.nlm.nih.gov
       Status: new
  Ticket <URL: https://helpdesk.open-bio.org/rt/Ticket/Display.html?id=889 >


Dear Colleague:

There are two changes I'd like to make you aware of.

As you may or may not have noticed, we have been working on a new C++ 
version of the BLAST binaries. In the coming months we will be moving 
the C++ binaries into prominence and (slowly) phasing out the C toolkit 
binaries.

There are many changes not least of which is a move to individual 
binaries for each program (blastn, blastp, etc).  We are not sure how 
many of your users use BioPerl with the BLAST binaries, my understanding 
is that many use BioPerl to to remote BLAST. However, there isa change 
to the BLAST results in Text and presumably HTML. This could have an 
effect on any parsers which scrape these formats and do not use XML. For 
obvious reason, we want to support only the XML format for parsing, but 
we thought we should give you heads up on this.
blast 2.2.22

Query: 3307 ------------------------------------------------------------ 
3307

Sbjct: 390  GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP 449

blast 2.2.22+

Query        ------------------------------------------------------------

Sbjct  390 
GSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGPEAFRGSGP  449

A single line of gaps lacks the Query numbering in the blast+ output. 
The C version of blast has numbering in this case. Sample alignment 
shown below. According to users the blast+ output without the numbering 
breaks bioperl parsers. Wehave heard forma few but I think they may be 
older parsers?
The second issue is a policy concerning E-utilities. This was announced 
on the utilities-announce at ncbi.nlm.nih.gov mail-list but you may not 
have seen it.

As part of an ongoing effort to ensure efficient access to the Entrez 
Utilities (E-utilities) by all users, NCBI has decided to change the 
usage policy for the E-utilities effective June 1, 2010. Effective on 
June 1, 2010, all E-utility requests, either using standard URLs or 
SOAP, must contain non-null values for both the &tool and &email 
parameters. Any E-utility request made after June 1, 2010 that does not 
contain values for both parameters will return an error explaining that 
these parameters must be included in E-utility requests.

The value of the &tool parameter should be a URI-safe string that is the 
name of the software package, script or web page producing the E-utility 
request.

The value of the &email parameter should be a valid e-mail address for 
the appropriate contact person or group responsible for maintaining the 
tool producing the E-utility request.

NCBI uses these parameters to contact users whose use of the E-utilities 
violates the standard usage policies described 
athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements. 
These usage policies are designed to prevent excessive requests from a 
small group of users from reducing or eliminating the wider community's 
access to the E-utilities. NCBI will attempt to contact a user at the 
e-mail address provided in the &email parameter prior to blocking access 
to the E-utilities.

NCBI realizes that this policy change will require many of our users to 
change their code. Based on past experience, we anticipate that most of 
our users should be able to make the necessary changes before the June 
1, 2010 deadline. If you have any concerns about making these changes by 
that date, or if you have any questions about these policies, please 
contact eutilities at ncbi.nlm.nih.gov.

Thank you for your understanding and cooperation in helping us continue 
to deliver a reliable and efficient web service.

I think you already adhere to this policy but should a user's script not 
meet these requirements, than the script will fail and requests will be 
turned away with an error message.

Scott D. McGinnis M.A.
NCBI/NLM/NIH
45 Center Drive, MSC 6511
Bldg 45, Room 4AN.44C
Bethesda, MD 20892
mcginnis at ncbi.nlm.nih.gov