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

[Chris Fields]

Thanks Mauricio.  I think the only thing of impact will be the BLAST+ stuff (and Mark has developed a wrapper for it).  We'll need to update the SearchIO parser, so any BLAST+ output examples would be tremendously helpful.

chris

On Feb 5, 2010, at 9:48 AM, Mauricio Herrera Cuadra wrote:

> 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
> 
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