EMBL-EBI Web Services

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====== News (2009) ======

[[..:News|Current]]

==== 2010 ====

News for [[.:2010]].

==== 4th December 2009 ====

As detailed in the [[http://www.ebi.ac.uk/embl/Documentation/forthcomingchanges.html|EMBL-Bank Forthcoming Changes]] entries in the ANN data class in EMBL-Bank will be migrated into the CON data class in the next release (102; Dec 2009). Thus the ''emblann'' database in WSDbfetch ([[services:dbfetch|SOAP]] and [[services:dbfetch_rest|REST]]) will no longer be available once the release becomes available.

Queries which used ''emblann'' as the database will need to use ''emblcon'' or ''embl'' to get the equivalent data.

==== 17th November 2009 ====

REST and SOAP document/literal services for sequence similarity search and multiple sequence alignment are now available, see the following pages for details of the services:
  * REST
    * [[services:sss:fasta_rest|FASTA (REST)]]
    * [[services:sss:ncbi_blast_rest|NCBI BLAST (REST)]]
    * [[services:sss:psiblast_rest|PSI-BLAST (REST)]]
    * [[services:sss:psisearch_rest|PSI-Search (REST)]]
    * [[services:sss:wu_blast_rest|WU-BLAST (REST)]]
  * SOAP document/literal
    * [[services:sss:fasta_soap|FASTA (SOAP)]]
    * [[services:sss:ncbi_blast_soap|NCBI BLAST (SOAP)]]
    * [[services:sss:psiblast_soap|PSI-BLAST (SOAP)]]
    * [[services:sss:psisearch_soap|PSI-Search (SOAP)]]
    * [[services:sss:wu_blast_soap|WU-BLAST (SOAP)]]

Note: the SOAP RPC/encoded services will be phased out in favor of the SOAP document/literal services over the next year, so we encourage developers to evaluate the new services, and begin migration of their usage as soon as possible.

==== 1st October 2009 ====

WSDbfetch ([[services:dbfetch|SOAP]] and [[services:dbfetch_rest|REST]]) has been updated to provide two generic formats for the major sequence databases:
  - ''annot'': returns the annotation in the default format, the sequence is not included.
  - ''entrysize'': returns a tab delimited table describing the size of the entry. The four fields are:
    - entry identifier (in DB:ID format)
    - size of the annotation (bytes)
    - length of the sequence (nt or aa)
    - an estimate of the whole entry size (annotation size + sequence length)
These formats provide a mechanism to control the amount of data retrieved for an entry, this is important when dealing with databases which can contain very large entries (e.g. EMBL-Bank and RefSeq).

==== 30th September 2009 ====

[[services:clustalw2|WSClustalW2]] has been updated to use ClustalW 2.0.12. 

With the release of Ensembl release 56 WSDbfetch ([[services:dbfetch|SOAP]] and [[services:dbfetch_rest|REST]]) support for Ensembl Gene (''ensemblgene'') has been extended to restore support for the following formats: EMBL, GenBank, CSV, tab delimited, GFF and GFF 3.

==== 3rd September 2009 ====

[[services:ncbiblast|WSNCBIBlast]] has been updated to use NCBI BLAST 2.2.21. 

==== 20th August 2009 ====

[[services:tcoffee|WSTCoffee]] has been updated to use T-Coffee 8.06. 

==== 31st July 2009 ====

C#, Java and Perl sample clients are now available for the [[services:EB-eye]] service. See the [[services:EB-eye|service page]] for more details.

==== 29th July 2009 ====

REST web services for [[http://www.ebi.ac.uk/QuickGO/WebServices.html|QuickGO]], an interface to the [[http://www.geneontology.org/|Gene Ontology]] (GO) and [[http://www.ebi.ac.uk/GOA/|Gene Ontology Annotation]] (GOA) databases, are now available. 

==== 27th July 2009 ====

Sample Perl client using [[http://www.soaplite.com/|SOAP::Lite]] is now available for the [[services:eb-eye|EB-eye web service]].

==== 13th July 2009 ====

[[services:clustalw2|WSClustalW2]] has been updated to use ClustalW 2.0.11. 

==== 9th July 2009 ====

[[services:fasta|WSFasta]] has been updated to use FASTA 35.4.8. 

[[services:ncbiblast|WSNCBIBlast]] has been updated to use NCBI BLAST 2.2.20. 

==== 22nd June 2009 ====

The [[services:InterProScan|WSInterProScan]] service now uses the faster and more accurate PatternScan method, by default, to perform PROSITE pattern searches. The older ScanRegEx method can be used by specifying it in the list of methods to be performed.


In most cases the only difference in the output is the replacement of the "ScanRegEx" method name with "PatternScan" for PROSITE pattern matches. If your are parsing the output and explicitly search for the ScanRegEx name you will need to update your parser to allow for the change in method name.

If you have comments or feedback regarding InterProScan, please let us know by using the [[http://www.ebi.ac.uk/support|feedback form]].

==== 15th May 2009 ====

The [[services:dalilite|WSDaliLite]] service has been changed to return a ZIP archive containing all the files generated by the program, rather then just the HTML index page. If you want the service to be able to return individual files please [[http://www.ebi.ac.uk/support/index.php?query=WebServices|contact us]] providing details of the relevant use case.

==== 15th May 2009 ====

[[services:interproscan|WSInterProScan]] and [[services:wublast|WSWUBlast]] documentation updated for the addition of service methods to get parameter information from the service. The C#, Java and Perl, [[clients:interproscan|WSInterProScan]] and [[clients:wublast|WSWUBlast]] have been updated to provide options to access this additional information.

==== 13th March 2009 ====

[[services:fasta|WSFasta]] has been updated to use FASTA 35.4.6.

==== 17th February 2009 ====

The WSDbfetch ([[services:dbfetch|SOAP]] and [[services:dbfetch_rest|REST]]) services have been updated to provide six new citation formats for [[http://www.ebi.ac.uk/Databases/MEDLINE/medline.html|MEDLINE]] entries. These are:
  - ''bibtex'': [[http://www.bibtex.org/|BibTeX]]
  - ''endnote'': [[http://www.endnote.com/|EndNote]] text format
  - ''isi'': ISI format, as used in [[http://www.isiwebofknowledge.com/|ISI Web of Knowledge]]
  - ''modsxml'': [[http://www.loc.gov/standards/mods/|MODS XML]]
  - ''ris'': [[http://www.refman.com/support/risformat_intro.asp|RIS]], as used by [[http://www.refman.com/|Reference Manager]] and [[http://www.procite.com/|ProCite]]
  - ''wordbibxml'': MS Word bibliography XML (see http://mahbub.wordpress.com/2007/03/22/deciphering-microsoft-office-2007-bibliography-format/)

These formats are provided using [[http://www.scripps.edu/~cdputnam/software/bibutils/|bibutils]], a set of open source tools for bibliography format interconversion.

==== 4th February 2009 ====

Advance notice: on 3rd March 2009 the database prefixes used in BLAST and FASTA results for the UniProtKB data will be changed to from "SW" to "SP" for UniProtKB/SwissProt and from "TREMBL" to "TR" for UniProtKB/TrEMBL. Searches against the whole of UniProtKB will return a mixture of these prefixes, indicating which entries come from the human curated section of the database.

==== 27th January 2009 ====

The MSD group has changed its name to the PDBe to reflect is close partnership with the wwPDB project. This change is also taken into account by the EB-eye:the domain name has been changed from 'msd' to 'pdbe'.

==== 14th January 2009 ====

Due to hardware changes at EBI the SignalP method in the [[services:interproscan|InterProScan service]] is currently failing. The problem is being investigated and we hope to have a fix in place soon. In the meantime we suggest running without the SignalP method.

**Update**: the SignalP method in the InterProScan service is now working again.

==== 2008 ====

News for [[.:2008]].
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