Here is a quick summary of what worked and what didn't worked.
Doesn't work: (has at least the 3 problems described in this thread)
- Using BioMart 0.7's Perl API with the registry containing MartURLLocation's
(section 6.4 in http://www.biomart.org/other/user-docs.pdf)
Works:
- Using BioMart 0.7's Perl API with the registry
containing MartDBLocation's (section 6.4
in http://www.biomart.org/other/user-docs.pdf)
- Using BioMart's Web Services API – RESTful Access (section 6.6
in http://www.biomart.org/other/user-docs.pdf)
Hope this helps clarify.
________________________________
From: Syed Haider <[email protected]>
To: pip pipster <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Thursday, December 29, 2011 11:36 AM
Subject: Re: [BioMart Users] problem with getting sequence data
So, when does it not work ? i assumed from your first email that
webservice does not work for some sequences - correct ?
On 29/12/2011 16:06, pip pipster wrote:
> Hi Syed,
> FYI, just to clarify using direct Web Services (without going through the 0.7
> BioMart Perl API's) seems to work. For example, using the XML file below as
> a POST request. If you know of any serious bugs crossing db boundries with
> this approach please let me know. Thank you for your help!!
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query virtualSchemaName = "default" formatter = "FASTA" header = "0"
> uniqueRows = "1" count = "" datasetConfigVersion = "0.6">
> <Dataset name = "hsapiens_gene_ensembl" interface = "default">
> <Filter name = "with_protein_id" excluded = "0"/>
> <Filter name = "chromosome_name" value = "1"/>
> <Attribute name = "ensembl_gene_id" />
> <Attribute name = "ensembl_transcript_id" />
> <Attribute name = "chromosome_name" />
> <Attribute name = "strand" />
> <Attribute name = "external_gene_id" />
> <Attribute name = "5utr" />
> </Dataset>
> </Query>
>
>
>
>
> ________________________________
> From: Syed Haider<[email protected]>
> To: pip pipster<[email protected]>
> Cc: "[email protected]"<[email protected]>
> Sent: Thursday, December 29, 2011 10:24 AM
> Subject: Re: [BioMart Users] problem with getting sequence data
>
> Hi Phillipe,
>
> Web services are certainly the way to go forward except the current
> (v0.7) queries that span genomic sequences such as your request. These
> sequences seem to have a bug which is triggered only through the
> webservices. The v0.8 does not have the perl API, but an equivalent in
> Java, which is essentially identical to its webservice equivalent.
>
> Best,
> Syed
>
> On 29/12/2011 02:02, pip pipster wrote:
>> Hi Syed,
>> Thanks for the suggestion. I had to wait until the evening to try your
>> suggestion because my University's firewall apparently block the 53xx
>> ports. The results look more pormising using DBLocation. Also, when using
>> Web Services (instead of the BioMart Perl API), I seem to get the correct
>> results though I still have more testing to do. Would you expect Web
>> Services to be the more reliable mechanism when it comes to data integrity
>> issues such as this? I wonder if this is one of many reasons why Biomart
>> 0.8 may drop support (is that true?) for the BioMart PERL API's.
>>
>> Do you know why changing the Mart type to MartDBLocation works better than
>> MartURLLocation? Given the firewall issues I may have no choice but to
>> switch to using the Web Services method.
>>
>> Thank you,
>> Phillipe
>>
>> ________________________________
>> From: Syed Haider<[email protected]<mailto:[email protected]>>
>> To: pip pipster<[email protected]<mailto:[email protected]>>
>> Cc:
>> "[email protected]<mailto:[email protected]>"<[email protected]<mailto:[email protected]>>
>> Sent: Wednesday, December 28, 2011 1:14 PM
>> Subject: Re: [BioMart Users] problem with getting sequence data
>>
>> Hi,
>>
>> what happens when you use the MartDBLocation type connection params in
>> registry file, e.g:
>>
>> <?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE MartRegistry>
>> <MartRegistry>
>>
>> <MartDBLocation databaseType="mysql"
>> host="martdb.ensembl.org<http://martdb.ensembl.org>"
>> database="ensembl_mart_65" name="ensembl" displayName="ENSEMBL 65 GENE
>> (SANGER UK)" port="5316" schema="ensembl_mart_65" user="anonymous"
>> password="" visible="1" default="1" martUser=""
>> includeDatasets="hsapiens_gene_ensembl" />
>>
>> <MartDBLocation databaseType="mysql"
>> host="martdb.ensembl.org<http://martdb.ensembl.org>"
>> database="sequence_mart_65" name="seq" displayName="ENSEMBL 65 SEQ (SANGER
>> UK)" port="5316" schema="sequence_mart_65" user="anonymous" password=""
>> visible="1" default="1" martUser="" includeDatasets="" />
>>
>> </MartRegistry>
>>
>>
>>
>> Syed
>>
>>
>>
>>
>>
>>
>>
>> On 27/12/2011 21:49, pip pipster wrote:
>>> <?xml version="1.0" encoding="UTF-8"?>
>>> <!DOCTYPE MartRegistry>
>>> <MartRegistry>
>>> <MartURLLocation database="ensembl_mart_65" default="1"
>>>displayName="Ensembl Genes 65"
>>>host="www.ensembl.org<http://www.ensembl.org>" includeDatasets=""
>>>martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice"
>>>port="80" serverVirtualSchema="default" visible="1" />
>>> <MartURLLocation database="sequence_mart_65" default=""
>>>displayName="Sequence" host="www.ensembl.org<http://www.ensembl.org>"
>>>includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE"
>>>path="/biomart/martservice" port="80" serverVirtualSchema="default"
>>>visible="" />
>>> </MartRegistry>
>>
>>
>>
>
>
>
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