Hi Syed,
I definitely have a way to proceed forward now, thanks for your help.
Any idea how to best suggest that Biomart do one of the following to help
others?
a. Fix issue with MartURLLocation so that others don't hit the same problems
b. If that's not possible, either prevent MartURLLocation from working - or
document the problem so others are aware?
Many thanks,
Phillipe
________________________________
From: Syed Haider <[email protected]>
To: pip pipster <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Thursday, December 29, 2011 3:23 PM
Subject: Re: [BioMart Users] problem with getting sequence data
All clear now Phillipe :) thanks.
So its the suspected issue as i suggested. Please try to avoid using
MartURLLocation type connection in registry as that has some bugs when
it comes to genomic sequences. You might wonder then how come the
website works (thats webservice access for you), thats because its using
the MartDBLocation behind the scenes.
And yes, if you use webservices (xml query based), you should be okay.
Just avoid the MartURLLocation driven webservice access.
Best,
Syed
On 29/12/2011 18:05, pip pipster wrote:
> 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]<mailto:[email protected]>>
>> To: pip pipster<[email protected]<mailto:[email protected]>>
>> Cc:
>> "[email protected]<mailto:[email protected]>"<[email protected]<mailto:[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]><mailto:[email protected]<mailto:[email protected]>>>
>>> To: pip
>>> pipster<[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>>
>>> Cc:
>>> "[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>"<[email protected]<mailto:[email protected]><mailto:[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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