NetAffx annotation and ortholog mart

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

NetAffx annotation and ortholog mart

Leandro Hermida-2
Hi BioMart community,

I don't know if this would be of interest to people, a long while ago
I made a single Perl script which would automatically download all the
annot and ortholog NetAffx files from Affymetrix, parse and process
all the annotations and create a BioMart mart out of it in one go.  I
don't know if the BioMart Central Portal or others would be interested
in this?  I would be more than happy to release this to the community

best,
Leandro
Reply | Threaded
Open this post in threaded view
|

Re: NetAffx annotation and ortholog mart

donghe
Hi Leandro,

I am very interested in it.  By using EnsMart, I can only get pairwise
orthologs, but I want to find all orthologs among homo, Mouse and rat, do
you know there is any easy way to get them?

Thanks,

Dong

> Hi BioMart community,
>
> I don't know if this would be of interest to people, a long while ago
> I made a single Perl script which would automatically download all the
> annot and ortholog NetAffx files from Affymetrix, parse and process
> all the annotations and create a BioMart mart out of it in one go.  I
> don't know if the BioMart Central Portal or others would be interested
> in this?  I would be more than happy to release this to the community
>
> best,
> Leandro
>


Reply | Threaded
Open this post in threaded view
|

Re: NetAffx annotation and ortholog mart

Leandro Hermida-2
Hi Dong,

My NetAffx mart can output a table like this (below), which can give
you all the orthologs between all human, rat and mouse chips with the
correct filters applied.  But isn't this pairwise too?  I don't know
why that would be a problem, you still get a table for each probe set
on one of the chips *all* the orthologs on the other chips.

-Leandro

Probe Set ID Chip Type Ortholog Probe Set ID Ortholog Chip Type
1007_s_at HG-U133A_2 1584561_at Canine
1007_s_at HG-U133A_2 1598717_at Canine
1007_s_at HG-U133A_2 cfa.18678.1.s1_s_at Canine_2
1007_s_at HG-U133A_2 cfa.7473.1.a1_at Canine_2
1007_s_at HG-U133A_2 cfaaffx.1636.1.s1_s_at Canine_2
1007_s_at HG-U133A_2 l57509_s_at Mu11KsubA
1007_s_at HG-U133A_2 1415797_at MOE430A
1007_s_at HG-U133A_2 1415797_at Mouse430_2
1007_s_at HG-U133A_2 1415797_at Mouse430A_2
1007_s_at HG-U133A_2 1415797_at HT_MG-430A
1007_s_at HG-U133A_2 1415798_at MOE430A
1007_s_at HG-U133A_2 1415798_at Mouse430_2
1007_s_at HG-U133A_2 1415798_at Mouse430A_2
1007_s_at HG-U133A_2 1415798_at HT_MG-430A
1007_s_at HG-U133A_2 1435820_x_at MOE430A
1007_s_at HG-U133A_2 1435820_x_at Mouse430_2
1007_s_at HG-U133A_2 1435820_x_at Mouse430A_2
1007_s_at HG-U133A_2 1435820_x_at HT_MG-430A
1007_s_at HG-U133A_2 1437619_x_at MOE430A
1007_s_at HG-U133A_2 1437619_x_at Mouse430_2
1007_s_at HG-U133A_2 1437619_x_at Mouse430A_2
1007_s_at HG-U133A_2 1437619_x_at HT_MG-430A
1007_s_at HG-U133A_2 1438367_x_at MOE430A
1007_s_at HG-U133A_2 1438367_x_at Mouse430_2
1007_s_at HG-U133A_2 1438367_x_at Mouse430A_2
1007_s_at HG-U133A_2 1438367_x_at HT_MG-430A
1007_s_at HG-U133A_2 1439382_x_at MOE430A
1007_s_at HG-U133A_2 1439382_x_at Mouse430_2
1007_s_at HG-U133A_2 1439382_x_at Mouse430A_2
1007_s_at HG-U133A_2 1439382_x_at HT_MG-430A
1007_s_at HG-U133A_2 1456226_x_at MOE430A
1007_s_at HG-U133A_2 1456226_x_at Mouse430_2
1007_s_at HG-U133A_2 1456226_x_at Mouse430A_2
1007_s_at HG-U133A_2 1456226_x_at HT_MG-430A
1007_s_at HG-U133A_2 100155_at MG_U74Av2
1007_s_at HG-U133A_2 1415797_pm_at HT_MG-430_PM
1007_s_at HG-U133A_2 1415798_pm_at HT_MG-430_PM
1007_s_at HG-U133A_2 1435820_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 1437619_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 1438367_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 1439382_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 1456226_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 tc16141_s_at Mu19KsubA
1007_s_at HG-U133A_2 tc23346_s_at Mu19KsubA
1007_s_at HG-U133A_2 1459990_at MOE430A
1007_s_at HG-U133A_2 1459990_at Mouse430_2
1007_s_at HG-U133A_2 1459990_at Mouse430A_2
1007_s_at HG-U133A_2 1459990_at HT_MG-430A
1007_s_at HG-U133A_2 1459990_pm_at HT_MG-430_PM
1007_s_at HG-U133A_2 1370216_at RAE230A
... ... ... ...

On Mon, Oct 25, 2010 at 6:55 PM,  <[hidden email]> wrote:

> Hi Leandro,
>
> I am very interested in it.  By using EnsMart, I can only get pairwise
> orthologs, but I want to find all orthologs among homo, Mouse and rat, do
> you know there is any easy way to get them?
>
> Thanks,
>
> Dong
>
>> Hi BioMart community,
>>
>> I don't know if this would be of interest to people, a long while ago
>> I made a single Perl script which would automatically download all the
>> annot and ortholog NetAffx files from Affymetrix, parse and process
>> all the annotations and create a BioMart mart out of it in one go.  I
>> don't know if the BioMart Central Portal or others would be interested
>> in this?  I would be more than happy to release this to the community
>>
>> best,
>> Leandro
>>
>
>
>
Reply | Threaded
Open this post in threaded view
|

Re: NetAffx annotation and ortholog mart

Syed Haider
Hi Leandro,

its indeed a very good resource. Could you send us the working URL when
you are happy with the data integrity and have certain degree of
confidence that you would be able to maintain it for BioMart user community.

Thanks
Syed

On 25/10/2010 18:21, Leandro Hermida wrote:

> Hi Dong,
>
> My NetAffx mart can output a table like this (below), which can give
> you all the orthologs between all human, rat and mouse chips with the
> correct filters applied.  But isn't this pairwise too?  I don't know
> why that would be a problem, you still get a table for each probe set
> on one of the chips *all* the orthologs on the other chips.
>
> -Leandro
>
> Probe Set ID Chip Type Ortholog Probe Set ID Ortholog Chip Type
> 1007_s_at HG-U133A_2 1584561_at Canine
> 1007_s_at HG-U133A_2 1598717_at Canine
> 1007_s_at HG-U133A_2 cfa.18678.1.s1_s_at Canine_2
> 1007_s_at HG-U133A_2 cfa.7473.1.a1_at Canine_2
> 1007_s_at HG-U133A_2 cfaaffx.1636.1.s1_s_at Canine_2
> 1007_s_at HG-U133A_2 l57509_s_at Mu11KsubA
> 1007_s_at HG-U133A_2 1415797_at MOE430A
> 1007_s_at HG-U133A_2 1415797_at Mouse430_2
> 1007_s_at HG-U133A_2 1415797_at Mouse430A_2
> 1007_s_at HG-U133A_2 1415797_at HT_MG-430A
> 1007_s_at HG-U133A_2 1415798_at MOE430A
> 1007_s_at HG-U133A_2 1415798_at Mouse430_2
> 1007_s_at HG-U133A_2 1415798_at Mouse430A_2
> 1007_s_at HG-U133A_2 1415798_at HT_MG-430A
> 1007_s_at HG-U133A_2 1435820_x_at MOE430A
> 1007_s_at HG-U133A_2 1435820_x_at Mouse430_2
> 1007_s_at HG-U133A_2 1435820_x_at Mouse430A_2
> 1007_s_at HG-U133A_2 1435820_x_at HT_MG-430A
> 1007_s_at HG-U133A_2 1437619_x_at MOE430A
> 1007_s_at HG-U133A_2 1437619_x_at Mouse430_2
> 1007_s_at HG-U133A_2 1437619_x_at Mouse430A_2
> 1007_s_at HG-U133A_2 1437619_x_at HT_MG-430A
> 1007_s_at HG-U133A_2 1438367_x_at MOE430A
> 1007_s_at HG-U133A_2 1438367_x_at Mouse430_2
> 1007_s_at HG-U133A_2 1438367_x_at Mouse430A_2
> 1007_s_at HG-U133A_2 1438367_x_at HT_MG-430A
> 1007_s_at HG-U133A_2 1439382_x_at MOE430A
> 1007_s_at HG-U133A_2 1439382_x_at Mouse430_2
> 1007_s_at HG-U133A_2 1439382_x_at Mouse430A_2
> 1007_s_at HG-U133A_2 1439382_x_at HT_MG-430A
> 1007_s_at HG-U133A_2 1456226_x_at MOE430A
> 1007_s_at HG-U133A_2 1456226_x_at Mouse430_2
> 1007_s_at HG-U133A_2 1456226_x_at Mouse430A_2
> 1007_s_at HG-U133A_2 1456226_x_at HT_MG-430A
> 1007_s_at HG-U133A_2 100155_at MG_U74Av2
> 1007_s_at HG-U133A_2 1415797_pm_at HT_MG-430_PM
> 1007_s_at HG-U133A_2 1415798_pm_at HT_MG-430_PM
> 1007_s_at HG-U133A_2 1435820_pm_x_at HT_MG-430_PM
> 1007_s_at HG-U133A_2 1437619_pm_x_at HT_MG-430_PM
> 1007_s_at HG-U133A_2 1438367_pm_x_at HT_MG-430_PM
> 1007_s_at HG-U133A_2 1439382_pm_x_at HT_MG-430_PM
> 1007_s_at HG-U133A_2 1456226_pm_x_at HT_MG-430_PM
> 1007_s_at HG-U133A_2 tc16141_s_at Mu19KsubA
> 1007_s_at HG-U133A_2 tc23346_s_at Mu19KsubA
> 1007_s_at HG-U133A_2 1459990_at MOE430A
> 1007_s_at HG-U133A_2 1459990_at Mouse430_2
> 1007_s_at HG-U133A_2 1459990_at Mouse430A_2
> 1007_s_at HG-U133A_2 1459990_at HT_MG-430A
> 1007_s_at HG-U133A_2 1459990_pm_at HT_MG-430_PM
> 1007_s_at HG-U133A_2 1370216_at RAE230A
> ... ... ... ...
>
> On Mon, Oct 25, 2010 at 6:55 PM,<[hidden email]>  wrote:
>> Hi Leandro,
>>
>> I am very interested in it.  By using EnsMart, I can only get pairwise
>> orthologs, but I want to find all orthologs among homo, Mouse and rat, do
>> you know there is any easy way to get them?
>>
>> Thanks,
>>
>> Dong
>>
>>> Hi BioMart community,
>>>
>>> I don't know if this would be of interest to people, a long while ago
>>> I made a single Perl script which would automatically download all the
>>> annot and ortholog NetAffx files from Affymetrix, parse and process
>>> all the annotations and create a BioMart mart out of it in one go.  I
>>> don't know if the BioMart Central Portal or others would be interested
>>> in this?  I would be more than happy to release this to the community
>>>
>>> best,
>>> Leandro
>>>
>>
>>
>>
Reply | Threaded
Open this post in threaded view
|

Re: NetAffx annotation and ortholog mart

Leandro Hermida-2
Hi Syed,

I have it running on an internal server and unfortunately don't have
one that can be exposed to the public on a general basis, would it be
possible that it's hosted at the EBI like many of the other marts? I
will do all the work of course like maintaining the script used to
create everything etc. All they would have to do is run the script
with local configuration command line parameters (e.g. db host, user,
password, etc) and it does everything automatically. If they don't
want that I can send them the entire MySQL mart database dump
compressed and they would just have to load it. NetAffx only updates
once every 6 months or so so this is feasible.  Also I would give them
the necessary completed MartEditor configuration XML files (.xml and
.template.xml) for it and they would just need to do an "Upload All"
to create and populate the meta tables.

what do you think?
Leandro

On Mon, Oct 25, 2010 at 8:36 PM, Syed Haider <[hidden email]> wrote:

> Hi Leandro,
>
> its indeed a very good resource. Could you send us the working URL when you
> are happy with the data integrity and have certain degree of confidence that
> you would be able to maintain it for BioMart user community.
>
> Thanks
> Syed
>
> On 25/10/2010 18:21, Leandro Hermida wrote:
>>
>> Hi Dong,
>>
>> My NetAffx mart can output a table like this (below), which can give
>> you all the orthologs between all human, rat and mouse chips with the
>> correct filters applied.  But isn't this pairwise too?  I don't know
>> why that would be a problem, you still get a table for each probe set
>> on one of the chips *all* the orthologs on the other chips.
>>
>> -Leandro
>>
>> Probe Set ID    Chip Type       Ortholog Probe Set ID   Ortholog Chip Type
>> 1007_s_at       HG-U133A_2      1584561_at      Canine
>> 1007_s_at       HG-U133A_2      1598717_at      Canine
>> 1007_s_at       HG-U133A_2      cfa.18678.1.s1_s_at     Canine_2
>> 1007_s_at       HG-U133A_2      cfa.7473.1.a1_at        Canine_2
>> 1007_s_at       HG-U133A_2      cfaaffx.1636.1.s1_s_at  Canine_2
>> 1007_s_at       HG-U133A_2      l57509_s_at     Mu11KsubA
>> 1007_s_at       HG-U133A_2      1415797_at      MOE430A
>> 1007_s_at       HG-U133A_2      1415797_at      Mouse430_2
>> 1007_s_at       HG-U133A_2      1415797_at      Mouse430A_2
>> 1007_s_at       HG-U133A_2      1415797_at      HT_MG-430A
>> 1007_s_at       HG-U133A_2      1415798_at      MOE430A
>> 1007_s_at       HG-U133A_2      1415798_at      Mouse430_2
>> 1007_s_at       HG-U133A_2      1415798_at      Mouse430A_2
>> 1007_s_at       HG-U133A_2      1415798_at      HT_MG-430A
>> 1007_s_at       HG-U133A_2      1435820_x_at    MOE430A
>> 1007_s_at       HG-U133A_2      1435820_x_at    Mouse430_2
>> 1007_s_at       HG-U133A_2      1435820_x_at    Mouse430A_2
>> 1007_s_at       HG-U133A_2      1435820_x_at    HT_MG-430A
>> 1007_s_at       HG-U133A_2      1437619_x_at    MOE430A
>> 1007_s_at       HG-U133A_2      1437619_x_at    Mouse430_2
>> 1007_s_at       HG-U133A_2      1437619_x_at    Mouse430A_2
>> 1007_s_at       HG-U133A_2      1437619_x_at    HT_MG-430A
>> 1007_s_at       HG-U133A_2      1438367_x_at    MOE430A
>> 1007_s_at       HG-U133A_2      1438367_x_at    Mouse430_2
>> 1007_s_at       HG-U133A_2      1438367_x_at    Mouse430A_2
>> 1007_s_at       HG-U133A_2      1438367_x_at    HT_MG-430A
>> 1007_s_at       HG-U133A_2      1439382_x_at    MOE430A
>> 1007_s_at       HG-U133A_2      1439382_x_at    Mouse430_2
>> 1007_s_at       HG-U133A_2      1439382_x_at    Mouse430A_2
>> 1007_s_at       HG-U133A_2      1439382_x_at    HT_MG-430A
>> 1007_s_at       HG-U133A_2      1456226_x_at    MOE430A
>> 1007_s_at       HG-U133A_2      1456226_x_at    Mouse430_2
>> 1007_s_at       HG-U133A_2      1456226_x_at    Mouse430A_2
>> 1007_s_at       HG-U133A_2      1456226_x_at    HT_MG-430A
>> 1007_s_at       HG-U133A_2      100155_at       MG_U74Av2
>> 1007_s_at       HG-U133A_2      1415797_pm_at   HT_MG-430_PM
>> 1007_s_at       HG-U133A_2      1415798_pm_at   HT_MG-430_PM
>> 1007_s_at       HG-U133A_2      1435820_pm_x_at HT_MG-430_PM
>> 1007_s_at       HG-U133A_2      1437619_pm_x_at HT_MG-430_PM
>> 1007_s_at       HG-U133A_2      1438367_pm_x_at HT_MG-430_PM
>> 1007_s_at       HG-U133A_2      1439382_pm_x_at HT_MG-430_PM
>> 1007_s_at       HG-U133A_2      1456226_pm_x_at HT_MG-430_PM
>> 1007_s_at       HG-U133A_2      tc16141_s_at    Mu19KsubA
>> 1007_s_at       HG-U133A_2      tc23346_s_at    Mu19KsubA
>> 1007_s_at       HG-U133A_2      1459990_at      MOE430A
>> 1007_s_at       HG-U133A_2      1459990_at      Mouse430_2
>> 1007_s_at       HG-U133A_2      1459990_at      Mouse430A_2
>> 1007_s_at       HG-U133A_2      1459990_at      HT_MG-430A
>> 1007_s_at       HG-U133A_2      1459990_pm_at   HT_MG-430_PM
>> 1007_s_at       HG-U133A_2      1370216_at      RAE230A
>> ...     ...     ...     ...
>>
>> On Mon, Oct 25, 2010 at 6:55 PM,<[hidden email]>  wrote:
>>>
>>> Hi Leandro,
>>>
>>> I am very interested in it.  By using EnsMart, I can only get pairwise
>>> orthologs, but I want to find all orthologs among homo, Mouse and rat, do
>>> you know there is any easy way to get them?
>>>
>>> Thanks,
>>>
>>> Dong
>>>
>>>> Hi BioMart community,
>>>>
>>>> I don't know if this would be of interest to people, a long while ago
>>>> I made a single Perl script which would automatically download all the
>>>> annot and ortholog NetAffx files from Affymetrix, parse and process
>>>> all the annotations and create a BioMart mart out of it in one go.  I
>>>> don't know if the BioMart Central Portal or others would be interested
>>>> in this?  I would be more than happy to release this to the community
>>>>
>>>> best,
>>>> Leandro
>>>>
>>>
>>>
>>>
>