[BioMart Users] format and load own data into Biomart?

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[BioMart Users] format and load own data into Biomart?

zhilianghu
Maybe I was not careful enough but by scanning through Biomart user manual
and online tutorial I don't seem to find how to build own data sets into
a local Biomart install.  We wish to share some large sets of own mapping
data with Biomart among our consortium members.  Any hint on steps/tools
to format, load and configure own data is appreciated.

Thank you,
Zhiliang
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Re: [BioMart Users] format and load own data into Biomart?

Arek Kasprzyk
Hi Zhiliang,
It does not really matter how you load data into BioMart as long as it ends up in a relational database containing BioMart schema. You can therefore use standard loading approaches e.g. the data import tools that come with the database and then use MConfigurator tool to configure it.  If you already have a relational database that you are trying to convert to BioMart spec, you can use the MConfigurator tool to do it for you.

My favourite approach to quickly learning how to set up a BioMart database is to simply create a database with one table and a few rows of data on your laptop and then configure it with MConfigurator and launch the server there. It will give you an immediate feel how the software works

a


On Wed, Dec 14, 2011 at 10:17 AM, Zhiliang <[hidden email]> wrote:
Maybe I was not careful enough but by scanning through Biomart user manual and online tutorial I don't seem to find how to build own data sets into a local Biomart install.  We wish to share some large sets of own mapping data with Biomart among our consortium members.  Any hint on steps/tools to format, load and configure own data is appreciated.

Thank you,
Zhiliang
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Re: [BioMart Users] format and load own data into Biomart?

zhilianghu
In reply to this post by zhilianghu
Hi Arek,

Thank you for your quick reply.  I suppose your "MConfigurator" refers to
"scripts/martconfigurator.sh" on the local installation.  I did a test and
now have a feel how to get my MySQL to it.

(It sees all my other databases besides the one I wish to give to it.
A quick question: what's the biomart's user agent name on a local system
that can be granted an access to a database on my MySQL?
(I started the biomart on my user account and it runs with my uid).

I found this tutorial useful - http://gmod.org/wiki/BioMart_Tutorial
It could be better if it comes with a simple sample data set to scroll
along :)  I am still trying to close the gap between my flat map data file
and ... a mart db.  It's interesting the tutorial says it can build mart
schema.  I have not found how the keys between (supposedly my custom)
tables are recognized...

Best regards,

Zhiliang


On Wed, 14 Dec 2011, Arek Kasprzyk wrote:

> Date: Wed, 14 Dec 2011 10:42:39 -0500
> From: Arek Kasprzyk <[hidden email]>
> To: Zhiliang <[hidden email]>
> Cc: [hidden email]
> Subject: Re: [BioMart Users] format and load own data into Biomart?
>
> Hi Zhiliang,
> It does not really matter how you load data into BioMart as long as it ends
> up in a relational database containing BioMart schema. You can therefore
> use standard loading approaches e.g. the data import tools that come with
> the database and then use MConfigurator tool to configure it.  If you
> already have a relational database that you are trying to convert to
> BioMart spec, you can use the MConfigurator tool to do it for you.
>
> My favourite approach to quickly learning how to set up a BioMart database
> is to simply create a database with one table and a few rows of data on
> your laptop and then configure it with MConfigurator and launch the server
> there. It will give you an immediate feel how the software works
>
> a
>
>
> On Wed, Dec 14, 2011 at 10:17 AM, Zhiliang <[hidden email]> wrote:
>
>> Maybe I was not careful enough but by scanning through Biomart user manual
>> and online tutorial I don't seem to find how to build own data sets into a
>> local Biomart install.  We wish to share some large sets of own mapping
>> data with Biomart among our consortium members.  Any hint on steps/tools to
>> format, load and configure own data is appreciated.
>>
>> Thank you,
>> Zhiliang
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Re: [BioMart Users] format and load own data into Biomart?

Arek Kasprzyk
Hi Zhiliang,
The GMOD tutorial looks very complicated to me. It mixes 0.7 and 0.8 software,  needs VM etc.
Installing and running 0.8 is much simpler, just follow the docs from 0.8.

Please start with section 4 on page 6 ("Quick Start"). If you can get it to work, the next step is create an empty table in your database and populate with a bit of data. Please follow section 5.4.1 on page 16. If you can do that, then the next step is to create a 'real' table and populate it with your 'real' data using a database import tool (e.g for mysql it is mysqlimport) and repeat the procedure. If you having problems with connecting to your database through MConfigurator, please use database commandline tool running on the same host as MConfigurator to make sure that you have sufficient privileges

a


On Wed, Dec 14, 2011 at 4:30 PM, Zhiliang <[hidden email]> wrote:
Hi Arek,

Thank you for your quick reply.  I suppose your "MConfigurator" refers to
"scripts/martconfigurator.sh" on the local installation.  I did a test and
now have a feel how to get my MySQL to it.

(It sees all my other databases besides the one I wish to give to it.
A quick question: what's the biomart's user agent name on a local system
that can be granted an access to a database on my MySQL?
(I started the biomart on my user account and it runs with my uid).

I found this tutorial useful - http://gmod.org/wiki/BioMart_Tutorial
It could be better if it comes with a simple sample data set to scroll
along :)  I am still trying to close the gap between my flat map data file
and ... a mart db.  It's interesting the tutorial says it can build mart
schema.  I have not found how the keys between (supposedly my custom)
tables are recognized...

Best regards,

Zhiliang


On Wed, 14 Dec 2011, Arek Kasprzyk wrote:

Date: Wed, 14 Dec 2011 10:42:39 -0500
From: Arek Kasprzyk <[hidden email]>
To: Zhiliang <[hidden email]>
Cc: [hidden email]
Subject: Re: [BioMart Users] format and load own data into Biomart?


Hi Zhiliang,
It does not really matter how you load data into BioMart as long as it ends
up in a relational database containing BioMart schema. You can therefore
use standard loading approaches e.g. the data import tools that come with
the database and then use MConfigurator tool to configure it.  If you
already have a relational database that you are trying to convert to
BioMart spec, you can use the MConfigurator tool to do it for you.

My favourite approach to quickly learning how to set up a BioMart database
is to simply create a database with one table and a few rows of data on
your laptop and then configure it with MConfigurator and launch the server
there. It will give you an immediate feel how the software works

a


On Wed, Dec 14, 2011 at 10:17 AM, Zhiliang <[hidden email]> wrote:

Maybe I was not careful enough but by scanning through Biomart user manual
and online tutorial I don't seem to find how to build own data sets into a
local Biomart install.  We wish to share some large sets of own mapping
data with Biomart among our consortium members.  Any hint on steps/tools to
format, load and configure own data is appreciated.

Thank you,
Zhiliang


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Re: [BioMart Users] format and load own data into Biomart?

zhilianghu
In reply to this post by zhilianghu
Hi Arek,

Thank you for the comments.  It sounds straight forward.
Let me try it out.

Zhiliang

On Thu, 15 Dec 2011, Arek Kasprzyk wrote:

> Date: Thu, 15 Dec 2011 09:07:39 -0500
> From: Arek Kasprzyk <[hidden email]>
> To: Zhiliang <[hidden email]>
> Cc: [hidden email]
> Subject: Re: [BioMart Users] format and load own data into Biomart?
>
> --f46d04428260da939604b422013e
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Zhiliang,
> The GMOD tutorial looks very complicated to me. It mixes 0.7 and 0.8
> software,  needs VM etc.
> Installing and running 0.8 is much simpler, just follow the docs from 0.8.
>
> Please start with section 4 on page 6 ("Quick Start"). If you can get it to
> work, the next step is create an empty table in your database and populate
> with a bit of data. Please follow section 5.4.1 on page 16. If you can do
> that, then the next step is to create a 'real' table and populate it with
> your 'real' data using a database import tool (e.g for mysql it is
> mysqlimport) and repeat the procedure. If you having problems with
> connecting to your database through MConfigurator, please use database
> commandline tool running on the same host as MConfigurator to make sure
> that you have sufficient privileges
>
> a
>
>
> On Wed, Dec 14, 2011 at 4:30 PM, Zhiliang <[hidden email]> wrote:
>
>> Hi Arek,
>>
>> Thank you for your quick reply.  I suppose your "MConfigurator" refers to
>> "scripts/martconfigurator.sh" on the local installation.  I did a test and
>> now have a feel how to get my MySQL to it.
>>
>> (It sees all my other databases besides the one I wish to give to it.
>> A quick question: what's the biomart's user agent name on a local system
>> that can be granted an access to a database on my MySQL?
>> (I started the biomart on my user account and it runs with my uid).
>>
>> I found this tutorial useful - http://gmod.org/wiki/BioMart_**Tutorial<http://gmod.org/wiki/BioMart_Tutorial>
>> It could be better if it comes with a simple sample data set to scroll
>> along :)  I am still trying to close the gap between my flat map data file
>> and ... a mart db.  It's interesting the tutorial says it can build mart
>> schema.  I have not found how the keys between (supposedly my custom)
>> tables are recognized...
>>
>> Best regards,
>>
>> Zhiliang
>>
>>
>> On Wed, 14 Dec 2011, Arek Kasprzyk wrote:
>>
>>  Date: Wed, 14 Dec 2011 10:42:39 -0500
>>> From: Arek Kasprzyk <[hidden email]>
>>> To: Zhiliang <[hidden email]>
>>> Cc: [hidden email]
>>> Subject: Re: [BioMart Users] format and load own data into Biomart?
>>>
>>>
>>> Hi Zhiliang,
>>> It does not really matter how you load data into BioMart as long as it
>>> ends
>>> up in a relational database containing BioMart schema. You can therefore
>>> use standard loading approaches e.g. the data import tools that come with
>>> the database and then use MConfigurator tool to configure it.  If you
>>> already have a relational database that you are trying to convert to
>>> BioMart spec, you can use the MConfigurator tool to do it for you.
>>>
>>> My favourite approach to quickly learning how to set up a BioMart database
>>> is to simply create a database with one table and a few rows of data on
>>> your laptop and then configure it with MConfigurator and launch the server
>>> there. It will give you an immediate feel how the software works
>>>
>>> a
>>>
>>>
>>> On Wed, Dec 14, 2011 at 10:17 AM, Zhiliang <[hidden email]> wrote:
>>>
>>>  Maybe I was not careful enough but by scanning through Biomart user
>>>> manual
>>>> and online tutorial I don't seem to find how to build own data sets into
>>>> a
>>>> local Biomart install.  We wish to share some large sets of own mapping
>>>> data with Biomart among our consortium members.  Any hint on steps/tools
>>>> to
>>>> format, load and configure own data is appreciated.
>>>>
>>>> Thank you,
>>>> Zhiliang
>>>>
>>>
>
> --f46d04428260da939604b422013e
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
>
> Hi Zhiliang,<br>The GMOD tutorial looks very complicated to me. It mixes 0.=
> 7 and 0.8 software,=A0 needs VM etc.<br>Installing and running 0.8 is much =
> simpler, just follow the docs from 0.8.<br><br>Please start with section 4 =
> on page 6 (&quot;Quick Start&quot;). If you can get it to work, the next st=
> ep is create an empty table in your database and populate with a bit of dat=
> a. Please follow section 5.4.1 on page 16. If you can do that, then the nex=
> t step is to create a &#39;real&#39; table and populate it with your &#39;r=
> eal&#39; data using a database import tool (e.g for mysql it is mysqlimport=
> ) and repeat the procedure. If you having problems with connecting to your =
> database through MConfigurator, please use database commandline tool runnin=
> g on the same host as MConfigurator to make sure that you have sufficient p=
> rivileges<br>
> <br>a<br><br><br><div class=3D"gmail_quote">On Wed, Dec 14, 2011 at 4:30 PM=
> , Zhiliang <span dir=3D"ltr">&lt;<a href=3D"mailto:[hidden email]">hu@=
> animalgenome.org</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote"=
> style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
> Hi Arek,<br>
> <br>
> Thank you for your quick reply. =A0I suppose your &quot;MConfigurator&quot;=
> refers to<br>
> &quot;scripts/martconfigurator.sh&quot; on the local installation. =A0I did=
> a test and<br>
> now have a feel how to get my MySQL to it.<br>
> <br>
> (It sees all my other databases besides the one I wish to give to it.<br>
> A quick question: what&#39;s the biomart&#39;s user agent name on a local s=
> ystem<br>
> that can be granted an access to a database on my MySQL?<br>
> (I started the biomart on my user account and it runs with my uid).<br>
> <br>
> I found this tutorial useful - <a href=3D"http://gmod.org/wiki/BioMart_Tuto=
> rial" target=3D"_blank">http://gmod.org/wiki/BioMart_<u></u>Tutorial</a><br=
>>
> It could be better if it comes with a simple sample data set to scroll<br>
> along :) =A0I am still trying to close the gap between my flat map data fil=
> e<br>
> and ... a mart db. =A0It&#39;s interesting the tutorial says it can build m=
> art<br>
> schema. =A0I have not found how the keys between (supposedly my custom)<br>
> tables are recognized...<br>
> <br>
> Best regards,<br>
> <br>
> Zhiliang<br>
> <br>
> <br>
> On Wed, 14 Dec 2011, Arek Kasprzyk wrote:<br>
> <br>
> <blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
> x #ccc solid;padding-left:1ex">
> Date: Wed, 14 Dec 2011 10:42:39 -0500<br>
> From: Arek Kasprzyk &lt;<a href=3D"mailto:[hidden email]" target=
> =3D"_blank">[hidden email]</a>&gt;<br>
> To: Zhiliang &lt;<a href=3D"mailto:[hidden email]" target=3D"_blank">h=
> [hidden email]</a>&gt;<br>
> Cc: <a href=3D"mailto:[hidden email]" target=3D"_blank">[hidden email]=
> g</a><br>
> Subject: Re: [BioMart Users] format and load own data into Biomart?<div cla=
> ss=3D"im"><br>
> <br>
> Hi Zhiliang,<br>
> It does not really matter how you load data into BioMart as long as it ends=
> <br>
> up in a relational database containing BioMart schema. You can therefore<br=
>>
> use standard loading approaches e.g. the data import tools that come with<b=
> r>
> the database and then use MConfigurator tool to configure it. =A0If you<br>
> already have a relational database that you are trying to convert to<br>
> BioMart spec, you can use the MConfigurator tool to do it for you.<br>
> <br>
> My favourite approach to quickly learning how to set up a BioMart database<=
> br>
> is to simply create a database with one table and a few rows of data on<br>
> your laptop and then configure it with MConfigurator and launch the server<=
> br>
> there. It will give you an immediate feel how the software works<br>
> <br>
> a<br>
> <br>
> <br>
> On Wed, Dec 14, 2011 at 10:17 AM, Zhiliang &lt;<a href=3D"mailto:hu@animalg=
> enome.org" target=3D"_blank">[hidden email]</a>&gt; wrote:<br>
> <br>
> <blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
> x #ccc solid;padding-left:1ex">
> Maybe I was not careful enough but by scanning through Biomart user manual<=
> br>
> and online tutorial I don&#39;t seem to find how to build own data sets int=
> o a<br>
> local Biomart install. =A0We wish to share some large sets of own mapping<b=
> r>
> data with Biomart among our consortium members. =A0Any hint on steps/tools =
> to<br>
> format, load and configure own data is appreciated.<br>
> <br>
> Thank you,<br>
> Zhiliang<br>
> </blockquote></div></blockquote>
> </blockquote></div><br>
>
> --f46d04428260da939604b422013e--
>
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