[biomart-users] create database using biomart

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

[biomart-users] create database using biomart

Mohd Amin Azuwar
is it posible to use our own data and create database using biomart. from the tutroial most of it we import data from others database then how can we use our own data ?

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] create database using biomart

Arek Kasprzyk
Hi,

yes of course. All you have to do is to put your data into a relational schema conforming to our spec. For an example of such schema look at this paper:


in the section 'data mart'.


Some more information in this paper:


in the section 'database'.


Please remember that in the simplest scenario this schema simply reduces to one central table. It is probably best to start with that and get everything going.

Please also watch out for the naming convention if you are using MySQL MyISAM. More details in this post:




a.




On 5 May 2016 at 05:21, Mohd Amin Azuwar <[hidden email]> wrote:
is it posible to use our own data and create database using biomart. from the tutroial most of it we import data from others database then how can we use our own data ?

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] create database using biomart

Mohd Amin Azuwar
thanks arek

On Friday, May 6, 2016 at 5:12:41 PM UTC+8, Arek Kasprzyk wrote:
Hi,

yes of course. All you have to do is to put your data into a relational schema conforming to our spec. For an example of such schema look at this paper:

<a href="http://genome.cshlp.org/content/14/1/160.full" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fgenome.cshlp.org%2Fcontent%2F14%2F1%2F160.full\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF7ttUiO3QjWQcMt8RrgCqS73z1sg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fgenome.cshlp.org%2Fcontent%2F14%2F1%2F160.full\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF7ttUiO3QjWQcMt8RrgCqS73z1sg&#39;;return true;">http://genome.cshlp.org/content/14/1/160.full

in the section 'data mart'.


Some more information in this paper:

<a href="http://database.oxfordjournals.org/content/2011/bar038.full" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdatabase.oxfordjournals.org%2Fcontent%2F2011%2Fbar038.full\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG0Df1JWYXOgRqxdj7JoQ7Icg6txg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fdatabase.oxfordjournals.org%2Fcontent%2F2011%2Fbar038.full\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG0Df1JWYXOgRqxdj7JoQ7Icg6txg&#39;;return true;">http://database.oxfordjournals.org/content/2011/bar038.full

in the section 'database'.


Please remember that in the simplest scenario this schema simply reduces to one central table. It is probably best to start with that and get everything going.

Please also watch out for the naming convention if you are using MySQL MyISAM. More details in this post:

<a href="https://groups.google.com/forum/?fromgroups#!searchin/biomart-users/naming/biomart-users/z2InoVYeN30/2_ogh90WDjAJ" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/forum/?fromgroups#!searchin/biomart-users/naming/biomart-users/z2InoVYeN30/2_ogh90WDjAJ&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/forum/?fromgroups#!searchin/biomart-users/naming/biomart-users/z2InoVYeN30/2_ogh90WDjAJ&#39;;return true;">https://groups.google.com/forum/?fromgroups#!searchin/biomart-users/naming/biomart-users/z2InoVYeN30/2_ogh90WDjAJ



a.




On 5 May 2016 at 05:21, Mohd Amin Azuwar <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="2dkNSYKMBgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">amina...@...> wrote:
is it posible to use our own data and create database using biomart. from the tutroial most of it we import data from others database then how can we use our own data ?

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="2dkNSYKMBgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">biomart-user...@googlegroups.com.
Visit this group at <a href="https://groups.google.com/group/biomart-users" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/group/biomart-users&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/group/biomart-users&#39;;return true;">https://groups.google.com/group/biomart-users.
For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;">https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] create database using biomart

Mohd Amin Azuwar
In reply to this post by Arek Kasprzyk
Btw thank for the article Arek . i'm still new using biomart and non of my colleague have used it before. so still blur how to start. i'm using V0.9, my data gene data are from cancer patient sand i'm doing exome analysis 
1. how to edit my own scheme?
2. how to import my own data to that scheme?

is there any tutorial step by step for that. sorry it's look like i'm asking very basic question 
and when i follow the tutorial there is an connection error to connect to dabase. 

Thanks again


--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] create database using biomart

Arek Kasprzyk
Hi,

I am afraid there is no specific tutorial for loading different types of data into marts. These procedures will differ dependent on your data. In general, if you have some exposure to relational database you should be able to cope with that. If you are just trying to test the set up, it is easiest to create some dummy data upload it into a database with a single table and then connect with  MartConfigurator, configure it and hit the button 'start server'. Once you are comfortable with that you can start working on more sophisticated data models

a.

On 9 May 2016 at 04:50, Mohd Amin Azuwar <[hidden email]> wrote:
Btw thank for the article Arek . i'm still new using biomart and non of my colleague have used it before. so still blur how to start. i'm using V0.9, my data gene data are from cancer patient sand i'm doing exome analysis 
1. how to edit my own scheme?
2. how to import my own data to that scheme?

is there any tutorial step by step for that. sorry it's look like i'm asking very basic question 
and when i follow the tutorial there is an connection error to connect to dabase. 

Thanks again


--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] create database using biomart

Mohd Amin Azuwar

okay, i have created my own database using AMPPS, i try to link Mysql to biomartconfigurator, the result is error. the setting  as showed above. is it right?
by the way thanks for your feedback Arek

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [biomart-users] create database using biomart

Arek Kasprzyk
Hi Mohd,

One thing that i notice right away is the port. Your MySQL server is most likely running on 3306 not port 80

a.

On 19 May 2016 at 08:58, Mohd Amin Azuwar <[hidden email]> wrote:

okay, i have created my own database using AMPPS, i try to link Mysql to biomartconfigurator, the result is error. the setting  as showed above. is it right?
by the way thanks for your feedback Arek

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.