QTL missing position data

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

QTL missing position data

Vallejos, Andrew

Sequence Features should still have a chromosomeid and chromosomelocationid values correct?  I am trying to figure out why QTLs do not have any position data, even though the data is in the items.xml file.

 

-Andrew

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: QTL missing position data

Richard Smith
Yes, absolutely.  Have you run just the source that loads QTLs on it's
own?  If locations are stored correctly in XML then they should load.

Please send some example XML if you're still having problems.

Richard.




Vallejos, Andrew wrote:

> Sequence Features should still have a chromosomeid and
> chromosomelocationid values correct?  I am trying to figure out why QTLs
> do not have any position data, even though the data is in the items.xml
> file.
>
>  
>
> -Andrew
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: QTL missing position data

Vallejos, Andrew


-----Original Message-----
From: Richard Smith [mailto:[hidden email]]
Sent: Friday, November 19, 2010 10:45 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] QTL missing position data

Yes, absolutely.  Have you run just the source that loads QTLs on it's
own?  If locations are stored correctly in XML then they should load.

Please send some example XML if you're still having problems.

Richard.




Vallejos, Andrew wrote:
> Sequence Features should still have a chromosomeid and
> chromosomelocationid values correct?  I am trying to figure out why
QTLs
> do not have any position data, even though the data is in the
items.xml

> file.
>
>  
>
> -Andrew
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
>
>
------------------------------------------------------------------------
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

rgd_qtls.xml (2M) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: QTL missing position data

Richard Smith
This is the old issue where for a one-many collections you need to
set the one end not the many end.  So in this case you should set
Location.feature not QTL.locations.

    <item id="0_30" class="" implements="Location">
       <attribute name="end" value="110718848" />
       <reference name="locatedOn" ref_id="0_11" />
****  <reference name="feature" ref_id="0_32" /> ****
       <attribute name="start" value="24006429" />
    </item>
    <item id="0_31" class="" implements="Publication">
       <attribute name="pubMedId" value="11953987" />
    </item>
    <item id="0_32" class="" implements="QTL">
       <attribute name="symbol" value="Aia5" />
       <attribute name="primaryIdentifier" value="61325" />
       <attribute name="name" value="Adjuvant induced arthritis QTL 5" />
       <attribute name="trait" value="Joint/bone inflammation" />
       <attribute name="pValue" value="0.01" />
       <collection name="publications">
          <reference ref_id="0_31" />
       </collection>
       <reference name="organism" ref_id="0_1" />
    </item>


Cheers,
Richard.




Vallejos, Andrew wrote:

>
> -----Original Message-----
> From: Richard Smith [mailto:[hidden email]]
> Sent: Friday, November 19, 2010 10:45 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] QTL missing position data
>
> Yes, absolutely.  Have you run just the source that loads QTLs on it's
> own?  If locations are stored correctly in XML then they should load.
>
> Please send some example XML if you're still having problems.
>
> Richard.
>
>
>
>
> Vallejos, Andrew wrote:
>> Sequence Features should still have a chromosomeid and
>> chromosomelocationid values correct?  I am trying to figure out why
> QTLs
>> do not have any position data, even though the data is in the
> items.xml
>> file.
>>
>>  
>>
>> -Andrew
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
>>
> ------------------------------------------------------------------------
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: QTL missing position data

Vallejos, Andrew
Heh...I knew that I should be setting them that way too...

Thanks!

-----Original Message-----
From: Richard Smith [mailto:[hidden email]]
Sent: Friday, November 19, 2010 11:07 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] QTL missing position data

This is the old issue where for a one-many collections you need to
set the one end not the many end.  So in this case you should set
Location.feature not QTL.locations.

    <item id="0_30" class="" implements="Location">
       <attribute name="end" value="110718848" />
       <reference name="locatedOn" ref_id="0_11" />
****  <reference name="feature" ref_id="0_32" /> ****
       <attribute name="start" value="24006429" />
    </item>
    <item id="0_31" class="" implements="Publication">
       <attribute name="pubMedId" value="11953987" />
    </item>
    <item id="0_32" class="" implements="QTL">
       <attribute name="symbol" value="Aia5" />
       <attribute name="primaryIdentifier" value="61325" />
       <attribute name="name" value="Adjuvant induced arthritis QTL 5"
/>
       <attribute name="trait" value="Joint/bone inflammation" />
       <attribute name="pValue" value="0.01" />
       <collection name="publications">
          <reference ref_id="0_31" />
       </collection>
       <reference name="organism" ref_id="0_1" />
    </item>


Cheers,
Richard.




Vallejos, Andrew wrote:

>
> -----Original Message-----
> From: Richard Smith [mailto:[hidden email]]
> Sent: Friday, November 19, 2010 10:45 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] QTL missing position data
>
> Yes, absolutely.  Have you run just the source that loads QTLs on it's
> own?  If locations are stored correctly in XML then they should load.
>
> Please send some example XML if you're still having problems.
>
> Richard.
>
>
>
>
> Vallejos, Andrew wrote:
>> Sequence Features should still have a chromosomeid and
>> chromosomelocationid values correct?  I am trying to figure out why
> QTLs
>> do not have any position data, even though the data is in the
> items.xml
>> file.
>>
>>  
>>
>> -Andrew
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
>>
>
------------------------------------------------------------------------
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev