Missing Sequence Table

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Missing Sequence Table

Alex Batchelor
Hi,

I'm building a mouse-knockout intermine as part of an internship over
the summer.

I've just loaded protein sequence data from Uniprot.  When I checked
whether the data had loaded I found there was no Sequence table in my
database despite there being a class "Sequence" in my genomic_model.xml:

<class name="Sequence" is-interface="true">
<attribute name="md5checksum" type="java.lang.String"/>
<attribute name="length" type="int"/>
<attribute name="residues"
type="org.intermine.objectstore.query.ClobAccess"/>
</class>

Should there be a sequence table or is sequence data stored elsewhere?

Thanks

Alex Batchelor


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Re: Missing Sequence Table

Julie Sullivan
I think "sequence" was a reserved word so we used "intermine_sequence".  Do you
have that table?

On 08/02/2011 01:52 PM, Alex Batchelor wrote:

> Hi,
>
> I'm building a mouse-knockout intermine as part of an internship over the summer.
>
> I've just loaded protein sequence data from Uniprot. When I checked whether the
> data had loaded I found there was no Sequence table in my database despite there
> being a class "Sequence" in my genomic_model.xml:
>
> <class name="Sequence" is-interface="true">
> <attribute name="md5checksum" type="java.lang.String"/>
> <attribute name="length" type="int"/>
> <attribute name="residues" type="org.intermine.objectstore.query.ClobAccess"/>
> </class>
>
> Should there be a sequence table or is sequence data stored elsewhere?
>
> Thanks
>
> Alex Batchelor
>
>

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