Correct element types for bulk loader?

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Correct element types for bulk loader?

Hans Kraus
Hi,

I got a GFF3 file which contains some lines like:
FR839628 GenBank mobile_element 756481 757197 . - .
Parent=PP7435_Chr1-0412;locus_tag=PP7435_Chr1-0412;mobile_element_type=other:ISA1

'mobile_element' is no recognized cvterm element; this gives an error
during loading into Chado with the bulk loader.

I thought I can use every element in the cvterm table instead of it.
I found: 'DNA_transposon' and used it for a first try.

I get the error:
MSG: The following tag(s) are illegal and are causing this parser to
die: DNA_transposon_type

What are the rules for allowed terms then?

Any help appreciated,
Hans

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Re: Correct element types for bulk loader?

Scott Cain
Hi Hans,

The terms have to be in the sequence ontology.

Scott

Sent from my iPhone

On May 25, 2012, at 4:36 PM, Hans Kraus <[hidden email]> wrote:

> Hi,
>
> I got a GFF3 file which contains some lines like:
> FR839628    GenBank    mobile_element    756481    757197    .    -    .
> Parent=PP7435_Chr1-0412;locus_tag=PP7435_Chr1-0412;mobile_element_type=other:ISA1
>
> 'mobile_element' is no recognized cvterm element; this gives an error
> during loading into Chado with the bulk loader.
>
> I thought I can use every element in the cvterm table instead of it.
> I found: 'DNA_transposon' and used it for a first try.
>
> I get the error:
> MSG: The following tag(s) are illegal and are causing this parser to
> die: DNA_transposon_type
>
> What are the rules for allowed terms then?
>
> Any help appreciated,
> Hans
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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