#138 Problem loading

[Anonymous]

Hello,

We are trying to add the Disease Ontology to our Chado load but we are having issues

I'm still working on getting the disease ontology loaded. It's currently failing because the DO OBO file defines the "is_a" relation (other OBO files don't). When it's loaded we end up with two "is_a" relations in Chado. That doesn't work out very well. :-)

does the DO OBO file need to define the "is_a" relation is this is not done for other ontologies?

Cheers
Antonia.

https://github.com/pombase/website/issues/989

[Antonia Lock]

Hi sorry, I'm trying to edit the subject of this ticket to something more informative but I can't seem to edit the ticket

[Lynn_Schriml]

Hello Antonia,
Sorry to hear you are having problems with the DO file.
Which file are you trying to load ?
doid.obo ?

We define each of the relations we use. Would it be possible for you to remove the is_a definition ?
Or could your loader skip any relations it already has defined ?

I could also create a separate file for you, without the relation.

Cheers,
Lynn

Sent from my iPhone

On Oct 26, 2018, at 5:01 AM, Antonia Lock antonialock@users.sourceforge.net wrote:

Hi sorry, I'm trying to edit the subject of this ticket to something more informative but I can't seem to edit the ticket

[feature-requests:#138] Problem loading

Status: open
Group: Next Release (example)
Created: Fri Oct 26, 2018 09:59 AM UTC by Anonymous
Last Updated: Fri Oct 26, 2018 09:59 AM UTC
Owner: nobody

Hello,

We are trying to add the Disease Ontology to our Chado load but we are having issues

I'm still working on getting the disease ontology loaded. It's currently failing because the DO OBO file defines the "is_a" relation (other OBO files don't). When it's loaded we end up with two "is_a" relations in Chado. That doesn't work out very well. :-)

does the DO OBO file need to define the "is_a" relation is this is not done for other ontologies?

Cheers
Antonia.

https://github.com/pombase/website/issues/989

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[Antonia Lock]

Hi Lynn,

Cheers. The problem was that the other OBO files that we load don't have the is_a relation defined explicitly, but this one does. Our developer says he can work around it.

This can close.

Thanks
Antonia.