GO source - use go-basic.obo

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GO source - use go-basic.obo

Julie Sullivan-2
Hi all,

GO has updated their files, if you are using the InterMine GO source
you'll want to update yours as well. I haven't had a chance to
investigate but it seems like we want to load "go-basic.obo" instead of
"go.obo" now.

The go.obo file still loads but takes 3 hours (instead of minutes). I
don't see any detailed release notes -- maybe someone can point me to
those? But from the description I guess they've added more complex
relationships into go.obo, we likely aren't handling these new
relationships correctly.

See for details and comments:

https://github.com/intermine/intermine/issues/1774

Cheers
Julie
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Re: GO source - use go-basic.obo

Deepak Unni
Hi Julie,

We switched to go-basic.obo for BovineMine, HymenopteraMine and MaizeMine after the InterMine Conference and Hackathon back in 2017.
Thats when I realized that loading GO shouldn't take 3 hours, and we have seen this behavior since 2016 (or maybe even 2015).

GO Handbook suggests to use go-basic.obo for applications that rely on traversal of ontology graph. Also, it is the go-basic.obo file that is completely acyclic.
The full version go.obo would have ontology terms from Molecular Function, Cellular Component and Biological Process linked together via has_part and occurs_in relationship types.


Hope this helps :)

Cheers,

Deepak


On Thu, Mar 8, 2018 at 6:14 AM, Julie Sullivan <[hidden email]> wrote:
Hi all,

GO has updated their files, if you are using the InterMine GO source you'll want to update yours as well. I haven't had a chance to investigate but it seems like we want to load "go-basic.obo" instead of "go.obo" now.

The go.obo file still loads but takes 3 hours (instead of minutes). I don't see any detailed release notes -- maybe someone can point me to those? But from the description I guess they've added more complex relationships into go.obo, we likely aren't handling these new relationships correctly.

See for details and comments:

https://github.com/intermine/intermine/issues/1774

Cheers
Julie
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--
Deepak Unni

Bioinformatics Software Developer,
Berkeley BOP,
Lawrence Berkeley National Laboratory,
Berkeley, CA

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