OBO Foundry: Normalise PURLs?

[ontoneo-project]

OBO Foundry: Normalise PURLs?

[FernandaFarinelli]

Thanks for letting me know.
I'm in the process to generate a new version of ONTONEO adjusting any issues. I'll verify this too.

[matentzn]

Hey @FernandaFarinelli looks better :) Thanks. Not quite right yet: You have:
http://purl.obolibrary.org/obo/ontoneo/ONTONEO_00100001

But the correct IRI should be:

http://purl.obolibrary.org/obo/ONTONEO_00100001

Thank you very much for doing it, this will greatly help with including ONTONEO in other projects!

[matentzn]

@FernandaFarinelli That looks great. The only thing i noticed about the IRIs is inconsistent length, which can lead to some errors:

http://purl.obolibrary.org/obo/ONTONEO_1000000
http://purl.obolibrary.org/obo/ONTONEO_1000001
http://purl.obolibrary.org/obo/ONTONEO_1000002

These three properties have 7 digits, while all your other terms have 8. I recommend prepending a 0 or something to make them 8 digits to be consistent across the ontology Otherwise, great.

[matentzn]

Its up to you @FernandaFarinelli
these IRIs are perfectly valid - but it may be confusing to some tools that chop the URI into a number and prefix part:
Imagine this:
ONTONEO:1000000
ONTONEO:01000000

These are definitely two different IRIs, but if you were to check "which one is higher", and you go with the numeric id, they would end up as being the same.. which may cause problems. That said, you did not anything wrong and can chose to leave it as is. My recommendation: Obsolete the three ids and replace by new ones.

[FernandaFarinelli]

Nico Matentzoglu,
I did some updates on Ontoneo.
Could you check again? Feel free to let me know about any other issue in Ontoneo.
I'll wait your reply to close this issue.
Thanks.

[zhengj2007]

The incorrect IRI still used in the latest ONTONEO release.

For example,
gestational age measurement datum
http://purl.obolibrary.org/obo/ontoneo/ONTONEO_00000255

Could all the ONTONEO terms use the OBO normalized IRI? Thanks!

[FernandaFarinelli]

I'm working on this.

[zhengj2007]

@FernandaFarinelli Thanks a lot!

[FernandaFarinelli]

@matentzn and @zhengj2007
I made such changes on ontoneo.
Please let me know if everything is ok.
Thanks for your patient.
Fernanda

[FernandaFarinelli]

@matentzn I have a doubt about this strategy. If I prepending a 0 it will be a new IRI ?

Maybe, to be stable IRIs I should create these three properties again, with a new 8 digits IRI and replace them in all my ontology.

In addition, I should transform these three properties in the obsolete class as a subclass of http://www.geneontology.org/formats/oboInOwl#ObsoleteClass, and inform in these old properties the annotation "term replace by" (IAO_0100001) and maybe the annotation "has obsolescence reason"(IAO_0000231).

What do you think about it? What is the best and simple strategy?

Thanks for your contribution.