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OntoZoo / ontobee

Ontobee is a linked data server for ontologies. See: http://www.ontobee.org.
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Sequence Ontology properties do not resolve #91

Closed arnikz closed 7 years ago

arnikz commented 7 years ago

Hi,

I get blank pages when requesting SO properties (e.g. http://purl.obolibrary.org/obo/SO_has_part). Could you please look into this? Thank you.

e4ong1031 commented 7 years ago

Hi arnikz,

The object property does exist in the Ontobee system, http://www.ontobee.org/ontology/SO?iri=http://purl.obolibrary.org/obo/so-xp.obo%23has_part.

When you go to the http://purl.obolibrary.org/obo/SO_has_part, this link redirected to http://www.ontobee.org/ontology/SO_has?iri=http://purl.obolibrary.org/obo/SO_has_part, which pointed to SO_has instead of SO. Seems like there is a misdirection in the PURL obolibrary. For now, please visit the Ontobee main page to browse the SO terms.

Thanks.

arnikz commented 7 years ago

Thanks @e4ong1031 for clarifying. I will then post this issue to purl.obolibrary.org.

cmungall commented 7 years ago

I recommend SO uses the standard RO/BFO properties

If the source version of SO is .obo, there is a quick fix for this. Just add an xref next to each term (for the gory details see owlcollab.github.io/oboformat/doc/obo-syntax.html#4.4)

See any other ontology for details. E.g. in GO:

[Typedef]
id: part_of
name: part of
xref: BFO:0000050
is_transitive: true
jamesaoverton commented 7 years ago

The PURL system is working as designed, matching term IDs that conform to the OBO ID policy: ontology ID space + underscore + digits.

It's possible to add a special case for SO_has_part (here obo.yml), but once added it has to be supported forever. It would be better to follow @cmungall's recommendation.