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The home of the Drosophila anatomy ontology
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RO ID clash needs to be fixed ASAP [sf#48] #48

Closed mmc46 closed 9 years ago

mmc46 commented 9 years ago

Reported by djs93 on 2015-01-23 16:32 UTC RO_0002000 'boundary of' and RO_0002002 'has boundary'are being reused for other terms in FBbt

This is likely the result of some historical screw up. 'has function in part of' is no longer used in FBbt and so can be deleted. For 'capable of part of', the RO xref should be switched to RO:0002215.

Please fix for next public release, as this potentially causes some nasty problems for integration with Uberon, GO, CL.

mmc46 commented 9 years ago

Commented by djs93 on 2015-01-23 16:34 UTC FYI - first reported here: https://sourceforge.net/p/obo/mailman/message/33261369/

mmc46 commented 9 years ago

Commented by mmc46 on 2015-01-23 16:47 UTC I've done the changes you list, but I'm getting problems in the oort build. Reason: multiple name tags not allowed

Though I can't see where the problem might be. Do you have an idea?

mmc46 commented 9 years ago

Commented by djs93 on 2015-01-23 16:49 UTC Doesn't oort give you an ID of the term where the problem arises?

mmc46 commented 9 years ago

Commented by djs93 on 2015-01-23 16:53 UTC Just had a look at the output. I suspect you have two Typedefs with xrefs to RO:0002215

These will get merged into one object property when converting to OWL, and so end up with two labels.

You need to end up with a single Typedef with an obo style ID (name with underscores) = the one used throughout the ontology.

mmc46 commented 9 years ago

Commented by mmc46 on 2015-01-23 16:54 UTC Yes, the other one is capable_of. Do you know what xref that should have?

mmc46 commented 9 years ago

Commented by djs93 on 2015-01-23 16:55 UTC Checking now.

mmc46 commented 9 years ago

Commented by djs93 on 2015-01-23 16:57 UTC My screw up on ticket

'capable of part of': RO_0002216 'capable of': RO_0002215

Sorry

mmc46 commented 9 years ago

Commented by mmc46 on 2015-01-23 17:02 UTC Still multiple name tags.

xref: RO:0002216 is on has_function_in

I'm guessing I can delete has_function_in? It's not used anywhere else, and mentioned in 2 obsolete typedfs (releases_neurotransmitter, secretes_hormone)?

mmc46 commented 9 years ago

Commented by djs93 on 2015-01-23 17:05 UTC Och. What a mess. Thinking about it - probably best to obsolete rather than delete both has_function_in and has_function_in_part_of. Deleting may cause headaches for loading into chado. If the stanzas remain, it is essential to delete the RO xrefs from both.

Cheers, David

mmc46 commented 9 years ago

Commented by mmc46 on 2015-01-26 10:47 UTC Ok, thanks. I've obsoleted both and deleted the xrefs. The builds are now working.

Thanks, Marta

mmc46 commented 9 years ago

Updated by mmc46 on 2015-01-26 10:48 UTC