Closed mmc46 closed 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/
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?
Commented by djs93 on 2015-01-23 16:49 UTC Doesn't oort give you an ID of the term where the problem arises?
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.
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?
Commented by djs93 on 2015-01-23 16:55 UTC Checking now.
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
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)?
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
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
Updated by mmc46 on 2015-01-26 10:48 UTC
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.