Incorrect ID for 'planned process' in cob-to-external

[beckyjackson]

In cob-to-external.tsv, 'planned process' has the ID COB:0000035:

COB/src/ontology/components/cob-to-external.tsv

Line 69 in a2f7141

COB:0000035 planned process owl:equivalentClass OBI:0000011 planned process . HumanCurated

... but in the COB file, this is COB:0000082:

COB/cob.owl

Lines 726 to 744 in a2f7141

	<!-- http://purl.obolibrary.org/obo/COB_0000082 -->
	<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000082">
	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
	<rdfs:subClassOf>
	<owl:Restriction>
	<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000081"/>
	<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000260"/>
	</owl:Restriction>
	</rdfs:subClassOf>
	<rdfs:subClassOf>
	<owl:Restriction>
	<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000087"/>
	<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/SEPIO_0000048"/>
	</owl:Restriction>
	</rdfs:subClassOf>
	<obo:IAO_0000115>A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.</obo:IAO_0000115>
	<rdfs:label>planned process</rdfs:label>
	</owl:Class>

In cob-edit.owl, COB:0000035 is 'completely executed planned process' so can we either update the ID or label in the external mapping file? I don't know if this mapping was intended to be to the completely-executed one or not. @cmungall ?

[bpeters42]

I would bet that this was an accident. But it reminds me that we have to be careful when doing the mapping to OBI, where what we have as 'planned process' is really 'completely executed'. Which further reminds me that we should do an OBI-COB alignment.

[bpeters42]

@sebastianduesing - can you check if this is still a thing?

[cmungall]

I made the PR but I kept this as exact, I think the misalignment deserves it's own issue

[sebastianduesing]

I might be misunderstanding this issue, but I'm not sure that #282 is the right fix. My reading of this issue is:

• In cob-edit.owl, COB:0000035 is 'completely executed planned process'.
• In cob-edit.owl, COB:0000082 is 'planned process'.
• OBI:0000011, which is called 'planned process' in OBI, is actually equivalent to COB:0000035, 'completely executed planned process'.
• The problem with cob-to-external.tsv is that the mapping for OBI:0000011 says it is mapped to a term with the IRI COB:0000035 ('completely executed planned process') but the COB term label in that row is simply 'planned process.'

The change in #282 changes the IRI to align with the label in cob-to-external.tsv. I believe that, because we do want OBI:'planned process' to map to COB:'completely executed planned process', the right fix would actually be to change the label to align with the IRI.

[cmungall]

you're right!

…

On Wed, Sep 18, 2024 at 8:46 AM Sebastian Duesing ***@***.***> wrote: I might be misunderstanding this issue, but I'm not sure that #282 <#282> is the right fix. My reading of this issue is: - In cob-edit.owl, COB:0000035 is 'completely executed planned process'. - In cob-edit.owl, COB:0000082 is 'planned process'. - OBI:0000011, which is called 'planned process' in OBI, is actually equivalent to COB:0000035, 'completely executed planned process'. - The problem with cob-to-external.tsv is that the mapping for OBI:0000011 says it is mapped to a term with the IRI COB:0000035 ('completely executed planned process') but the COB term label in that row is simply 'planned process.' The change in #282 <#282> *changes the IRI to align with the label* in cob-to-external.tsv. I believe that, because we do want OBI:'planned process' to map to COB:'completely executed planned process', the right fix would actually be to *change the label to align with the IRI*. — Reply to this email directly, view it on GitHub <#191 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMON5FNY6F7H2JLQDLBLZXGN4RAVCNFSM6AAAAABOMTQZ6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJYHAZDQOBTGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>