treat-xrefs-as-equivalent

obo-behavior / behavior-ontology

Neuro Behaviour Ontology: an ontology for human and animal behaviour processes and behaviour phenotypes

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treat-xrefs-as-equivalent #193

Closed DitchingIt closed 10 months ago

DitchingIt commented 10 months ago

@gouttegd pointed out recently on Slack that this notation treats entries as exact matches whether or not we want them to be. I am gradually introducing changes to cross referencing in parts of NBO, with skos:exactMatch being my preferred form of exact referencing.

Recently I noticed that our basic ontology information notes: treat-xrefs-as-equivalent GO

I am not comfortable assuming every GO Xref in NBO is an exact match. I suggest that we remove the general equivalence and only assert exact cross references case by case, using a skos:exactMatch annotation.

Assuming no disagreement, I don't know how to do this and would appreciate some advice @pmidford @sbello @matentzn @gouttegd

gouttegd commented 10 months ago

Related to this issue: I believe there is something wrong NBO’s GO xrefs.

There is only one such proper cross-reference: NBO:0000415 oboInOwl:hasDbXref "GO:0060082".

All the other “cross-references” to GO are using a oboInOwl:xref annotation property, which as far as I know is not correct and will be ignored by most tools (contrary to oboInOwl:hasDbXref).

DitchingIt commented 10 months ago

[x] @gouttegd I appreciate your input. This one was added by me in response to issue #8. Do you have a solution which can convert all these incorrect annotation properties in one go? I will only get to these references if they crop up as I gradually work my way through the 400 or so classes most closely allied to Ethology in the process branch of NBO. The rest will only be looked at if other volunteer editors take on the task.
[x] Meanwhile, it would be good to know how to tackle the prior problem I raised at a structural level, or whether it is only a text note which someone knows how to remove?

gouttegd commented 10 months ago

Do you have a solution which can convert all these incorrect annotation properties in one go?

For this kind of things, there’s hardly anything more efficient than a good old search-and-replace with any text editor you’re familiar with. Just replace any instance of oboInOwl:xref by oboInOwl:hasDbXref. The only caveat to be aware of is that you need to “re-serialise” the file with ROBOT afterwards.

To do everything on the command line:

Replace oboInOwl:xref by oboInOwl:hasDbXref in a new tmp.owl file:

sed 's/oboInOwl:xref/oboInOwl:hasDbXref/g' nbo-edit.owl > tmp.owl

Reserialise the tmp.owl into nbo-edit.owl again:

robot convert -i tmp.owl -f ofn -o nbo-edit.owl

DitchingIt commented 10 months ago

@gouttegd Thanks. I have next to no experience of using the command line.

I'd be happier with the manual approach but would be grateful for a quick (and probably obvious) basic walk through including:

which file I'm editing (NBO-EDIT?)
presumably I will turn it into a pull request?
how to reserialise with ROBOT

matentzn commented 10 months ago

Dealt with xref issue here: https://github.com/obo-behavior/behavior-ontology/pull/194

DitchingIt commented 10 months ago

@matentzn Is removing the treat-xrefs-as-equivalent statement just as easy? It only pointed to GO which I would rather specifiy on a case by case basis.

DitchingIt commented 10 months ago

Issues fixed by #194 and #197