Re: [protege-user] Merging Imported Ontologies

Well I'm not sure I'm understanding your point yet, but since merging a
specific version of an imported ontology with your own ontology will stick
the data from that specific version to your own ontology, and considering
that the discussion (as far as I understood) is about the case in which the
changes in the imported ontologies do matter and therefore import statement
is not removed, if the imported ontology gets updated, then the newer
version will be loaded from the web while the older version is locally
loaded too, possibly causing conflicts. It doesn't seem a sensible approach
at least to me.

And if the ontologies are merged and the import statement is removed, then
there is no loading of data from outside the current file, and the ontology
is effectively offline and not updated which is seemingly not wanted here.

By the way, In case the updates are not always wanted, what I usually do is
placing the main ontology file and the ontologies which are to be imported
in a single folder and doing local imports. In this case, Protégé usually
addresses the local files using relative paths so that if I move the whole
folder containing all of the ontologies (and the catalog file containing
the mapping of ontology IRIs to local paths) to another location or share
it with another person, the paths won't be broken. And any time I want to
see the updates to the imported ontologies, I temporarily move the catalog
file to another place or simply rename it, so that all the imported
ontologies will be loaded from the web and if I want to go offline again, I
take the catalog file back to it's former state. Anyway I'm not properly
understanding the purpose of merging, actually.

On Thu, Feb 13, 2025 at 7:21 PM Michael DeBellis <[email protected]>
wrote:

> Why not saving an offline version (as .ttl file(s), say) of the ontology
>> (or each of the ontologies) you want to import, and then importing the
>> files locally into your ontology (rather than importing them from the web)?
>> This way, if the imported ontology gets updated, the changes won't be
>> applied unless you manually update the saved version on your local system.
>> So you can update the imported ontology(s) at your will, but things won't
>> get out of hand if sudden dramatic changes happen to the imported ontology.
>
>
> That's what I do now and it's always worked for me, because usually what I
> care about is an application (which is built on an ontology) so issues
> about staying consistent with the imported ontologies never mattered much.
> I just use them and then I don't care if they change in the future because
> it won't affect the system, and that's usually what I care about. Also,
> usually when I import ontologies like SKOS or Prov, I don't use the entire
> ontology anyway so even more reason, I'm not that concerned about future
> evolutions. The difference is this time I'm helping someone who doesn't
> want to build an application but a new reusable vocabulary that imports
> several other vocabularies. So I thought it might make sense to be a big
> more rigorous and thoughtful about imports and to see if anyone had any
> suggestions, if there were issues I wasn't thinking about, etc.
>
> On Thu, Feb 13, 2025 at 3:54 AM Hyacinth <[email protected]> wrote:
>
>> Greetings
>>
>> Why not saving an offline version (as .ttl file(s), say) of the ontology
>> (or each of the ontologies) you want to import, and then importing the
>> files locally into your ontology (rather than importing them from the web)?
>> This way, if the imported ontology gets updated, the changes won't be
>> applied unless you manually update the saved version on your local system.
>> So you can update the imported ontology(s) at your will, but things won't
>> get out of hand if sudden dramatic changes happen to the imported ontology.
>>
>> I remember to have experienced some bugs in using local imports in the
>> past, though not remembering exactly what the problem was and not sure
>> whether it still exists.
>>
>> On Thu, Feb 13, 2025 at 3:44 AM Michael DeBellis <[email protected]>
>> wrote:
>>
>>> I was helping someone start a new research project today where she is
>>> going to start by leveraging several diverse vocabularies from different
>>> domains. I showed her how to import an ontology.
>>>
>>> When I do this, I typically merge the ontologies because in the past
>>> I've had issues with imported ontologies. In the worst case, I often
>>> download things like Prov to my local drive and then import that way. Of
>>> course that leads to problems if I share the ontology because that path
>>> won't exist on someone else's machine. So one bit of advice I gave my
>>> colleague was to not do that and import from the URL rather than their
>>> local drive.
>>>
>>> But I'm wondering should one still merge the ontologies in this
>>> situation or not? After I do the Merge I usually delete the ontology import
>>> that shows up at the bottom of the Active Ontology tab. That way there
>>> won't be any issues with loading an ontology and not being able to load it
>>> because a server for an imported ontology is down. On the other hand, it
>>> seems that to have an audit trail, it is better to leave those import
>>> statements. I think (although I haven't tested this) if you do the merge
>>> and an imported (and merged) ontology isn't available it won't matter
>>> because you can just say skip finding that import and the entities will
>>> still be there.
>>>
>>> A related issue is what if an imported ontology changes? Not merging and
>>> having the Import statement seems the "right" way to do it because you
>>> would get the new version. On the other hand, if you are under a deadline
>>> and you suddenly have to deal with a bunch of changes to one of the
>>> imported ontologies that could be a pain.
>>>
>>> Just wondering what people think are the trade offs here between:
>>> 1) Whether or not to merge an imported ontology and
>>> 2) Whether or not to delete the import statement if you do merge the
>>> imported ontology?
>>>
>>> Thanks in advance for any opinions,
>>> Michael
>>> https://www.michaeldebellis.com/blog
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