Re: [protege-user] Merging Imported Ontologies

>
> 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...


Thanks, that's the kind of practical ideas I was looking for.

On Thu, Feb 13, 2025 at 11:20 AM Hyacinth <[email protected]> wrote:

> 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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