Re: [protege-user] Merging Imported Ontologies

Hello Igor,

Thanks a lot for what seems to me a sound advice. Could you be more 
explicit about "Git" as a modern tool for version control. I have this 
problem when I want to developp a multilingual version of LEXEAU, for 
example adding Spanish to the actual bilingual version ( French and 
English ), stored on its ontology repository under my administration, 
aiming at the edition of a Spanish and French Water lexicon on the web 
out of the revised LEXEAU version in three languages, with a specific 
software.

What should be the scenario of LEXEAU updating after some translation in 
Spanish proposed by Mr Z, in Madrid, completing locally the actual 
version of LEXEAU downloaded from its repository ? What do you mean by 
"a clone of a Git repository" ? Would you have some bibliography available ?

Regards,

Jean-Louis Janin


Le 14/02/2025 à 23:46, Igor Toujilov via protege-user a écrit :
> Hi All,
> I want to suggest my solution as a software engineer. I mainly agree 
> with Hyacinth's opinion (with few exceptions).
> First of all, I strongly encourage considering the ontology 
> development as a software engineering activity which had already 
> provided commonly accepted industrial solutions and tools for the 
> change management, merging, version tracking, etc. decades ago. If you 
> really want to develop ontologies in a professional way, think of 
> ontologies as software products. And for doing so, you need to look at 
> modern tools for version control, mostly Git.
> Well developed ontologies have a modular structure like programming 
> modules. OWL has the import mechanism for managing the modules. Do not 
> ignore this mechanism.
> Protege has ontology merge functionality. But do not use it as a 
> replacement of the import mechanism. I use the merge functionality 
> from time to time when I need a temporary snapshot of a combined 
> ontology. For example, Stardog does not support the OWL import 
> directive. So, I sometimes, very infrequently, use the merge to load 
> my ontology to Stardog.
> Create a directory under Git control and put there all your ontologies 
> and imported ones for your project.
> Do not import ontologies from URLs in your production environment, as 
> this will jeopardise stability. Always import ontologies from a clone 
> of a Git repository.
> Regards,
> Igor
> *Sent:* Thursday, February 13, 2025 at 8:17 PM
> *From:* "Michael DeBellis" <[email protected]>
> *To:* "User support for WebProtege and Protege Desktop" 
> <[email protected]>
> *Subject:* 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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