Restarting . . .

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Restarting . . .

David Hay-2
I was away from Protege for a few months, but I have signed up for Dave
McComb's course in September.  Today I fired it up again. Dave had told
me to load version 5.0 which I did.  One problem is that the tutorial
from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in
the attached file (Pizza1.owl).  I have also attached the main windows
from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
- Dwight Eisenhower


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Re: Restarting . . .

Dave McComb-2
Well that is certainly bizarre looking. 

I looked at the owl, and loaded it in protege.  Have to admit I’ve never seen anything quite like this.

Do you still have it open in Protege? 

What’s odd, of course is the long repetitions of ontologies/www.pizza.com over and over again.  

The other thing that is odd, is the owl file only has ten lines and has no classes, and yet many of them showed up when I opened the file. (no explanation for that)

But where a clue might exist: in your screen shot there are valid subclasses of Pizza_Topping.  when its loaded anew from the file all the subclass of Pizza_Topping are the weird repetitive ontologies/www.pizza.com .  if you could click on the Pizza_Topping we might see a clue as to what sent it in this tizzy. 


On Aug 5, 2016, at 1:03 PM, David Hay <[hidden email]> wrote:

I was away from Protege for a few months, but I have signed up for Dave McComb's course in September.  Today I fired it up again. Dave had told me to load version 5.0 which I did.  One problem is that the tutorial from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in the attached file (Pizza1.owl).  I have also attached the main windows from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
- Dwight Eisenhower

<Pizza Dashboard.JPG><Pizza1.owl>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Restarting . . .

Rafael Gonçalves
Hi David,

It might be an issue with the Turtle serializer in the OWL API. Do you happen to have a version of the ontology before whatever changes preceded the Save? 

Cheers,
Rafael

On Aug 5, 2016, at 12:58, Dave McComb <[hidden email]> wrote:

Well that is certainly bizarre looking. 

I looked at the owl, and loaded it in protege.  Have to admit I’ve never seen anything quite like this.

Do you still have it open in Protege? 

What’s odd, of course is the long repetitions of ontologies/www.pizza.com over and over again.  

The other thing that is odd, is the owl file only has ten lines and has no classes, and yet many of them showed up when I opened the file. (no explanation for that)

But where a clue might exist: in your screen shot there are valid subclasses of Pizza_Topping.  when its loaded anew from the file all the subclass of Pizza_Topping are the weird repetitive ontologies/www.pizza.com .  if you could click on the Pizza_Topping we might see a clue as to what sent it in this tizzy. 


On Aug 5, 2016, at 1:03 PM, David Hay <[hidden email]> wrote:

I was away from Protege for a few months, but I have signed up for Dave McComb's course in September.  Today I fired it up again. Dave had told me to load version 5.0 which I did.  One problem is that the tutorial from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in the attached file (Pizza1.owl).  I have also attached the main windows from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
- Dwight Eisenhower

<Pizza Dashboard.JPG><Pizza1.owl>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Restarting . . .

Csongor Nyulas
Administrator
Rafael is probably right about the turtle serialization causing this. Even if it is not the turtle serialization, per se, this is what is happening:

When you open the OWL file in Protege, it will set the ontology IRI and the default prefix to whatever the ontology path was REPEATED TWICE, then appends the local ontology name.
So, in case you open the attached ontology, which I generated from your ontology by collapsing the 512 times repetition of "www.pizza.com/ontologies/" to "www.pizza.com/ontologiesX512/", you can see that the ontology IRI will be set as:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl
and the default prefix to:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl#
despite the fact that in the OWL file both the ontology IRI, the default prefix and the XML base is specified as:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl

If you modify and save your file, the length of the ontology IRI and default prefix will be doubled. Next time you open it, it will doubled again.

The clue for me was that you had "www.pizza.com/ontologies/" repeated 1024 times in the ontology IRI and default prefix, and some of your entities had a prefix with "www.pizza.com/ontologies/" repeated 512 times. So apparently you opened, modified and saved your ontologies 10 times, to get to an ontology IRI that contain "www.pizza.com/ontologies/" repeated 2^10 times.

I hope this helps the debugging.

Csongor


On 08/05/2016 04:26 PM, Rafael Gonçalves wrote:
Hi David,

It might be an issue with the Turtle serializer in the OWL API. Do you happen to have a version of the ontology before whatever changes preceded the Save? 

Cheers,
Rafael

On Aug 5, 2016, at 12:58, Dave McComb <[hidden email]> wrote:

Well that is certainly bizarre looking. 

I looked at the owl, and loaded it in protege.  Have to admit I’ve never seen anything quite like this.

Do you still have it open in Protege? 

What’s odd, of course is the long repetitions of ontologies/www.pizza.com over and over again.  

The other thing that is odd, is the owl file only has ten lines and has no classes, and yet many of them showed up when I opened the file. (no explanation for that)

But where a clue might exist: in your screen shot there are valid subclasses of Pizza_Topping.  when its loaded anew from the file all the subclass of Pizza_Topping are the weird repetitive ontologies/www.pizza.com .  if you could click on the Pizza_Topping we might see a clue as to what sent it in this tizzy. 


On Aug 5, 2016, at 1:03 PM, David Hay <[hidden email]> wrote:

I was away from Protege for a few months, but I have signed up for Dave McComb's course in September.  Today I fired it up again. Dave had told me to load version 5.0 which I did.  One problem is that the tutorial from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in the attached file (Pizza1.owl).  I have also attached the main windows from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
- Dwight Eisenhower

<Pizza Dashboard.JPG><Pizza1.owl>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Restarting . . .

Dave McComb-2
Csongor, excellent sleuthing. 

Are you suggesting that David put the domain name in the prefix field ( in the Ontology Prefixes tab?)  

David can you confirm that (or at least that that may have been the cause)  (the left hand column in that window should be the qname which is usually 3 or 4 letters.  That window is especially fiddly and often changes don’t take the first time you type them in.  

David, you do seem to come up with creative use cases that somehow never occur to anyone else. 



On Aug 5, 2016, at 6:27 PM, Csongor Nyulas <[hidden email]> wrote:

Rafael is probably right about the turtle serialization causing this. Even if it is not the turtle serialization, per se, this is what is happening:

When you open the OWL file in Protege, it will set the ontology IRI and the default prefix to whatever the ontology path was REPEATED TWICE, then appends the local ontology name.
So, in case you open the attached ontology, which I generated from your ontology by collapsing the 512 times repetition of "www.pizza.com/ontologies/" to "www.pizza.com/ontologiesX512/", you can see that the ontology IRI will be set as:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl
and the default prefix to:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl#
despite the fact that in the OWL file both the ontology IRI, the default prefix and the XML base is specified as:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl

If you modify and save your file, the length of the ontology IRI and default prefix will be doubled. Next time you open it, it will doubled again.

The clue for me was that you had "www.pizza.com/ontologies/" repeated 1024 times in the ontology IRI and default prefix, and some of your entities had a prefix with "www.pizza.com/ontologies/" repeated 512 times. So apparently you opened, modified and saved your ontologies 10 times, to get to an ontology IRI that contain "www.pizza.com/ontologies/" repeated 2^10 times.

I hope this helps the debugging.

Csongor


On 08/05/2016 04:26 PM, Rafael Gonçalves wrote:
Hi David,

It might be an issue with the Turtle serializer in the OWL API. Do you happen to have a version of the ontology before whatever changes preceded the Save? 

Cheers,
Rafael

On Aug 5, 2016, at 12:58, Dave McComb <[hidden email]> wrote:

Well that is certainly bizarre looking. 

I looked at the owl, and loaded it in protege.  Have to admit I’ve never seen anything quite like this.

Do you still have it open in Protege? 

What’s odd, of course is the long repetitions of ontologies/www.pizza.com over and over again.  

The other thing that is odd, is the owl file only has ten lines and has no classes, and yet many of them showed up when I opened the file. (no explanation for that)

But where a clue might exist: in your screen shot there are valid subclasses of Pizza_Topping.  when its loaded anew from the file all the subclass of Pizza_Topping are the weird repetitive ontologies/www.pizza.com .  if you could click on the Pizza_Topping we might see a clue as to what sent it in this tizzy. 


On Aug 5, 2016, at 1:03 PM, David Hay <[hidden email]> wrote:

I was away from Protege for a few months, but I have signed up for Dave McComb's course in September.  Today I fired it up again. Dave had told me to load version 5.0 which I did.  One problem is that the tutorial from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in the attached file (Pizza1.owl).  I have also attached the main windows from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
- Dwight Eisenhower

<Pizza Dashboard.JPG><Pizza1.owl>_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Restarting . . .

sanju tiwari
In reply to this post by David Hay-2
Hello 
somebody can help me to put my own ontology on serverside.
my ontology is stored in my computer and I want to show it in URI. So how can I do that


On Sat, Aug 6, 2016 at 12:33 AM, David Hay <[hidden email]> wrote:
I was away from Protege for a few months, but I have signed up for Dave McComb's course in September.  Today I fired it up again. Dave had told me to load version 5.0 which I did.  One problem is that the tutorial from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in the attached file (Pizza1.owl).  I have also attached the main windows from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
-       Dwight Eisenhower


_______________________________________________
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--
Regards
Sanju Mishra Tiwari
TMU Moradabad

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Re: Restarting . . .

Lorenz Buehmann
Wrong mailing list and wrong thread.
Hello 
somebody can help me to put my own ontology on serverside.
my ontology is stored in my computer and I want to show it in URI. So how can I do that


On Sat, Aug 6, 2016 at 12:33 AM, David Hay <[hidden email]> wrote:
I was away from Protege for a few months, but I have signed up for Dave McComb's course in September.  Today I fired it up again. Dave had told me to load version 5.0 which I did.  One problem is that the tutorial from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in the attached file (Pizza1.owl).  I have also attached the main windows from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
-       Dwight Eisenhower


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user




--
Regards
Sanju Mishra Tiwari
TMU Moradabad


_______________________________________________
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[hidden email]
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-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

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Re: Restarting . . .

Csongor Nyulas
Administrator
In reply to this post by Dave McComb-2

Just to clarify,


I did not suggest any particular solution/workaround for this. I was just trying to help understand what is going on, in the hope that we can reproduce it, explain it, and at some point even fix it.


Csongor


From: protege-user <[hidden email]> on behalf of Dave McComb <[hidden email]>
Sent: Friday, August 5, 2016 5:57:15 PM
To: User support for WebProtege and Protege Desktop
Cc: David C. Hay
Subject: Re: [protege-user] Restarting . . .
 
Csongor, excellent sleuthing. 

Are you suggesting that David put the domain name in the prefix field ( in the Ontology Prefixes tab?)  

David can you confirm that (or at least that that may have been the cause)  (the left hand column in that window should be the qname which is usually 3 or 4 letters.  That window is especially fiddly and often changes don’t take the first time you type them in.  

David, you do seem to come up with creative use cases that somehow never occur to anyone else. 



On Aug 5, 2016, at 6:27 PM, Csongor Nyulas <[hidden email]> wrote:

Rafael is probably right about the turtle serialization causing this. Even if it is not the turtle serialization, per se, this is what is happening:

When you open the OWL file in Protege, it will set the ontology IRI and the default prefix to whatever the ontology path was REPEATED TWICE, then appends the local ontology name.
So, in case you open the attached ontology, which I generated from your ontology by collapsing the 512 times repetition of "www.pizza.com/ontologies/" to "www.pizza.com/ontologiesX512/", you can see that the ontology IRI will be set as:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl
and the default prefix to:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl#
despite the fact that in the OWL file both the ontology IRI, the default prefix and the XML base is specified as:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl

If you modify and save your file, the length of the ontology IRI and default prefix will be doubled. Next time you open it, it will doubled again.

The clue for me was that you had "www.pizza.com/ontologies/" repeated 1024 times in the ontology IRI and default prefix, and some of your entities had a prefix with "www.pizza.com/ontologies/" repeated 512 times. So apparently you opened, modified and saved your ontologies 10 times, to get to an ontology IRI that contain "www.pizza.com/ontologies/" repeated 2^10 times.

I hope this helps the debugging.

Csongor


On 08/05/2016 04:26 PM, Rafael Gonçalves wrote:
Hi David,

It might be an issue with the Turtle serializer in the OWL API. Do you happen to have a version of the ontology before whatever changes preceded the Save? 

Cheers,
Rafael

On Aug 5, 2016, at 12:58, Dave McComb <[hidden email]> wrote:

Well that is certainly bizarre looking. 

I looked at the owl, and loaded it in protege.  Have to admit I’ve never seen anything quite like this.

Do you still have it open in Protege? 

What’s odd, of course is the long repetitions of ontologies/www.pizza.com over and over again.  

The other thing that is odd, is the owl file only has ten lines and has no classes, and yet many of them showed up when I opened the file. (no explanation for that)

But where a clue might exist: in your screen shot there are valid subclasses of Pizza_Topping.  when its loaded anew from the file all the subclass of Pizza_Topping are the weird repetitive ontologies/www.pizza.com .  if you could click on the Pizza_Topping we might see a clue as to what sent it in this tizzy. 


On Aug 5, 2016, at 1:03 PM, David Hay <[hidden email]> wrote:

I was away from Protege for a few months, but I have signed up for Dave McComb's course in September.  Today I fired it up again. Dave had told me to load version 5.0 which I did.  One problem is that the tutorial from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in the attached file (Pizza1.owl).  I have also attached the main windows from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
- Dwight Eisenhower

<Pizza Dashboard.JPG><Pizza1.owl>_______________________________________________
protege-user mailing list
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Re: Restarting . . .

Csongor Nyulas
Administrator
In reply to this post by Csongor Nyulas

Hi David Hay (copying the mailing list too)


please see my inline answers below...


From: David Hay <[hidden email]>
Sent: Sunday, August 7, 2016 1:59 PM
To: Csongor Nyulas
Cc: Dave McComb
Subject: Re: [protege-user] Restarting . . .
 
Csongor,

Thank you for your analysis.  I see that your result gave me a manuscript that I can now read.  I don't quite understand why this is so, but thanks.

Basically every time I found 512 times repetition of "www.pizza.com/ontologies/" I replaced it with "www.pizza.com/ontologiesX512/" so that you can have a better overview of the statement in your ontology.

Forgetting for a moment why you had to rename .../ontologies to .../ontologies512, why was it doubled?  In your note you said it had actually been doubled again, but I don't see that in the script.

As I said above, I did not just replaced .../ontologies with /ontolgies512, but 512 consequent occurances of .../ontologies with .../ontologiesX512, to shorten the file.
When you see "www.pizza.com/ontologiesX512/" followed by another "www.pizza.com/ontologiesX512/" in the file, it means that there were 1024 repetitions on "www.pizza.com/ontologies/" in a row in your file. That's what I mean by doubled, and it is caused by saving the file after being modified in Protege.

I did open Pizza4.owl and saved it back immediately as Pizza5.owl.  Nothing changed. If I start making changes to it, will that set this off again?

It is not enough to open the file and save it back immediately (at least it wasn't enough in my case). After opening the file, you need to make at least one change (try to create a class, for example), and then save it to the disk. I am not sure whether saving it under a different name, as you did, exhibits the problem, but if you just save it under the same name (with CTRL+S or File -> Save) you will see that the ontology IRI and your defaul prefix will be doubled, i.e. "www.pizza.com/ontologiesX512/" will appear 4 times, which means that if we would not have shortened the namespaces already, you would see 2048 repetitions of "www.pizza.com/ontologies/".

Thanks again for your help.

Dave

On 8/5/2016 7:27 PM, Csongor Nyulas wrote:
Rafael is probably right about the turtle serialization causing this. Even if it is not the turtle serialization, per se, this is what is happening:

When you open the OWL file in Protege, it will set the ontology IRI and the default prefix to whatever the ontology path was REPEATED TWICE, then appends the local ontology name.
So, in case you open the attached ontology, which I generated from your ontology by collapsing the 512 times repetition of "www.pizza.com/ontologies/" to "www.pizza.com/ontologiesX512/", you can see that the ontology IRI will be set as:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl
and the default prefix to:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl#
despite the fact that in the OWL file both the ontology IRI, the default prefix and the XML base is specified as:
www.pizza.com/ontologiesX512/www.pizza.com/ontologiesX512/pizza.owl

If you modify and save your file, the length of the ontology IRI and default prefix will be doubled. Next time you open it, it will doubled again.

The clue for me was that you had "www.pizza.com/ontologies/" repeated 1024 times in the ontology IRI and default prefix, and some of your entities had a prefix with "www.pizza.com/ontologies/" repeated 512 times. So apparently you opened, modified and saved your ontologies 10 times, to get to an ontology IRI that contain "www.pizza.com/ontologies/" repeated 2^10 times.

I hope this helps the debugging.

Csongor


On 08/05/2016 04:26 PM, Rafael Gonçalves wrote:
Hi David,

It might be an issue with the Turtle serializer in the OWL API. Do you happen to have a version of the ontology before whatever changes preceded the Save? 

Cheers,
Rafael

On Aug 5, 2016, at 12:58, Dave McComb <[hidden email]> wrote:

Well that is certainly bizarre looking. 

I looked at the owl, and loaded it in protege.  Have to admit I’ve never seen anything quite like this.

Do you still have it open in Protege? 

What’s odd, of course is the long repetitions of ontologies/www.pizza.com over and over again.  

The other thing that is odd, is the owl file only has ten lines and has no classes, and yet many of them showed up when I opened the file. (no explanation for that)

But where a clue might exist: in your screen shot there are valid subclasses of Pizza_Topping.  when its loaded anew from the file all the subclass of Pizza_Topping are the weird repetitive ontologies/www.pizza.com .  if you could click on the Pizza_Topping we might see a clue as to what sent it in this tizzy. 


On Aug 5, 2016, at 1:03 PM, David Hay <[hidden email]> wrote:

I was away from Protege for a few months, but I have signed up for Dave McComb's course in September.  Today I fired it up again. Dave had told me to load version 5.0 which I did.  One problem is that the tutorial from 2011 is even further from the prompts on the screen.

But I persevered, and just finished Step 4.10. Yaay!  However . . .

When I saved it and looked at my Turtle file I got what you'll see in the attached file (Pizza1.owl).  I have also attached the main windows from the dashboard.

Any ideas what's going on?

Thanks,

Dave Hay

(713) 464-8316

Things are more like they are now
Than they ever were before.
- Dwight Eisenhower

<Pizza Dashboard.JPG><Pizza1.owl>_______________________________________________
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_______________________________________________
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-- 
Dave Hay
(713) 464-8316

Things are more like they are now
Than they ever were before.
-	Dwight Eisenhower

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user