Importing SNOMED Ontology

classic Classic list List threaded Threaded
7 messages Options
Reply | Threaded
Open this post in threaded view
|

Importing SNOMED Ontology

ozairbajwa
Hi,

I am new to Protege and Ontology Development

I am building on an existing owl Ontology in Health Care. There are two owl
files and one of them refers the second one and is supposed to import it.
However I am struggling to understand how the two ontologies are linked and
where is the reference.  The second ontology that is supposed to be imported
is the large SNOMED Ontolog. Basically I am confused when one ontology
imports other, how are they linked and how to put the pieces together.







--
Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Importing SNOMED Ontology

sanju tiwari
Hi
After importing the other ontology, it will have a different reference than main ontology. All concepts will be with its different URI. So there will not be any conflict with main ontoloy. Both will have a different address.
For example, Protein class in main ontology and also exist in Snomed ontology that will imported so  
Class in main: Protein
While in imported it will be:
snom:Protein. So both are different classes.
I hope it will work for you.

On Sun, 29 Mar 2020, 04:58 ozairbajwa, <[hidden email]> wrote:
Hi,

I am new to Protege and Ontology Development

I am building on an existing owl Ontology in Health Care. There are two owl
files and one of them refers the second one and is supposed to import it.
However I am struggling to understand how the two ontologies are linked and
where is the reference.  The second ontology that is supposed to be imported
is the large SNOMED Ontolog. Basically I am confused when one ontology
imports other, how are they linked and how to put the pieces together.







--
Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Importing SNOMED Ontology

ozairbajwa
Hi,
Thanks for your response.
May be I did not state it correctly. I understand both Ontologies have a
different address and won't overlap. I wanted to know how is Ontology A
using the imported SNOMED ontology. If I understand it correctly the idea of
importing an ontology is to be able to use it or refer to it's concepts. A
class/concept in Ontology A should be able to refer to or access the
relevant class/concept in the SNOMED ontology.

Appreciate the feedback



--
Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Importing SNOMED Ontology

samsontu
Hi,

On Mar 28, 2020, at 4:58 PM, ozairbajwa <[hidden email]> wrote:

Hi,
Thanks for your response.
May be I did not state it correctly. I understand both Ontologies have a
different address and won't overlap. I wanted to know how is Ontology A
using the imported SNOMED ontology. If I understand it correctly the idea of
importing an ontology is to be able to use it or refer to it's concepts. A
class/concept in Ontology A should be able to refer to or access the
relevant class/concept in the SNOMED ontology.

Ontology A imports Ontology B when Ontology A has an import statement like:
...
    <owl:Ontology rdf:about="http://www.semanticweb.org/ontologies/A">
        <owl:imports rdf:resource="http://www.semanticweb.org/ontologies/B"/>
    </owl:Ontology>

In Protege Desktop user interface, it looks like 

In Protege, once A imports B, you can do anything with entities in Ontology B as you would any other entity in Ontology A.

With best regards,
Samson


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Importing SNOMED Ontology

sanju tiwari
Thanks Samson
You have cleared very well with a simple example.


On Sun, 29 Mar 2020, 06:30 Samson Tu, <[hidden email]> wrote:
Hi,

On Mar 28, 2020, at 4:58 PM, ozairbajwa <[hidden email]> wrote:

Hi,
Thanks for your response.
May be I did not state it correctly. I understand both Ontologies have a
different address and won't overlap. I wanted to know how is Ontology A
using the imported SNOMED ontology. If I understand it correctly the idea of
importing an ontology is to be able to use it or refer to it's concepts. A
class/concept in Ontology A should be able to refer to or access the
relevant class/concept in the SNOMED ontology.

Ontology A imports Ontology B when Ontology A has an import statement like:
...
    <owl:Ontology rdf:about="http://www.semanticweb.org/ontologies/A">
        <owl:imports rdf:resource="http://www.semanticweb.org/ontologies/B"/>
    </owl:Ontology>

In Protege Desktop user interface, it looks like 

In Protege, once A imports B, you can do anything with entities in Ontology B as you would any other entity in Ontology A.

With best regards,
Samson

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

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

PastedGraphic-1.png (75K) Download Attachment
PastedGraphic-1.png (75K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Importing SNOMED Ontology

ozairbajwa
Hi Samson and Dr. Tiwari,

Thanks a lot for the clarification.
After your response I checked my two ontology files and there was an issue
with the import statement and hence second ontology was not imported. After
resolving that now it seems to be working.
I am building on an existing ontology that imports the SNOMED ontology. I
understand SNOMED CT quite well but I am not able to connect the dots in
Protege. I just finished a basic course in Protege but could not find any
tutorials related to SNOMED ontology in Protege. Can somebody guide or point
me to the relevant resources?
Is this the right forum to post questions related to SNOMED in Protege?

Really appreciate the feedback.

Thanks
Ozair



--
Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: Importing SNOMED Ontology

samsontu


On Mar 31, 2020, at 3:30 PM, ozairbajwa <[hidden email]> wrote:

Hi Samson and Dr. Tiwari,

Thanks a lot for the clarification.
After your response I checked my two ontology files and there was an issue
with the import statement and hence second ontology was not imported. After
resolving that now it seems to be working.
I am building on an existing ontology that imports the SNOMED ontology. I
understand SNOMED CT quite well but I am not able to connect the dots in
Protege. I just finished a basic course in Protege but could not find any
tutorials related to SNOMED ontology in Protege. Can somebody guide or point
me to the relevant resources?
Is this the right forum to post questions related to SNOMED in Protege?

I am not aware of any tutorial on how to work with SNOMED in Protege. However, I’ve worked with SNOMED in Protege before and I don’t think SNOMED CT poses any special issue for Protege. Just allocation a lot of memory to the Java heap space (the Java -Xmx setting), as you would for any large ontology.

This is the mailing list for using Protege. Any Protege-related usage question is appropriate.

With best regards,
Samson



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