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Regarding the MYSQL Connection in PROTEGE 4.3

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Regarding the MYSQL Connection in PROTEGE 4.3

aashna verma
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

Lorenz B.
And once you connected to MySQL you still need a mapping from your database schema to the ontology. Do you have this already? You can have a look at the Ontop plugin but in any case you have to create the mapping since this is non-trivial and depends you.

Respected Sir,

How can we connect an owl file with database.Is it feasible to connect to
jdbc and mysql in Protege 4.3.I am working in eclipse and added all jars of
protege in eclipse.But I want to connect my Owl file with Mysql database,so
that i can retreive information through MYSQL.Thanking You in advance for
your help 



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Re: Regarding the MYSQL Connection in PROTEGE 4.3

aashna verma
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

samsontu
Hi,

Is there a compelling reason for you to use Protege 4.3? 

In Protege 5.x, you can use the Ontop plugin [1] to connect your ontology to a relational database, i.e., create mappings from the ontology to the database so that you can make SPARQL queries against the combined ontology/database information content.

Neither Protege 4.3 nor Protege 5.x supports the "database backend” (i.e., storage of ontology in a relational database) that Protege 3.x had.

With best regards,
Samson


On Apr 8, 2017, at 10:49 AM, aashna verma <[hidden email]> wrote:

Thank you sir for your reply.I am new to ontologies.Despite of reading papers
and research,I cannot understand how owl file is connected to mysql.There
are some tutorials like
https://protegewiki.stanford.edu/wiki/Working_with_the_Database_Backend_in_OWL
but these are based on protege 3x,and i am working on protege 4.3(Build
304).

Sir,I am able to connect
1. protege with eclipse with the help of plugin and OWLAPI.
2. I am able to connect MYSQL with Eclipse.
3.I am able to work with .OWL file in eclipse.

But My main Problem is,How can we connect MySQL with protege 4.3.I dont
know,whether I am on the riight track or not.Sir,Please guide me briefly.



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Re: Regarding the MYSQL Connection in PROTEGE 4.3

aashna verma
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

samsontu

On Apr 11, 2017, at 9:43 AM, aashna verma <[hidden email]> wrote:

Thank you so much sir.By Using Ontop i am able to connect protege5 with
database MySQL.Sir, I dont know whether what i am thinking to do with
ontology is posible or not.

Now my question is, if we have ontology linked with data properties,and the
MYSQL database contains all the classes of the ontology as attribute.If we
want to retrieve the information by coding it with java.Is it feasible that
we search by sql query in java.and that searching is done by MYSQL Which is
connected to Ontology.Kindly answer.It solves a big problem of mine.


It sounds like you want to store some description of an ontology in MySQL, programmatically query the database and materialize the ontology description in OWL. You can use Java and OWL API to do whatever you want, but I don’t know what you want to do with such an ontology. You can write such custom Java code independently of Protege. The Ontop plugin won’t help you in this approach.

With best regards,
Samson

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Center for Biomedical Informatics Research  phone: 1-650-725-3391
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

aashna verma
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

aashna verma
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

Csongor Nyulas
Administrator
In reply to this post by aashna verma
The sort answer to your question is: No.

To understand better the available techniques (possibly) relevant to
your problem I would recommend that you study the ontop documentation
[1] and tutorial [2], and think about:
(1) Why do you need to ask SQL queries (instead of DL or SPARQL queries)?
(2) Why do you need ontologies at all?
(3) Why do you want to keep your classes (and not only your instances)
in databases, rather than bringing those into the ontologies?

Csongor

[1] https://github.com/ontop/ontop#links
[2] https://www.youtube.com/watch?v=KHtlARfex4c



On 04/11/2017 11:09 AM, aashna verma wrote:

> Sir,i want to retrieve the information from ontology.I am thinking of making
> a general ontology like for eg pizza ontology.I am making an ontology like
> pizza functionality,pizza spices etc.and linked with hermit reasoner.
> I am making a MYSQL databse in which all the classes defined like pizza
> functionality,pizza spices are the attributes or the first column.
> Now i want that if i enter a simple SQL query in java .Then firstly it
> connects with MYSQL and the upper attributes connect with ontology,so that
> the information becomes precise for retrieval.Sir,It is feasible to do so.
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Regarding-the-MYSQL-Connection-in-PROTEGE-4-3-tp4668073p4668110.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
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> [hidden email]
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

samsontu
In reply to this post by aashna verma

On Apr 11, 2017, at 11:19 AM, aashna verma <[hidden email]> wrote:

Sir,i want to retrieve the information from ontology.I am thinking of making
a general ontology like for eg pizza ontology.I am making an ontology like
pizza functionality,pizza spices etc.and linked with hermit reasoner.
I am making a MYSQL databse in which all the classes defined like pizza
functionality,pizza spices are the attributes or the first row.
Now i want that if i enter a simple SQL query in java .Then firstly it
connects with MYSQL and the upper attributes connect with ontology,so that
the information becomes precise for retrieval.Sir,It is feasible to do so.


It sounds like you want to develop an ontology in Protege, export a portion of it to a MYSQL, and query the exported portion using SQL.

If that’s what you want to do, yes, it is feasible, just understand that you have to manage the export yourself, using the standard Java/SQL API.

With best regards,
Samson


-- 
Samson Tu                                                      email: [hidden email]
Senior Research Engineer                              web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                                          fax: 1-650-725-7944




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Re: Regarding the MYSQL Connection in PROTEGE 4.3

aashna verma
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

Lorenz B.
I think this is out of scope here. It looks like you want to do OBDA, but nobody here can do the project together with you.

Yes Sir,I want to do the same thing.Please explain me more briefly about
this.Like if i mapped owl classes with attributes,the various relationships
build with that classes also linked with the MYSQL database.And i have to
add JAVA/SQL Connector or write some code for that.Kindly Help.
Your answers really solved my queries well.Thank You so much sir.



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AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

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Re: Regarding the MYSQL Connection in PROTEGE 4.3

aashna verma
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

Wei Zhao
In reply to this post by aashna verma
We created our ontology in Protege.  Is there a way to map our XML data
to this ontology and out put the data in RDF in Portege?

Any ideas, suggestions are much appreciated!

Wei

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Metadata Librarian
OCUL/Scholars Portal
Phone: 416 946-0951
Fax: 416 978-1668
[hidden email]

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Re: Regarding the MYSQL Connection in PROTEGE 4.3

Csongor Nyulas
Administrator
Hi Wei,
Is this related to Aashna's question or project?

If not, can you please start a new thread (with an appropriate subject)?

You may also want to check out the mailing list archive where there were
several questions similar to yours:
http://protege-project.136.n4.nabble.com/template/NamlServlet.jtp?macro=search_page&node=136&query=XML+export

Regards,
Csongor


On 04/12/2017 11:37 AM, Wei Zhao wrote:
> We created our ontology in Protege.  Is there a way to map our XML
> data to this ontology and out put the data in RDF in Portege?
>
> Any ideas, suggestions are much appreciated!
>
> Wei
>


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Re: Regarding the MYSQL Connection in PROTEGE 4.3

Csongor Nyulas
Administrator
In reply to this post by aashna verma
Aashna,
What I think is Lorenz is saying (and what I also see looking at the
long back-and-forth on this thread) is that you seem to need much more
than just a simple direction or advise here. We gave you several advises
already, pointing you to different, but somewhat related, directions.
Unfortunately it seems that you are not familiar with how all these
technologies work and relate to each other. You are trying to accomplish
a (potentially very) difficult task, without a good understanding of the
complex tools/languages/paradigms necessary to achieve this. A mailing
list is not the ideal place to teach you all these. Can you talk to your
supervisor/advisor, or consult a semantic web expert, who can help you
define your goals and ways to approach it?

Csongor



On 04/12/2017 09:26 AM, aashna verma wrote:

> Ok .thanku sir.I only need a direction or advise that clear my goal of
> retreival.
>
>
>
> --
> View this message in context: http://protege-project.136.n4.nabble.com/Regarding-the-MYSQL-Connection-in-PROTEGE-4-3-tp4668073p4668119.html
> Sent from the Protege User mailing list archive at Nabble.com.
> _______________________________________________
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> [hidden email]
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import XML and output RDF

Wei Zhao
In reply to this post by Csongor Nyulas
We created our ontology in Protege.  Is there a way to map our XML data
to this ontology and out put the data in RDF in Portege?

Any ideas, suggestions are much appreciated!

Wei

--
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Metadata Librarian
OCUL/Scholars Portal
Phone: 416 946-0951
Fax: 416 978-1668
[hidden email]

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Re: Regarding the MYSQL Connection in PROTEGE 4.3

aashna verma
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Re: Regarding the MYSQL Connection in PROTEGE 4.3

Lorenz B.


Ok..Thanku Sir.I am a researcher and i have a bit knowledge of all these
tools.I am studying all these tools in details.But some things like
retreival from ontology using SQL 
You cannot simply retrieve something from an ontology using SQL. Who would translate the SQL query to the corresponding parts of the OWL ontology? And to be honest, I don't understand WHY you want to use SQL to get something from an ontology. The only useful thing would be query expansion which means query rewriting - but this is non-trivial and ongoing research although there are for sure some promising approaches out there.

is not given on internet.And this mailing
list provide me answer,thats the reason i enter my next question.But thanku
sir for your kind help.



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Group: http://aksw.org - semantic web research center

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Re: import XML and output RDF

Lorenz B.
In reply to this post by Wei Zhao
Any transformation language like XSLT can be used - but the mapping is your task, i.e. you have to decide which XML tag is supposed to be what type of entity in your ontology.

We created our ontology in Protege.  Is there a way to map our XML data to this ontology and out put the data in RDF in Portege?

Any ideas, suggestions are much appreciated!

Wei

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

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