Namespace and RDF/XML Serialisation

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Namespace and RDF/XML Serialisation

Christian Knuepfer-2
Hi,

since Protege 4.1 the default namespace is repeated in each Class
statement. E.g. if I have an ontology with


xmlns="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl#"
xml:base="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl"


the I got the following statement in the RDF/XML file:


<owl:Class rdf:about="&ontology1297094364376;test"/>


Why is the default/base namespace repeated here? This was not the case
in Protege 4.0.x. There the statement looks like:


<owl:Class rdf:about="#test"/>


Is there a way to get back the old statement style?


Best,

Christian.


--
Christian Knuepfer
Friedrich-Schiller-Universitaet Jena
Institut fuer Informatik
Ernst-Abbe-Platz 1-4
D-07743 Jena, Germany

Office: R. 3237
Phone: Intl.+49-3641-9-46353
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Re: Namespace and RDF/XML Serialisation

Timothy Redmond

This is really an OWL api question (owlapi.sourceforge.net).  
Fortunately the Protege developers by and large don't have to deal with
the low level details of rdf serialization.

My personal feeling about this is that I think it makes more sense to
focus on the OWL content rather than the low level details of the rdf
serialization.   But the OWL api developers have made other user
requested changes to the serialization such as alphabetizing the results
to make svn diffs more useful.

-Timothy


On 02/07/2011 08:14 AM, Christian Knuepfer wrote:

> Hi,
>
> since Protege 4.1 the default namespace is repeated in each Class
> statement. E.g. if I have an ontology with
>
>
> xmlns="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl#"
> xml:base="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl"
>
>
> the I got the following statement in the RDF/XML file:
>
>
> <owl:Class rdf:about="&ontology1297094364376;test"/>
>
>
> Why is the default/base namespace repeated here? This was not the case
> in Protege 4.0.x. There the statement looks like:
>
>
> <owl:Class rdf:about="#test"/>
>
>
> Is there a way to get back the old statement style?
>
>
> Best,
>
> Christian.
>
>

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Re: Namespace and RDF/XML Serialisation

Christian Knuepfer-2
In reply to this post by Christian Knuepfer-2
Hi Timothy,

Thank you for the response!

Usually, I also don't care about serialisation. My problem is exactly
what you mentioned: If I just open and save an owl-file in 4.1 I got a
huge number of changes in svn diff because of the changed rdf:about style.

So hopefully this scheme for rdf:about will now be stable...


Cheers,

Christian.

> Message: 5 Date: Mon, 07 Feb 2011 09:25:50 -0800 From: Timothy
> Redmond <[hidden email]> To: [hidden email]
> Subject: Re: [p4-feedback] Namespace and RDF/XML Serialisation
> Message-ID: <[hidden email]> Content-Type: text/plain;
> charset=ISO-8859-1; format=flowed
>
>
> This is really an OWL api question (owlapi.sourceforge.net).
> Fortunately the Protege developers by and large don't have to deal
> with the low level details of rdf serialization.
>
> My personal feeling about this is that I think it makes more sense to
> focus on the OWL content rather than the low level details of the rdf
> serialization.   But the OWL api developers have made other user
> requested changes to the serialization such as alphabetizing the
> results to make svn diffs more useful.
>
> -Timothy
>
>
> On 02/07/2011 08:14 AM, Christian Knuepfer wrote:
>> Hi,
>>
>> since Protege 4.1 the default namespace is repeated in each Class
>> statement. E.g. if I have an ontology with
>>
>>
>> xmlns="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl#"
>>
>> xml:base="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl"
>>
>>
>> the I got the following statement in the RDF/XML file:
>>
>>
>> <owl:Class rdf:about="&ontology1297094364376;test"/>
>>
>>
>> Why is the default/base namespace repeated here? This was not the
>> case in Protege 4.0.x. There the statement looks like:
>>
>>
>> <owl:Class rdf:about="#test"/>
>>
>>
>> Is there a way to get back the old statement style?
>>
>>
>> Best,
>>
>> Christian.
>>
>>


--
Christian Knuepfer
Friedrich-Schiller-Universitaet Jena
Institut fuer Informatik
Ernst-Abbe-Platz 1-4
D-07743 Jena, Germany

Office: R. 3237
Phone: Intl.+49-3641-9-46353
Fax: Intl.+49-3641-9-46302

e-mail: [hidden email]
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Re: Namespace and RDF/XML Serialisation

Timothy Redmond
On 02/07/2011 11:59 PM, Christian Knuepfer wrote:
> Hi Timothy,
>
> Thank you for the response!
>
> Usually, I also don't care about serialisation. My problem is exactly
> what you mentioned: If I just open and save an owl-file in 4.1 I got a
> huge number of changes in svn diff because of the changed rdf:about style.
>
> So hopefully this scheme for rdf:about will now be stable...

Yes - this is a problem in need of a good solution.   The best thing
would be if an OWL aware diff tool was integrated into svn.  This would
allow you to edit with whatever tool suited your purpose at the time and
still be sure that the calculated diffs are reasonable.  I believe that
OWL diff can do this but I haven't actually configured this so I don't
know how well this combination works.

-Timothy

>
> Cheers,
>
> Christian.
>
>> Message: 5 Date: Mon, 07 Feb 2011 09:25:50 -0800 From: Timothy
>> Redmond<[hidden email]>  To: [hidden email]
>> Subject: Re: [p4-feedback] Namespace and RDF/XML Serialisation
>> Message-ID:<[hidden email]>  Content-Type: text/plain;
>> charset=ISO-8859-1; format=flowed
>>
>>
>> This is really an OWL api question (owlapi.sourceforge.net).
>> Fortunately the Protege developers by and large don't have to deal
>> with the low level details of rdf serialization.
>>
>> My personal feeling about this is that I think it makes more sense to
>> focus on the OWL content rather than the low level details of the rdf
>> serialization.   But the OWL api developers have made other user
>> requested changes to the serialization such as alphabetizing the
>> results to make svn diffs more useful.
>>
>> -Timothy
>>
>>
>> On 02/07/2011 08:14 AM, Christian Knuepfer wrote:
>>> Hi,
>>>
>>> since Protege 4.1 the default namespace is repeated in each Class
>>> statement. E.g. if I have an ontology with
>>>
>>>
>>> xmlns="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl#"
>>>
>>> xml:base="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl"
>>>
>>>
>>> the I got the following statement in the RDF/XML file:
>>>
>>>
>>> <owl:Class rdf:about="&ontology1297094364376;test"/>
>>>
>>>
>>> Why is the default/base namespace repeated here? This was not the
>>> case in Protege 4.0.x. There the statement looks like:
>>>
>>>
>>> <owl:Class rdf:about="#test"/>
>>>
>>>
>>> Is there a way to get back the old statement style?
>>>
>>>
>>> Best,
>>>
>>> Christian.
>>>
>>>
>

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Re: Namespace and RDF/XML Serialisation

alexz
In reply to this post by Christian Knuepfer-2
Wouldn't it be nice if there were a "semantic svn". It would allow you
to define an equivalence relation corresponding to your interest and
would maintain a tree in which there is no change when a commit is
equivalent to the previous under that relation, and perhaps another
tree for the current equivalence, which is character-wise identical.
In fact, why stop at just these two equivalence relations. The repo
could support multiple such.

Bob Morris

On Tue, Feb 8, 2011 at 2:59 AM, Christian Knuepfer
<[hidden email]> wrote:

> Hi Timothy,
>
> Thank you for the response!
>
> Usually, I also don't care about serialisation. My problem is exactly
> what you mentioned: If I just open and save an owl-file in 4.1 I got a
> huge number of changes in svn diff because of the changed rdf:about style.
>
> So hopefully this scheme for rdf:about will now be stable...
>
>
> Cheers,
>
> Christian.
>
>> Message: 5 Date: Mon, 07 Feb 2011 09:25:50 -0800 From: Timothy
>> Redmond <[hidden email]> To: [hidden email]
>> Subject: Re: [p4-feedback] Namespace and RDF/XML Serialisation
>> Message-ID: <[hidden email]> Content-Type: text/plain;
>> charset=ISO-8859-1; format=flowed
>>
>>
>> This is really an OWL api question (owlapi.sourceforge.net).
>> Fortunately the Protege developers by and large don't have to deal
>> with the low level details of rdf serialization.
>>
>> My personal feeling about this is that I think it makes more sense to
>> focus on the OWL content rather than the low level details of the rdf
>> serialization.   But the OWL api developers have made other user
>> requested changes to the serialization such as alphabetizing the
>> results to make svn diffs more useful.
>>
>> -Timothy
>>
>>
>> On 02/07/2011 08:14 AM, Christian Knuepfer wrote:
>>> Hi,
>>>
>>> since Protege 4.1 the default namespace is repeated in each Class
>>> statement. E.g. if I have an ontology with
>>>
>>>
>>> xmlns="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl#"
>>>
>>> xml:base="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl"
>>>
>>>
>>> the I got the following statement in the RDF/XML file:
>>>
>>>
>>> <owl:Class rdf:about="&ontology1297094364376;test"/>
>>>
>>>
>>> Why is the default/base namespace repeated here? This was not the
>>> case in Protege 4.0.x. There the statement looks like:
>>>
>>>
>>> <owl:Class rdf:about="#test"/>
>>>
>>>
>>> Is there a way to get back the old statement style?
>>>
>>>
>>> Best,
>>>
>>> Christian.
>>>
>>>
>
>
> --
> Christian Knuepfer
> Friedrich-Schiller-Universitaet Jena
> Institut fuer Informatik
> Ernst-Abbe-Platz 1-4
> D-07743 Jena, Germany
>
> Office: R. 3237
> Phone: Intl.+49-3641-9-46353
> Fax: Intl.+49-3641-9-46302
>
> e-mail: [hidden email]
> WWW: http://www.informatik.uni-jena.de/~tral
>
> PGP Key-ID: 0xC3329342
> PGP Public Key:
>  http://www.minet.uni-jena.de/~tral/data/christian_knuepfer_pub.asc
> Fingerprint 5656 7F57 8E58 FC7B AC58 6714 3DA4 3181 C332 9342
> --
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>



--
Robert A. Morris
Emeritus Professor  of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390
Associate, Harvard University Herbaria
email: [hidden email]
web: http://efg.cs.umb.edu/
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Re: Namespace and RDF/XML Serialisation

Rich Morin
At 8:35 AM -0500 2/8/11, Bob Morris wrote:
> Wouldn't it be nice if there were a "semantic svn".

If one wanted to build such a thing, Git might be a
better starting point.  It is very modular and has a
very solid foundation ("blobs" of data and metadata
are stored by their cryptographic checksums).

By creating sets of canonical "signature files" for
RDF data, one might well be able to leverage Git's
organizational capabilities.

-r
--
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http://www.cfcl.com/rdm/resume     [hidden email]
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Software system design, development, and documentation
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Re: Namespace and RDF/XML Serialisation

Melanie Courtot-2
In reply to this post by Christian Knuepfer-2
Hi Christian,

If you are looking for a diff tool: I have been using Bubastis, http://wwwdev.ebi.ac.uk/efo/bubastis/ 
, developed by James Malone at the EBI, and found it worked quite well  
in my case. A standalone version is also available at http://www.ebi.ac.uk/efo/tools

Cheers,
Melanie


On 7-Feb-11, at 11:59 PM, Christian Knuepfer wrote:

> Hi Timothy,
>
> Thank you for the response!
>
> Usually, I also don't care about serialisation. My problem is exactly
> what you mentioned: If I just open and save an owl-file in 4.1 I got a
> huge number of changes in svn diff because of the changed rdf:about  
> style.
>
> So hopefully this scheme for rdf:about will now be stable...
>
>
> Cheers,
>
> Christian.
>
>> Message: 5 Date: Mon, 07 Feb 2011 09:25:50 -0800 From: Timothy
>> Redmond <[hidden email]> To: [hidden email]
>> Subject: Re: [p4-feedback] Namespace and RDF/XML Serialisation
>> Message-ID: <[hidden email]> Content-Type: text/plain;
>> charset=ISO-8859-1; format=flowed
>>
>>
>> This is really an OWL api question (owlapi.sourceforge.net).
>> Fortunately the Protege developers by and large don't have to deal
>> with the low level details of rdf serialization.
>>
>> My personal feeling about this is that I think it makes more sense to
>> focus on the OWL content rather than the low level details of the rdf
>> serialization.   But the OWL api developers have made other user
>> requested changes to the serialization such as alphabetizing the
>> results to make svn diffs more useful.
>>
>> -Timothy
>>
>>
>> On 02/07/2011 08:14 AM, Christian Knuepfer wrote:
>>> Hi,
>>>
>>> since Protege 4.1 the default namespace is repeated in each Class
>>> statement. E.g. if I have an ontology with
>>>
>>>
>>> xmlns="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl# 
>>> "
>>>
>>> xml:base="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl 
>>> "
>>>
>>>
>>> the I got the following statement in the RDF/XML file:
>>>
>>>
>>> <owl:Class rdf:about="&ontology1297094364376;test"/>
>>>
>>>
>>> Why is the default/base namespace repeated here? This was not the
>>> case in Protege 4.0.x. There the statement looks like:
>>>
>>>
>>> <owl:Class rdf:about="#test"/>
>>>
>>>
>>> Is there a way to get back the old statement style?
>>>
>>>
>>> Best,
>>>
>>> Christian.
>>>
>>>
>
>
> --
> Christian Knuepfer
> Friedrich-Schiller-Universitaet Jena
> Institut fuer Informatik
> Ernst-Abbe-Platz 1-4
> D-07743 Jena, Germany
>
> Office: R. 3237
> Phone: Intl.+49-3641-9-46353
> Fax: Intl.+49-3641-9-46302
>
> e-mail: [hidden email]
> WWW: http://www.informatik.uni-jena.de/~tral
>
> PGP Key-ID: 0xC3329342
> PGP Public Key:
>  http://www.minet.uni-jena.de/~tral/data/christian_knuepfer_pub.asc
> Fingerprint 5656 7F57 8E58 FC7B AC58 6714 3DA4 3181 C332 9342
> --
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

---
Mélanie Courtot
MSFHR trainee, TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada






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Re: Namespace and RDF/XML Serialisation

Christian Knuepfer-2
Hi Melanie,

Thank you for pointing me to Bubastis. Unfortunately, the standalone
version brings some parser error. More important, Bubastis doesn’t
consider changes in the annotations.

At the moment, I'm very happy with OWLDiff. It works really great, also
in connection with subversion! From their webpage:


"To run subversion diff on linux platform type
svn diff --diff-cmd ./svn-owldiff {R}

It performs the diff between local copy of {R} and repository HEAD. (of
course, you can use also other 'svn diff' options)." [1]



Thanks again,

Christian.

[1] http://krizik.felk.cvut.cz/km/owldiff/documentation.html



Am 08.02.2011 18:32, schrieb Melanie Courtot:

> Hi Christian,
>
> If you are looking for a diff tool: I have been using Bubastis,
> http://wwwdev.ebi.ac.uk/efo/bubastis/, developed by James Malone at the
> EBI, and found it worked quite well in my case. A standalone version is
> also available at http://www.ebi.ac.uk/efo/tools
>
> Cheers,
> Melanie
>
>
> On 7-Feb-11, at 11:59 PM, Christian Knuepfer wrote:
>
>> Hi Timothy,
>>
>> Thank you for the response!
>>
>> Usually, I also don't care about serialisation. My problem is exactly
>> what you mentioned: If I just open and save an owl-file in 4.1 I got a
>> huge number of changes in svn diff because of the changed rdf:about
>> style.
>>
>> So hopefully this scheme for rdf:about will now be stable...
>>
>>
>> Cheers,
>>
>> Christian.
>>
>>> Message: 5 Date: Mon, 07 Feb 2011 09:25:50 -0800 From: Timothy
>>> Redmond <[hidden email]> To: [hidden email]
>>> Subject: Re: [p4-feedback] Namespace and RDF/XML Serialisation
>>> Message-ID: <[hidden email]> Content-Type: text/plain;
>>> charset=ISO-8859-1; format=flowed
>>>
>>>
>>> This is really an OWL api question (owlapi.sourceforge.net).
>>> Fortunately the Protege developers by and large don't have to deal
>>> with the low level details of rdf serialization.
>>>
>>> My personal feeling about this is that I think it makes more sense to
>>> focus on the OWL content rather than the low level details of the rdf
>>> serialization.   But the OWL api developers have made other user
>>> requested changes to the serialization such as alphabetizing the
>>> results to make svn diffs more useful.
>>>
>>> -Timothy
>>>
>>>
>>> On 02/07/2011 08:14 AM, Christian Knuepfer wrote:
>>>> Hi,
>>>>
>>>> since Protege 4.1 the default namespace is repeated in each Class
>>>> statement. E.g. if I have an ontology with
>>>>
>>>>
>>>> xmlns="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl#"
>>>>
>>>>
>>>> xml:base="http://www.semanticweb.org/ontologies/2011/1/Ontology1297094364376.owl"
>>>>
>>>>
>>>>
>>>> the I got the following statement in the RDF/XML file:
>>>>
>>>>
>>>> <owl:Class rdf:about="&ontology1297094364376;test"/>
>>>>
>>>>
>>>> Why is the default/base namespace repeated here? This was not the
>>>> case in Protege 4.0.x. There the statement looks like:
>>>>
>>>>
>>>> <owl:Class rdf:about="#test"/>
>>>>
>>>>
>>>> Is there a way to get back the old statement style?
>>>>
>>>>
>>>> Best,
>>>>
>>>> Christian.
>>>>
>>>>
>>
>>
>
> ---
> Mélanie Courtot
> MSFHR trainee, TFL- BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>
>


--
Christian Knuepfer
Friedrich-Schiller-Universitaet Jena
Institut fuer Informatik
Ernst-Abbe-Platz 1-4
D-07743 Jena, Germany

Office: R. 3237
Phone: Intl.+49-3641-9-46353
Fax: Intl.+49-3641-9-46302

e-mail: [hidden email]
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  http://www.minet.uni-jena.de/~tral/data/christian_knuepfer_pub.asc
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