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[protege-discussion] Update of the MySQL backend database (Csongor Nyulas)

Eddy.VANDERLINDEN at ext.ec.europa.eu Eddy.VANDERLINDEN at ext.ec.europa.eu
Thu Apr 25 23:24:18 PDT 2013


Hi Csongor, 

MappingMaster is really great and works fine for my purpose! 

Some small hints I would like to share which took me some trials to find out: 
- if more than one Facts: or Annotations: attributes are entered, they need to be separated by a comma (,) 
- if Facts: and Annotations: need to be entered, they need to be entered in 2 separate descriptions. 

Further the tutorials on DSL and GUI of the MappingMaster  were of great help. 

Thanks a lot for all that (also for the DataMaster)!! 

Best regards 

Eddy  


-----Original Message-----
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Today's Topics:

   1. Re: Update of the MySQL backend database (Csongor Nyulas)
      (Csongor Nyulas)
   2.  Plugin development in 4.1 (Uri Shani)
   3. Cfp - 1st International Workshop on Data Mining on Linked
      Data (DMoLD'13) with Linked Data Mining Challenge @ ECML/PKDD
      (Claudia d'Amato)


----------------------------------------------------------------------

Message: 1
Date: Wed, 24 Apr 2013 14:47:02 -0700
From: Csongor Nyulas <csongor.nyulas at stanford.edu>
To: protege-discussion at lists.stanford.edu
Subject: Re: [protege-discussion] Update of the MySQL backend database
	(Csongor Nyulas)
Message-ID: <517852D6.6010809 at stanford.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Eddy,

You should definitely try out DataMaster [1] and MappingMaster [2]. Both 
should work with Protege 3.4.8 and later.
In DataMaster, class names and individual URIs are created automatically 
based on a pattern that ensure unique names based on the imported data 
source. If the class/individual URIs are important to you, you can 
rename them later in another process. DataMaster works with any database 
that has a JDBC driver, and with anything that can be served as an ODBC 
data source (such as CSV and text files).
MappingMaster works with Excel spread sheets, and has a very powerful 
mapping language that allows you to manipulate your input data, and it 
also allows you to specify how the created class/instance names should 
be generated based on the source content.

Another good alternative would be to write a small Java application 
using the Protege OWL API [3] that would do the import. In that case you 
would have the freedom to do custom processing of the data prior to 
import, and you could reuse the application in the future.

Csongor

[1] http://protegewiki.stanford.edu/wiki/DataMaster
[2] http://protege.cim3.net/cgi-bin/wiki.pl?MappingMaster
[3] http://protegewiki.stanford.edu/wiki/ProtegeOWL_API_Programmers_Guide


On 04/23/2013 11:15 PM, Eddy.VANDERLINDEN at ext.ec.europa.eu wrote:
> Hi Csongor,
>
> Thanks a lot for your advice.
>
> What I try to do is uploading new individuals, some hundreds.
>
> Configuring the Data master tab in Prot?g? 3.4.8 might help perhaps.
> I'm not sure if the tab supports 3.4.8 and as far as I remembered, new classes were created automatically based on the tab name of the Excel sheet.
> The direct import in MySQL seemed a swift alternative but, I would appreciate your advice for any alternative you judge better.
> The import may be from .CSV files too.
>
> Thanks in advance.
>
> Kind regards - Meilleures salutations - Mit freundlichen Gr?ssen - Met vriendelijke groeten
>
> Eddy Vanderlinden
>
> -------------
> DIGIT Unit 01, Brussels
> MIA - Methodologies, Interoperability and Architectures
> Tel.: +32 2 295 26 64
> -----Original Message-----
> From: protege-discussion-bounces at lists.stanford.edu [mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of protege-discussion-request at lists.stanford.edu
> Sent: Tuesday, April 23, 2013 9:04 PM
> To: protege-discussion at lists.stanford.edu
> Subject: protege-discussion Digest, Vol 81, Issue 25
>
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>
>     1. Re: Update of the MySQL backend database (Csongor Nyulas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Apr 2013 11:09:15 -0700
> From: Csongor Nyulas <csongor.nyulas at stanford.edu>
> To: protege-discussion at lists.stanford.edu
> Subject: Re: [protege-discussion] Update of the MySQL backend database
> Message-ID: <5176CE4B.1020003 at stanford.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Eddy,
>
> The Protege 3 database back-end is not meant to be edited directly
> (through SQL updates or Excel or anything). The adding of new
> information (new rows) is an especially bad idea, since it is very easy
> to break things.
> The Protege back-end is NOT a triple store, but rather a "proprietary"
> storage format developed originally for frames ontologies, and later
> adapted to be used to store OWL ontologies.
>
> You should use the Protege/WebProtege client or the Protege API to
> modify the content of your ontology.
>
> If you explain what you try to achieve, maybe we can provide even more
> specific advise.
>
> Regards,
> Csongor
>
>
> On 04/23/2013 02:15 AM, Eddy.VANDERLINDEN at ext.ec.europa.eu wrote:
>> Hello,
>> MS Excel offers in the 2010 version a nice feature.
>> When we have the MySQL workbench installed on the same PC, there is a
>> connection possible from Excel to MySQL.
>> This is accessible through the button as shown hereby .
>> We can retrieve and update information in the spreadsheet.
>> The possibility to upload triples is available too.
>> However, when we do so, they do not appear in the ontology (updates of
>> existing triples do).
>> We are using Prot?g? 3.4.8 with Webprot?g? 1 as user interface, the
>> collaborative version in the background does not show the new triples
>> neither.
>> An example of the uploaded data in the spreadsheet is shown here:
>> *frame* 	*frame_type* 	*slot* 	*facet* 	*is_template* 	*value_index*
>> *value_type* 	*short_value* 	*long_value*
>> ArisDiagram 	25 	:DIRECT-TYPE 	
>> 	0 	1 	9 	http://ec.europa.eu/ontologies/EC_Glossary.owl#EC_Concept 	
>> http://ec.europa.eu/ontologies/EC_Glossary.owl#EC_Concept 	9
>> :DIRECT-INSTANCES 	
>> 	0 	206 	25 	ArisDiagram 	
>> ArisDiagram 	25 	:NAME 	
>> 	0 	0 	3 	ArisDiagram 	
>> ArisDiagram 	25 	http://www.w3.org/1999/02/22-rdf-syntax-ns#type 	
>> 	0 	0 	9 	http://ec.europa.eu/ontologies/EC_Glossary.owl#EC_Concept 	
>> ArisDiagram 	25 	http://www.w3.org/2004/02/skos/core#prefLabel 	
>> 	0 	0 	3 	Aris diagram 	
>>
>> Is there anything we are missing here to make this function?
>> Thanks in advance.
>> Kind regards
>> Eddy Vanderlinden
>> -------------
>> DIGIT Unit 01, Brussels
>> MIA - Methodologies, Interoperability and Architectures
>> Tel.: +32 2 295 26 64
>>
>>
>> _______________________________________________
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------------------------------

Message: 2
Date: Thu, 25 Apr 2013 10:27:58 +0300
From: Uri Shani <SHANI at il.ibm.com>
To: protege-discussion at lists.stanford.edu
Subject: [protege-discussion]  Plugin development in 4.1
Message-ID:
	<OF5BFCA621.844A03F5-ONC2257B58.00289A1B-C2257B58.0029071E at il.ibm.com>
Content-Type: text/plain; charset="us-ascii"

Well, I have figured it out by myself after hacking around in all possible 
directions.
Seems that the tabs are initialized and shown only if enabled in the 
Preferences, so it turned out the Preferences have discovered my new 
plugin and once Protege opened and I checked the label of the new plugin, 
the tab appeared as well on the tabs row.
Still - I could not find where the extension points are documented so that 
the time I spent to discover that wisdom can be saved...
Thanks,
- Uri



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Message: 3
Date: Thu, 25 Apr 2013 18:41:40 +0200
From: Claudia d'Amato <claudia.damato at uniba.it>
To: destinatari-ignoti:;
Subject: [protege-discussion] Cfp - 1st International Workshop on Data
	Mining on Linked Data (DMoLD'13) with Linked Data Mining Challenge @
	ECML/PKDD
Message-ID: <51795CC4.5040304 at uniba.it>
Content-Type: text/plain; charset="iso-8859-15"; Format="flowed"

[Apologies for multiple postings]


---------------------------------------------------------------------------------
                           Call for Papers
                                for
              Data Mining on Linked Data (DMoLD'13) workshop
                   with Linked Data Mining Challenge
---------------------------------------------------------------------------------

To be held during the European Conference on Machine Learning and
Principles and Practice of Knowledge Discovery in Databases, ECML/PKDD 2013,
23-27 September 2013 Prague, Czech Republic (http://www.ecmlpkdd2013.org/)

The workshop  consists of an Open Track and of a Challenge Track.
The Open Track will expect submission of regular research papers, describing
novel approaches to applying Data Mining techniques on the Linked Data sources.
Participation in the Challenge Track will require the participants to download a
real-world RDF dataset from the domain of Public Contract Procurement, and
accomplish at least one of the three pre-defined tasks on it using their own or
publicly available data mining tool.

IMPORTANT DATES:
* May  1, 2013  - Challenge Track data for Task 1 and Task 3
* May 15, 2013  - Challenge Track data for Task 2
* June 21, 2013 - Deadline for Challenge Track results
* June 28, 2013 - Deadline for paper submissions (both Open Track and of a Challenge Track)

For more info about the Challenge, visit
http://keg.vse.cz/dmold2013
For more info about the ECML/PKDD 2013, visit
http://www.ecmlpkdd2013.org

Claudia d'?Amato, Petr Berka, Vojtech Svatek & Krzysztof Wecel
Workshop organizers

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