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

Csongor Nyulas csongor.nyulas at stanford.edu
Wed Apr 24 14:47:02 PDT 2013


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 Protégé 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 Grüssen - Met vriendelijke groeten
>
> Eddy Vanderlinden
>
> -------------
> DIGIT Unit 01, Brussels
> MIA - Methodologies, Interoperability and Architectures
> Tel.: +32 2 295 26 64
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>     1. Re: Update of the MySQL backend database (Csongor Nyulas)
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> ----------------------------------------------------------------------
>
> 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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