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[protege-discussion] populate my individuals from database : protege-discussion Digest, Vol 76, Issue 26

alaa hedib alaa_hedib at
Fri Nov 23 04:45:22 PST 2012

thanks Timothy and Slukaits really smart way , i already think in it , but to write it as java code.please Sluka if you can send to my sample sheet from your work .

--- On Tue, 11/13/12, Timothy Redmond <tredmond at> wrote:

From: Timothy Redmond <tredmond at>
Subject: Re: [protege-discussion] populate my individuals from database : protege-discussion Digest, Vol 76, Issue 26
To: protege-discussion at
Date: Tuesday, November 13, 2012, 12:23 PM

This is interesting and it is useful to know that you succeeded in making this work.  Hacky but I like it.

There is one possible gotcha and if you know the right technique it would be nice to know the workaround.  If some of the characters are non-ascii then windows might use the wrong character encoding on the paste.  We want it to use the UTF-8 encoding and windows tends to use some windows specific encoding. Often this might not be a problem but occasionally people have had trouble with the cut and paste.  If the basic text editor was smart enough there is a chance that it could be part of the solution.


On 11/13/12 12:10 PM, Sluka, James Patrick wrote:
>> can any one help me to find efficient  way to populate my ontology
>> individuals from database table or speared-sheet
> How often do you need to do this?
> --------------------------------
> IF this is a "one-of" process, that is you've got a big list of individuals and you just need to import it one time, then you can pretty much do it using Excel and a bit of cutting and pasting in a text editor.
> I've had to do this a few months ago; take a basic structure in Excel that has classes, subclasses, definitions, external links, edit dates etc. and convert it into an OWL-2 ontology.
> To do it, I built a very simple OWL-2 in Protege 4 with the basic types, qualities, links etc. and saved the ontology as RDF/XML.
> I then examined that file and extracted the syntax for, for example, creating a class (subClass of xxxx, definition etc.)
> In Excel you can use a spreadsheet cell to create a class (or individual) where the details for the class (individual) are values of other columns that are inserted into the correct RDF/XML syntax.
> To create many individuals it is likely that the syntax is exactly the same for all of them, just the details (name etc.) change. So the same Excel formula can be used for all the individuals. Write the formula once then paste it down an entire column.
> Here is the Excel formula I used to create classes, one class per row, info for the class from several cells in the same Excel row;
> ="<owl:Class rdf:about=""&CBO_0_9;"&Classes!E6&""">
>   <rdfs:label>"&Classes!E6&"</rdfs:label>
>   <rdfs:subClassOf rdf:resource=""&CBO_0_9;"&Classes!F6&"""/>
> <rdfs:comment>"&Classes!L6&"</rdfs:comment>"&C14&$C$1&B14&K14&L14&M14&"
> </owl:Class>"
> (In the above, Excel cell references were to another sheet in the workbook named "Classes".)
> You can put <cr>'s into an Excel cell with <alt><enter> and that's how I got the line breaks in the formula above. The formula above gives a cell with the text contents of (again, this is for one row of the Excel table and is creating an owl class for that row);
> "<owl:Class rdf:about=""&CBO_0_9;PhysicalEntityType"">
>   <rdfs:label>PhysicalEntityType</rdfs:label>
>   <rdfs:subClassOf rdf:resource=""&CBO_0_9;CBO_Object""/>
>   <rdfs:comment>A PhysicalEntityType is a CBO:Class (BFO:snap:quality) class of physical objects. For example, a Cell, a basement membrane of a diffusible Molecule.</rdfs:comment>
>   <dc:date rdf:datatype=""&xsd;date"">21 July 2011</dc:date>
>   <dc:creator>jps</dc:creator>
>   <rdfs:seeAlso>BFO:snap:quality</rdfs:seeAlso> <rdfs:isDefinedBy>urn:miriam:dummy:1</rdfs:isDefinedBy> <rdfs:isDefinedBy>urn:miriam:dummy:2</rdfs:isDefinedBy> <rdfs:isDefinedBy>urn:miriam:dummy:3</rdfs:isDefinedBy>
> </owl:Class>"
> I then copied the column with the results from Excel into a basic text editor and removed the extra quote marks. (Single " are removed and "" is converted into ").
> I then pasted that big chunk of XML into the original template OWL-2 file. If everything is done right that file can be opened in Protege2 and will be a valid OWL2 ontology. It took a few tries to get the syntax and quote marks correct so save your Excel worksheet so you can go back and fix any problems with the formulas.
> This is a pretty crude hack but if you only need to do it once (or perhaps only occasionally) it is probably easier than writing a Protege plugin to import from an Excel file.
> Jim Sluka
> Indiana Univ.
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