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

Timothy Redmond tredmond at stanford.edu
Tue Nov 13 12:23:04 PST 2012


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.

-Timothy.


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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