Re: populate my individuals from database : protege-discussion Digest, Vol 76, Issue 26
Timothy Redmond <[email protected]>
| Newsgroups | gmane.comp.misc.ontology.protege.general |
|---|---|
| Message-ID | <[email protected]> |
On 11/23/2012 04:45 AM, alaa hedib wrote:
> thanks Timothy and Sluka
> its 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 .
>
Writing some custom code to translate a database or a spreadsheet into
OWL should not be too difficult. To read the database you can use jdbc
[1] and there are a couple of good options for reading excel
spreadsheets in java (e.g. [2] but I believe apache has an option as
well). To write to the OWL ontology I would recommend the OWL api. The
functions shouldCreatePropertyAssertions and shouldCreateClassAssertions
from [4] show how to add statements that individuals have a particular
type and particular property values.
The hard work of course is making this more than a custom solution to
work with one particular database or spreadsheet. So you are forced to
choose between
1. writing and maintaining a graphical (or text based) program
(possibly a Protege plugin) such as datamaster or mapping master or
2. writing a one-off solution for one particular problem.
I have done the second option in the past but it must have been before
mapping master came out because I hope that I would have used mapping
master if it was there. If you are considering the first option then I
would think that exploring the Protege 3 solutions would be less work.
-Timothy
[1] http://docs.oracle.com/javase/tutorial/jdbc/basics/index.html
[2] http://jexcelapi.sourceforge.net/
[3] http://owlapi.sourceforge.net/
[4] http://owlapi.svn.sourceforge.net/viewvc/owlapi/v3/trunk/contract/src/test/java/org/coode/owlapi/examples/Examples.java?view=markup
>
> Alaa
>
>
> --- On *Tue, 11/13/12, Timothy Redmond /<[email protected]>/*wrote:
>
>
> From: Timothy Redmond <[email protected]>
> Subject: Re: [protege-discussion] populate my individuals from
> database : protege-discussion Digest, Vol 76, Issue 26
> To: [email protected]
> 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.
>
> -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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