Issue with Problem Oriented Medical Record OWL Ontology

This seems to be a common problem with FOAF / ontologies
importing FOAF and Protege, I have run into it several
times. Honestly, I have not yet figured out the cause of
this and almost suspect that Protege recognizes FOAF and
tries to handle it in a special way (with unwanted side
effects).

- Matthias


> Hi,
> 
> I'm new to Protege and ontologies, and I'm getting the
following issue
> with
> the POMR ontology from Chimezie.
> 
> I have protege version 3.2.1 build 365 and JDK 1.5.0
> 
> If I run this ontology through a verifier, it verifies
the ontology
> seemingly without a problem.
> 
> If i try to load the ontology directly from
> http://metacognition.info/ontologies/pro
blem-oriented-medical-record.owl I
> get some very interesting error:
> 
> WARNING: [ProtegeOWLParser] Warning: Trying to add
import for external
> resource:
>  http://purl.org/dc/e
lements/1.1/ --
> DefaultProtegeOWLParserLogger.logWarning()
> INFO: [ProtegeOWLParser] Importing http://purl.org/dc/e
lements/1.1/ (from
> Redire
> ct to http://protege.stanford.edu/plugins/owl/dc/protege-dc.o
wl)
> The resource p1:chime has the rdf:type
> http://xmlns.co
m/foaf/0.1/Personwhich is
>  not a class but a
>
edu.stanford.smi.protegex.owl.model.impl.DefaultRDFUntypedRe
s
> ource
> Suggestion: In many cases the problem is a missing
owl:imports statement
> to
> the
> classes file which defines the correct type of
> http://xmlns.com/foa
f/0.1/Person
> 
> 
> It seems to me that it cannot distinguish the foaf
Person class, with or
> without the foaf imports statement.
> 
> If someone could please assist here, it would be of
great help.  Thank you
> in advance,
> Noah

-- 
"Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat
...
Jetzt GMX TopMail testen: http://www.gmx.net/d
e/go/topmail

Noah Cohen wrote:
> Hi,
> 
> I'm new to Protege and ontologies, and I'm getting the
following issue 
> with the POMR ontology from Chimezie.

You may want to address the protege-owl mailing list with
this problem.

Also note that Protege is not the only ontology editor in
the world. 
For example TopBraid Composer [1] can open this file without
problems. 
While this is a commercial tool, you can exploit a free 30
days 
evaluation period.

Holger

[1] http://www.topbraidco
mposer.com


> I have protege version 3.2.1 build 365 and JDK 1.5.0
> 
> If I run this ontology through a verifier, it verifies
the ontology 
> seemingly without a problem. 
> 
> If i try to load the ontology directly from 
> http://metacognition.info/ontologies/pro
blem-oriented-medical-record.owl 
> I get some very interesting error:
> 
> WARNING: [ProtegeOWLParser] Warning: Trying to add
import for external 
> resource:
>  http://purl.org/dc/e
lements/1.1/ -- 
> DefaultProtegeOWLParserLogger.logWarning()
> INFO: [ProtegeOWLParser] Importing http://purl.org/dc/e
lements/1.1/ 
> (from Redire
> ct to http://protege.stanford.edu/plugins/owl/dc/protege-dc.o
wl 
> <http://protege.stanford.edu/plugins/owl/dc/protege-
dc.owl>)
> The resource p1:chime has the rdf:type http://xmlns.com/foa
f/0.1/Person 
> which is
>  not a class but a 
>
edu.stanford.smi.protegex.owl.model.impl.DefaultRDFUntypedRe
s
> ource
> Suggestion: In many cases the problem is a missing
owl:imports statement 
> to the
> classes file which defines the correct type of 
> http://xmlns.com/foa
f/0.1/Person
> 
> 
> It seems to me that it cannot distinguish the foaf
Person class, with or 
> without the foaf imports statement. 
>  
> If someone could please assist here, it would be of
great help.  Thank 
> you in advance,
> Noah
> 

At 6:18 PM -0700 4/11/07, Holger Knublauch wrote:
>Noah Cohen wrote:
>>  Hi,
>>  I'm new to Protege and ontologies, and I'm getting
the following 
>>issue with the POMR ontology from Chimezie.
>
>You may want to address the protege-owl mailing list
with this problem.
>
>Also note that Protege is not the only ontology editor
in the world. 
>For example TopBraid Composer [1] can open this file
without 
>problems. While this is a commercial tool, you can
exploit a free 30 
>days evaluation period.
>
>Holger
>
>[1] http://www.topbraidco
mposer.com
>
>

yes Holger,  (and if he wanted a free, open source editor
that could 
handle it I would recommend SWOOP [1])

However, I think the bigger issue here is that there were
(and I 
believe still are) some weirdnesses in the machine
readability of the 
FOAF namespace ( http://xmlns.com/foaf/0.1 ) and that a number of 
systems have problems with it (I notice if I try to load it
directly 
into SWOOP I still get XML parsing errors).  Lots of systems
have 
done various work arounds for this -- so when you report
your error 
to the Protege mailing list, you might also send it to the
FOAF one, 
we've been complaining about this for a couple years now,
maybe if 
some other folks yell as well we can get it so that the most
used 
Semantic Web vocabulary will actually conform to the
standards it 
promotes 
  -JH
[1] http://code.google.co
m/p/swoop/


>>  I have protege version 3.2.1 build 365 and JDK
1.5.0
>>  If I run this ontology through a verifier, it
verifies the 
>>ontology seemingly without a problem.
>>  If i try to load the ontology directly from 
>>http://metacognition.info/ontologies/pro
blem-oriented-medical-record.owl 
>>I get some very interesting error:
>>  WARNING: [ProtegeOWLParser] Warning: Trying to add
import for 
>>external resource:
>>   http://purl.org/dc/e
lements/1.1/ -- 
>>DefaultProtegeOWLParserLogger.logWarning()
>>  INFO: [ProtegeOWLParser] Importing 
>>http://purl.org/dc/e
lements/1.1/ (from Redire
>>  ct to http://protege.stanford.edu/plugins/owl/dc/protege-dc.o
wl 
>><http://protege.stanford.edu/plugins/owl/dc/protege-
dc.owl>)
>>  The resource p1:chime has the rdf:type 
>>http://xmlns.com/foa
f/0.1/Person which is
>>   not a class but a 
>>edu.stanford.smi.protegex.owl.model.impl.DefaultRDFU
ntypedRes
>>  ource
>>  Suggestion: In many cases the problem is a missing
owl:imports 
>>statement to the
>>  classes file which defines the correct type of 
>>http://xmlns.com/foa
f/0.1/Person
>>
>>  It seems to me that it cannot distinguish the foaf
Person class, 
>>with or without the foaf imports statement.  If
someone could 
>>please assist here, it would be of great help. 
Thank you in 
>>advance,
>>  Noah
>>

-- 
How can you be in two places at once if you're not anywhere
at all?
						(Firesign Theatre, 1969)
Prof James Hendler				http://www.cs.rpi.edu/
~hendler
Tetherless World Constellation Chair		301-405-2696 (work)
Computer Science Dept			301-405-6707 (Fax)
Rensselaer Polytechnic Institute, Troy NY 12180

Ho Ho. Funny you should mention this. I was just complaining
about it  
yesterday. In this snippet it is me first, alternating with
Richard  
Cyganiak. (The "weirdness" that Jim is referring
to is that even  
requests for content-type: application/rdf+xml to the foaf
URL return  
html)

>> For example I am terminally confused by FOAF. What
does the name   
>> "http://xmlns.com/foa
f/0.1/" refer to?
>
> That's the FOAF vocabulary specification. A document,
since GET  
> returns 200. It's available in HTML format, and may or
may not be  
> available in other formats.
>
>> What does this mean (from foaf rdf)?  
<rdfs:isDefinedBy  
>> rdf:resource="http://xmlns.co
m/foaf/0.1/"/>
>
> The subject is defined by the FOAF vocabulary
specification.  
> rdfs:isDefinedBy doesn't constrain the defining
document to any  
> particular format.
>
>> How does a SW agent get the rdf for http://xmlns.com/foaf/0.1/
 
>> Organization ?
>
> It can't get the RDF since the FOAF folks have do
neither GRDDL nor  
> a <link> header nor content negotiation. FOAF
gets away with this  
> because everybody has to support FOAF, and so everybody
just  
> hardcodes the URL to their RDF.

Guess FOAF isn't quite getting away with it   I'm not
sure why they  
ever thought they could.

Emanates from a criticism I make about content negotiation
being bad  
semantic web practice.

http://lists.w3.org/Archives/Public/semantic-w
eb/2007Apr/0060.html

It's my turn to respond. I'm reading about Content-Location
headers,  
from RFC2616 - HTTP1/1. Here's a bit I'm currently trying to
digest.  
It's not going down very well.
> The Content-Location value is not a replacement for the
original  
> requested URI; it is only a statement of the location
of the  
> resource corresponding to this particular entity at the
time of the  
> request. Future requests MAY specify the
Content-Location URI as  
> the request- URI if the desire is to identify the
source of that  
> particular entity.
>
> A cache cannot assume that an entity with a
Content-Location  
> different from the URI used to retrieve it can be used
to respond  
> to later requests on that Content-Location URI.
However, the  
> Content- Location can be used to differentiate between
multiple  
> entities retrieved from a single requested resource, as
described  
> in section 13.6.
Section 13.6 discusses the "Vary" header. More fun
(but only if you  
care about what URIs refer to).

-Alan



On Apr 11, 2007, at 9:34 PM, Jim Hendler wrote:
[snip]
> However, I think the bigger issue here is that there
were (and I  
> believe still are) some weirdnesses in the machine
readability of  
> the FOAF namespace ( http://xmlns.com/foaf/0.1 ) and that a number  
> of systems have problems with it (I notice if I try to
load it  
> directly into SWOOP I still get XML parsing errors). 
Lots of  
> systems have done various work arounds for this -- so
when you  
> report your error to the Protege mailing list, you
might also send  
> it to the FOAF one, we've been complaining about this
for a couple  
> years now, maybe if some other folks yell as well we
can get it so  
> that the most used Semantic Web vocabulary will
actually conform to  
> the standards it promotes 
>  -JH
>

On Apr 11, 2007, at 7:35 PM, Noah Cohen wrote:

>>>  I have protege version 3.2.1 build 365 and JDK
1.5.0
>>>  If I run this ontology through a verifier, it
verifies the  
>>> ontology seemingly without a problem.
>>>  If i try to load the ontology directly from
http:// 
>>>
metacognition.info/ontologies/problem-oriented-medical-recor
d.owl  
>>> I get some very interesting error:
>>>  WARNING: [ProtegeOWLParser] Warning: Trying to
add import for  
>>> external resource:
>>>   http://purl.org/dc/e
lements/1.1/ --  
>>> DefaultProtegeOWLParserLogger.logWarning()
>>>  INFO: [ProtegeOWLParser] Importing http://purl.org/dc/eleme
nts/ 
>>> 1.1/ (from Redire
>>>  ct to http://protege.stanford.edu/plugins/owl/dc/protege-dc.o
wl  
>>> <http://protege.stanford.edu/plugins/owl/dc/protege-
dc.owl>)
>>>  The resource p1:chime has the rdf:type http://xmlns.com/foaf/0.1/
 
>>> Person which is
>>>   not a class but a  
>>>
edu.stanford.smi.protegex.owl.model.impl.DefaultRDFUntypedRe
s
>>>  ource
>>>  Suggestion: In many cases the problem is a
missing owl:imports  
>>> statement to the
>>>  classes file which defines the correct type of
http://xmlns.com/ 
>>> foaf/0.1/Person
>>>
>>>  It seems to me that it cannot distinguish the
foaf Person class,  
>>> with or without the foaf imports statement.  If
someone could  
>>> please assist here, it would be of great help. 
Thank you in  
>>> advance,
>>>  Noah