ISSUE-102 (AnnotationProperty): URI cannot be declared to be an annotation property, which in turn means that annotation URIs can't have annotations on them

ISSUE-102 (AnnotationProperty): URI cannot be declared to be an annotation property, which in turn means that annotation URIs can't have annotations on them

http://www.w3.org/2007/OWL/tracker/issues/

Raised by: Alan Ruttenberg
On product: 

 From:    matthew.horridge@cs.man.ac.uk
 Subject:  Re: NCBO BioPortal Prototype Released
 Date:  March 7, 2008 4:39:39 AM EST
 To:    alanruttenberg@gmail.com
 Cc:    wbug@ncmir.ucsd.edu, noy@stanford.edu, maryann@ncmir.ucsd.edu, jgrethe@ncmir.ucsd.edu, ian.horrocks@comlab.ox.ac.uk

Hi,

I think a new issue has to be raised with the OWL 1.1 Working Group.  The issue pointed to by Alan doesn't represent the problem that we have here. I believe that the main problem stems from the fact that there are no longer annotation properties in OWL 1.1.  This means that a URI cannot be declared to be an annotation property, which in turn means that annotation URIs can't have annotations on them.

I think the following needs to be done,

1)  Add a new type of axiom for declaring annotation properties

2)  Add a new type of axiom for annotating annotation properties


Cheers,

Matthew



On 7 Mar 2008, at 06:36, Alan Ruttenberg wrote:

This appears to be http://www.w3.org/2007/OWL/tracker/issues/16
I've added a pointer to the thread to the issue.
Thanks,
Alan

On Mar 6, 2008, at 4:13 PM, Bill Bug wrote:

Oops.  My mistake.  Thanks, Natasha.

Sorry for misquoting you, Alan.

Cheers,
Bill

On Mar 6, 2008, at 3:23 PM, Natasha Noy wrote:

Bill,

Here is the current thread (started yesterday) on the OWL API mailing list, in case you want to point Alan to it. Basically, Matthew confirmed that the problem is with the current OWL 11 spec (not the OWL API, actually).
http://sourceforge.net/mailarchive/forum.php?thread_name=1204757310.7801.36.camel%40smi-tredmond-li.stanford.edu&forum_name=owlapi-developer

Natasha


On Mar 5, 2008, at 11:19 PM, Bill Bug wrote:

Many thanks, Natasha.

Yes - my understanding is this is an OWL API bug.  I've spoken with Alan Ruttenberg about this some time back.  Alan is co-chair with Ian H. on the OWL 1.1 spec committee.  Alan is also recommending one tread with great care, if one thinks of using P4, but must maintain compatibility with P3. He himself uses CLISP for most all his OWL work, so the problem is completely moot for him.

This along with other issues is why I've been avoiding P4 for now, as much as I must bite my lip in anticipation each time I spend a little time playing with it.  ;-)

Cheers,
Bill

On Mar 5, 2008, at 11:22 PM, Natasha Noy wrote:

Bill,

Tim and Tania have spent a bit of time today looking into this problem, and think they might know where the problem is coming from. Unfortunately, they think it might the OWL 11 API problem, which is out of our hands. We'll know more tomorrow when Manchester has time to look at it. Also, Tim says that the way things are now, you indeed should stay away from Protege 4: it will loose information if you load your files there and then save. Basically, it doesn't handle the case where annotation properties are declared in one ontology and used in another very well (ok, that's an understatement -- not at all).

We have posted the bug, and are hoping to hear from our Manchester friends tomorrow.

In the meantime, yes, send us what you have, and we'll try to get it into the BioPortal. Indeed, we need to come up with a good way to update BirnLex. For now though, it will probably have to be a push from your side. But once we have all the scripts to convert it into the form that BioPortal can digest, that should be doable, right?

Best,

Natasha


On Mar 5, 2008, at 4:46 PM, Bill Bug wrote:

Many thanks to you, Natasha.

I should have remember about this AnnotationProperty issue with P4.  I was just so excited to think we'd found a very easy and quick fix, my past experience with P4 didn't pop to mind.  This is one of the reasons I've avoided using P4, actually.  It's got so many useful conveniences for us OWL users, I know the more I use it, the more I'll become prey to the current bugs that have still to be worked out.

I needed to divert to a few writing tasks in the last day, but I should finish with the last outstanding item - a 3/4 finished manuscript review - this evening, so that I'll be able to get back to the Jena code to generate that file.  The only outstanding issue was to complete the "dumping" of the subsumptive graph, which I'd already begun to do.  What I'll then deliver is a 2D ASCII file with classes & instances as rows, and all the properties we'd want for this first pass into the Bioportal as columns, including an ID pointer to the parent class to capture the asserted graph. Each column with have the name of the actual AnnotationProperty as a header, except for the parent which will have the header "SuperClass".

Nothing fancy, just the basics.

Thank you again for jumping on this, as its extremely important to us - both for the BIRN and for the NIF projects.  One of the issues I'm most interested in is working out an update policy, so the BioPortal has the most current version of our OWL content, which will be turning over relatively rapidly.  As I mentioned, we've got an MD5 digest in place that makes it clear when some aspect of the file has changed.  This is run every evening at 3 AM PDT and only updated if there's been a change.

I should be able to get that to you by Friday at the latest with the other things in my queue.

Cheers,
Bill

On Mar 5, 2008, at 1:07 PM, Natasha Noy wrote:

Hi Bill,

I see - I wasn't aware of this discrepancy. I'll try to investigate. But then in the meantime, if you can give us an OWL file with everything merged, we will try to load it into BioPortal. Having such a file will certainly speed things up for us!

Thanks a lot in advance!

Natasha


On Mar 4, 2008, at 4:44 PM, Bill Bug wrote:

Dear Natasha,

Below are screen shots that help explain the problem here.  As I mentioned earlier, there are some known problems with P4 - one being the way it handles AnnotationProperties.  You will note that the two example classes given here - "Cerebral cortex" and "Bipolar disease" - have considerably more AnnotationProperties when viewed in P3 than when viewed in P4.  The bulk of the properties just don't get parsed in P4 for some reason.  I saw this a while back, and I and others have reported it.  Don't know when they'll get around to fixing it.

I've included the OWL/RDF/XML for these classes so you can see there is nothing non-standard about the way in which the AnnotationProperties are declared for these classes.

So - though the merge ontology feature in P4 is very very handy, it just won't help us right now.

I can still provide that CSV dump of BIRNLex, if you think that might provide an expeditious way to get BIRNLex into BioPortal as one big ontology file.

Cheers,
Bill

<Picture 21.png>
<Picture 18.png>
<Picture 19.png>
<Picture 20.png>

BIPOLAR DISORDER:
  <owl:Class rdf:about="#birnlex_12754">
    <obo_annot:synonym>Manic-Depressive Psychosis</obo_annot:synonym>
    <rdfs:label>Bipolar Disorder</rdfs:label>
    <birn_annot:hasBirnlexCurator>http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#BillBug</birn_annot:hasBirnlexCurator>
    <obo_annot:hasExternalSource>http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#MeSH</obo_annot:hasExternalSource>
    <core:prefLabel>Bipolar Disorder</core:prefLabel>
    <obo_annot:createdDate>2007-10-08</obo_annot:createdDate>
    <obo_annot:synonym>Affective Bipolar Psychosis</obo_annot:synonym>
    <obo_annot:usageNote>MeSH includes implied subcomponents</obo_annot:usageNote>
    <obo_annot:nifID>_8.3_11.3</obo_annot:nifID>
    <birn_annot:putativeClassExtension>Manic Disorder</birn_annot:putativeClassExtension>
    <rdfs:subClassOf rdf:resource="#birnlex_12753"/>
    <obo_annot:synonym>Bipolar Depression</obo_annot:synonym>
    <birn_annot:hasCurationStatus>http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#uncurated</birn_annot:hasCurationStatus>
    <core:definition>A major affective disorder marked by severe mood swings (manic or major depressive episodes) and a tendency to remission and recurrence (MeSH).</core:definition>
    <obo_annot:modifiedDate>2007-10-08</obo_annot:modifiedDate>
    <obo_annot:hasDefinitionSource>http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#MeSH_defSource</obo_annot:hasDefinitionSource>
    <birn_annot:putativeClassExtension>Mania</birn_annot:putativeClassExtension>
    <birn_annot:putativeClassExtension>Manic State</birn_annot:putativeClassExtension>
    <obo_annot:externalSourceId>D001714</obo_annot:externalSourceId>
  </owl:Class>

CEREBRAL CORTEX:
  <owl:Class rdf:about="#birnlex_1494">
    <birn_annot:hasBirnlexCurator>http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Bill_Bug</birn_annot:hasBirnlexCurator>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:ID="birnlex_1616"/>
        </owl:someValuesFrom>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <obo_annot:UmlsCui>C0007776</obo_annot:UmlsCui>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
        <owl:someValuesFrom>
          <owl:Class rdf:ID="birnlex_1072"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#birnlex_1128"/>
        </owl:someValuesFrom>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <birn_annot:hasCurationStatus>http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#pending_final_vetting</birn_annot:hasCurationStatus>
    <obo_annot:pendingActionNote>Find out what areas are included in cerebral cortex from Allan (2006-07-15).</obo_annot:pendingActionNote>
    <rdfs:label>Cerebral cortex</rdfs:label>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
        <owl:someValuesFrom rdf:resource="#birnlex_1079"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
        <owl:someValuesFrom>
          <owl:Class rdf:ID="birnlex_1475"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Class rdf:about="#birnlex_1700"/>
    </rdfs:subClassOf>
    <obo_annot:externallySourcedDefinition>The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon and folds into gyri. It reaches its highest development in man and is responsible for intellectual faculties and higher mental functions (MeSH &amp; CSP both).</obo_annot:externallySourcedDefinition>
    <birn_annot:hasBirnlexCurator>http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Allan_MacKenzie-Graham</birn_annot:hasBirnlexCurator>
    <obo_annot:createdDate>2006-07-15</obo_annot:createdDate>
    <birn_annot:neuronamesID>20</birn_annot:neuronamesID>
    <obo_annot:hasExternalSource>http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl#MeSH</obo_annot:hasExternalSource>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1136"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:allValuesFrom>
          <owl:Class>
            <owl:unionOf rdf:parseType="Collection">
              <owl:Class rdf:about="#birnlex_922"/>
              <owl:Class rdf:about="#birnlex_1063"/>
            </owl:unionOf>
          </owl:Class>
        </owl:allValuesFrom>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1422"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1468"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <obo_annot:modifiedDate>2006-10-05</obo_annot:modifiedDate>
    <obo_annot:nifID>_5.1_1.11.1.1</obo_annot:nifID>
    <birn_annot:birnlexDefinition>The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon and folds into gyri (adapted from MSH by Christine Fennema-Notestine).</birn_annot:birnlexDefinition>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
        <owl:someValuesFrom>
          <owl:Class rdf:ID="birnlex_1480"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1117"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1148"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1428"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1368"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
        <owl:someValuesFrom rdf:resource="#birnlex_1160"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <birn_annot:hasBirnlexCurator>http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#Christine_Fennema-Notestine</birn_annot:hasBirnlexCurator>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1487"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <core:changeNote>made a region of the telencephalon based on NN (BB).</core:changeNote>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
        <owl:someValuesFrom rdf:resource="#birnlex_1086"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <core:prefLabel>Cerebral cortex</core:prefLabel>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#birnlex_928"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#birnlex_1436"/>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_proper_part"/>
        <owl:someValuesFrom>
          <owl:Class rdf:ID="birnlex_1493"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
  </owl:Class>


On Mar 4, 2008, at 2:03 PM, Natasha Noy wrote:

Can you give me some examples of the properties that are not there, so that I can look them up and at least try to figure out at which stage the problem occurs?

For the moment, you can search through *all* properties. Eventually, we plan to have the ontology authors specify the *important* properties, such as where their synonyms are stored. It is high on the priority list. The issue is not so much the query itself, but the fact that different ontologies use diffirent properties for, say, synonyms. We want to enable ontology authors to tell us what those are at submission time.

Natasha


On Mar 4, 2008, at 10:18 AM, Bill Bug wrote:

Hi Natasha,

We still seem to be missing almost all the annotation properties - the most important ones like definition, prefLabel, synonyms

For some reasons, SOME of the properties defined in:

 xmlns:obo_annot="http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl#"

are getting through, but not all. Even for BIRNLex_annotation_properties.owl, only a few AnnotationProperties get through and even then, only intermittently.

Another important issue here - for us at least - is we want to make certain that users of the BioPortal will be able to search our ontology not only based on rdfs:label, but also on a small set of other AnnotationProps that we define (for us, that would primarily be skos:prefLabel and obo_annot:synonym).  That's definitely functionality we'd ultimately need from the BioPortal.  Given it would be trivial to implement in Jena, I assume its not a big problem.

Thanks again for being so responsive and acting so expeditiously.

Cheers,
Bill

On Mar 4, 2008, at 12:57 PM, Natasha Noy wrote:

[I am putting others on the thread in Bcc, so that this is the last message on the thread that you receive unless you ask us to keep you on the thread]

ok, here you go -- both BIRNLex and NIF. Can you check to see if everything seems to be there. If there are problems, let us know where they are.

Natasha

<nif.owl.zip><BIRNLex.owl.zip>
On Mar 4, 2008, at 9:33 AM, Bill Bug wrote:

So the best place to go for the latest, greatest is always the URL

 BIRNLex:
  http://purl.org/nbirn/birnlex/ontology/birnlex.owl

 NIF:
  http://purl.org/nif/ontology/nif.owl

Those are the "root" files in the import graph, so if you start with these, you automagically get everything.

Each of these locations includes an MD5 digest specifying the latest digest for the overall ontology:

 http://purl.org/nbirn/birnlex/ontology/birnlex-plus.md5

 http://purl.org/nif/ontology/nif-plus.md5

There's also an MD5 log to specifically indicate WHEN changes have taken place:

 http://purl.org/nbirn/birnlex/ontology/birnlex-plus.md5.log

 http://purl.org/nif/ontology/nif-plus.md5.log

(You'll note there's been a lot of updating in the last few days)

These were specifically put in place so that processes which needed to keep current with the latest version of BIRNLex (or NIF) could have a "hook" to make it easy to know when an automatic update should be run.  This provides a very light weight check to help consumers - like the BioPortal - avoid re-running a "heavy" process when its not necessary.

Cheers,
Bill
 
On Mar 4, 2008, at 12:20 PM, Natasha Noy wrote:

Sorry -- pushed the "send" button before replying to the whole thing.

I would also say this same mechanism should work for NIF as well.

Absolutely -- send us the files and we'll take care of it.

The one thing I would want to make clear to BioPortal users looking for ontologies to re-use is that BIRNLex expressly is designed for modular use.  We have extensive modules for organism taxonomy (a concordance of NCBI Tax + GBIF for organisms of interest to neuroscientists - and coverage sufficient for many other domains), Neuroanatomy, nerve cell types, neuro disease, OBI-related investigation, etc. - most of which are specifically designed to be used in isolation from one another, to help promote re-use.  If there were some way to indicate this and then point back to our BIRNLex Wiki pages for details, that would be great.

We will preserve the different prefixes; that's not perfect, but could give some indication of where the module boundaries are. Also, yes, we can point to the BIRNLex homepage in the ontology metadata, where all the other information about the ontology is.

Natasha







William Bug, M.S., M.Phil.                                            email: wbug@ncmir.ucsd.edu
Ontological Engineer         work: (610) 457-0443
Biomedical Informatics Research Network (BIRN)
and
National Center for Microscopy &
Imaging Research (NCMIR)
Dept. of Neuroscience, School of Medicine
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

Please note my email has recently changed





William Bug, M.S., M.Phil.                                            email: wbug@ncmir.ucsd.edu
Ontological Engineer         work: (610) 457-0443
Biomedical Informatics Research Network (BIRN)
and
National Center for Microscopy &
Imaging Research (NCMIR)
Dept. of Neuroscience, School of Medicine
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

Please note my email has recently changed





William Bug, M.S., M.Phil.                                            email: wbug@ncmir.ucsd.edu
Ontological Engineer         work: (610) 457-0443
Biomedical Informatics Research Network (BIRN)
and
National Center for Microscopy &
Imaging Research (NCMIR)
Dept. of Neuroscience, School of Medicine
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

Please note my email has recently changed





William Bug, M.S., M.Phil.                                            email: wbug@ncmir.ucsd.edu
Ontological Engineer         work: (610) 457-0443
Biomedical Informatics Research Network (BIRN)
and
National Center for Microscopy &
Imaging Research (NCMIR)
Dept. of Neuroscience, School of Medicine
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

Please note my email has recently changed





William Bug, M.S., M.Phil.                                            email: wbug@ncmir.ucsd.edu
Ontological Engineer         work: (610) 457-0443
Biomedical Informatics Research Network (BIRN)
and
National Center for Microscopy &
Imaging Research (NCMIR)
Dept. of Neuroscience, School of Medicine
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

Please note my email has recently changed





William Bug, M.S., M.Phil.                                            email: wbug@ncmir.ucsd.edu
Ontological Engineer         work: (610) 457-0443
Biomedical Informatics Research Network (BIRN)
and
National Center for Microscopy &
Imaging Research (NCMIR)
Dept. of Neuroscience, School of Medicine
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

Please note my email has recently changed

Received on Wednesday, 12 March 2008 04:07:20 UTC