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Re: ISSUE-102 (AnnotationProperty): RAISED - No Discussion

From: Deborah L. McGuinness <dlm@ksl.stanford.edu>
Date: Wed, 12 Mar 2008 13:00:06 -0400
Message-ID: <47D80C16.6030504@ksl.stanford.edu>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
CC: OWL Working Group WG <public-owl-wg@w3.org>

I thought we had come to agreement previously that we would allow 
annotations on all properties - and that would include annotation 
properties.
I intended to use this feature for provenance representation so that my 
applications could annotate the source of annotations.

Is there a way that we can reconsider dropping that capability?

thanks,
deborah

Alan Ruttenberg wrote:
>
> Grumble.
> -Alan
>
> On Mar 12, 2008, at 12:07 AM, OWL Working Group Issue Tracker wrote:
>
>>
>>
>> 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 17:08:31 GMT

This archive was generated by hypermail 2.2.0+W3C-0.50 : Wednesday, 12 March 2008 17:08:32 GMT