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[bioontology-support] mappings

Trish Whetzel whetzel at stanford.edu
Wed Dec 16 09:37:04 PST 2009


Hi Julia,

One item that looks like it may be problematic with the OWL derivative  
from below http://www.berkeleybop.org/ontologies/ is that there are  
multiple kinds of things in the property rdfs:label. For example,  
definition, Dbxrefs and are represented as subclasses versus values of  
properties. I believe that LOOM expects this content to be in  
different properties versus all being within one property with the  
same name.

Using Protege 4 to open the OBO format file and then saving as RDF/ 
XML, I get the following for the same term as represented below:
<!-- http://purl.org/obo/owl/pathway#PW_0000015 -->
     <owl:Class rdf:about="#PW_0000015">
         <rdfs:label>Alzheimer disease pathway</rdfs:label>
         <rdfs:subClassOf rdf:resource="#PW_0000014"/>
         <oboInOwl:def>"A mostly sporadic, late-onset condition  
affecting the central nervous system, is the most prevalent  
neurodegenerative disease and the most common form of dementia. It is  
characterized by the presence of amyloid plaques and fibril tangles.  
Possible pathways affected range from protein misfolding and  
aggregation, to oxidative stress and impaired metal homeostasis."  
[InHouse:InHouse PW dictionary "Definition provided by the PW  
editorial team"]</oboInOwl:def>
     </owl:Class>

I have not had a chance to check use of this file further following  
the instructions with LOOM. However, have you tried to generate an OWL  
version using Protege 4 and then using LOOM?

Trish



On Dec 15, 2009, at 8:46 AM, Julia Dmitrieva wrote:

> Dear Trish,
> I was not succeed with mapping of OBO ontologies with LOOM.
> I use the OWL variants from http://www.berkeleybop.org/ontologies/.
>
> I think that the problem is that syntax of those ontologies after  
> the convertion from OBO
> to OWL is not OK, I was also not succeed with preferred name  
> configuration from Protege 3.
>
> Further, I did the same as it was described at http://www.bioontology.org/wiki/index.php/LOOM 
> .
> Here I show how the classes are looking out in OWL variant, may be  
> you know how
> the problem can be solved:
>
> <owl:Class rdf:about="http://purl.org/obo/owl/PW#PW_0000015">
>     <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string 
> "
>     >pathway</oboInOwl:hasOBONamespace>
>     <oboInOwl:hasDefinition>
>       <oboInOwl:Definition>
>         <rdfs:label xml:lang="en">A mostly sporadic, late-onset  
> condition affecting the central nervous system, is the most  
> prevalent neurodegenerative disease and the most common form of  
> dementia. It is characterized by the presence of amyloid plaques and  
> fibril tangles. Possible pathways affected range from protein  
> misfolding and aggregation, to oxidative stress and impaired metal  
> homeostasis.</rdfs:label>
>         <oboInOwl:hasDbXref>
>           <oboInOwl:DbXref>
>             <oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI 
> "
>             >http://purl.org/obo/owl/InHouse#InHouse_InHouse_PW_dictionary 
> </oboInOwl:hasURI>
>             <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string 
> "
>             >InHouse:InHouse_PW_dictionary</rdfs:label>
>           </oboInOwl:DbXref>
>         </oboInOwl:hasDbXref>
>         <oboInOwl:hasDbXref>
>           <oboInOwl:DbXref>
>             <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string 
> "
>             >KEGG:map05010</rdfs:label>
>             <oboInOwl:hasURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI 
> "
>             >http://purl.org/obo/owl/KEGG#KEGG_map05010</ 
> oboInOwl:hasURI>
>           </oboInOwl:DbXref>
>         </oboInOwl:hasDbXref>
>       </oboInOwl:Definition>
>     </oboInOwl:hasDefinition>
>     <rdfs:subClassOf>
>       <owl:Class rdf:about="http://purl.org/obo/owl/PW#PW_0000014"/>
>     </rdfs:subClassOf>
>     <rdfs:label xml:lang="en">Alzheimer disease pathway</rdfs:label>
>   </owl:Class>
>
> Thank you
> Julia
>
> 2009/12/8 Trish Whetzel <whetzel at stanford.edu>
> Hi Julia,
>
> Just wanted to check back to see if you have any further questions  
> on using LOOM to generate mappings. In addition, once the mappings  
> are generated we can upload these to BioPortal if you like so that  
> they can be accessible via the mapping web services.
>
> Trish
>
>
> On Nov 21, 2009, at 9:10 AM, Julia Dmitrieva wrote:
>
>> Dear BioPortal community.
>>
>> I would like to create mappings in different ontologies with LOOM.
>> Is it possible to use OBO or OWL format (in description is written,
>> that I have to use .pprj file format).
>>
>> My second question is:
>> In the case of OBO ontology what will be the TargetSynonymSlotURI:
>>
>> for example,  what will be the TargetSynonymSlotURI in the  
>> following case:
>>
>> format-version: 1.0
>> date: 27:04:2009 14:30
>> saved-by: VPetri
>> auto-generated-by: OBO-Edit 1.101
>> default-namespace: pathway
>> .
>> .
>> .
>> .
>> [Term]
>> id: PW:0000416
>> name: sentrinization pathway
>> def: "A pathway of protein modification via conjugation with  
>> sentrin - a family of ubiquitin-like protein. Sentrinization does  
>> not target proteins to the proteasome, rather it targets proteins  
>> to particular cellular compartments." [PubMed:PMID\: 10806345;  
>> 15808504 "Review articles in PubMed"]
>> related_synonym: "SUMO modification pathway" []
>> related_synonym: "sumoylation pathway" []
>> is_a: PW:0000433 ! protein modification pathway via conjugation  
>> with ubiquitin and ubiqutin-like molecules
>>
>> Is it pathway#related_synonym?
>>
>> Thank you for your help,
>> with best regards,
>>
>> Julia
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> whetzel at stanford.edu
> http://www.bioontology.org
>
>
>
>

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org



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