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[bioontology-support] Relation URIs

Paul R Alexander palexander at stanford.edu
Thu Dec 13 13:44:53 PST 2012


Lorenz,

I've submitted a request to provide a list of properties defined by BioPortal, though hopefully future revisions of the REST API will make this clearer in the response output.

Even the RDF term services will contain the BioPortal-specific properties. The structure that we add is one of the main reasons you would choose to use BioPortal REST services over working with each ontology directly, so we almost always include it when we provide information about a term.

Paul


On Dec 10, 2012, at 1:13 AM, Lorenz Bühmann <buehmann at informatik.uni-leipzig.de> wrote:

> Hi Paul,
> 
> thanks for your answer. Maybe you could make a list of properties online available, which are only internally available in the BioPortal. There are also some other properties, which are not property specific, e.g. disjointWith which I guess means owl:disjointWith. 
> By the way, I currently recongnized that you provide a RDF term service. Maybe that could be another solution to get the information about a concept with the URIs in one step. Does it cover the same features as the non-RDF term service minus your internal properties?
> 
> Regards,
> Lorenz
> 
> 
> On 08/12/12 02:11, Paul R Alexander wrote:
>> Lorenz,
>> 
>> Are there specific relations that you are interested in? A few of the entries in relation are BioPortal-specific:
>> SubClass (child classes/terms)
>> SuperClass (parent classes/terms)
>> ChildCount (# of child classes/terms)
>> IndividualCount (# of instances/individuals of this class)
>> 
>> The others are supplied by the ontology itself. You should see them listed on the properties call that I sent earlier in most cases. It appears as though PAR doesn't show up there, and to be honest I'm not sure why. I'll file a bug report on that.
>> 
>> Let me know if you have other questions.
>> 
>> Paul
>> 
>> 
>> On Dec 5, 2012, at 1:15 PM, Lorenz Buehmann <buehmann at informatik.uni-leipzig.de> wrote:
>> 
>>> 
>>> -----BEGIN PGP SIGNED MESSAGE-----
>>> Hash: SHA1
>>> 
>>> Hi Paul,
>>> 
>>> thanks for your answer. I guess what you suggest is the service for getting all properties for an ontology. This properties can than be used by instances.
>>> What I want to know is, how to handle the relations which are contained in class beans, e.g.
>>> 
>>> <?xml version="1.0" encoding="UTF-8"?>
>>> <success>
>>>   <accessedResource>/bioportal/concepts/44103</accessedResource>
>>>   <accessDate>2010-12-08 16:57:43.763 PST</accessDate>
>>>   <data>
>>>     <classBean>
>>>       <id>O80-O84.9</id>
>>>       <fullId>http://purl.bioontology.org/ontology/ICD10/O80-O84.9</fullId>
>>> 
>>>       <label>Delivery</label>
>>>       <type>Class</type>
>>>       <relations>
>>>         <entry>
>>>           <string>SubClass</string>
>>>           <list>
>>>             <classBean>
>>> 
>>>               <id>O84</id>
>>>               <fullId>http://purl.bioontology.org/ontology/ICD10/O84</fullId>
>>>               <label>Multiple delivery</label>
>>>               <type>Class</type>
>>>               <relations>
>>>                 <entry>
>>>                   <string>ChildCount</string>
>>> 
>>>                   <int>5</int>
>>>                 </entry>
>>>               </relations>
>>>             </classBean>
>>>             <classBean>
>>>               <id>O83</id>
>>>               <fullId>http://purl.bioontology.org/ontology/ICD10/O83</fullId>
>>> 
>>>               <label>Other assisted single delivery</label>
>>>               <type>Class</type>
>>>               <relations>
>>>                 <entry>
>>>                   <string>ChildCount</string>
>>>                   <int>7</int>
>>>                 </entry>
>>> 
>>>               </relations>
>>>             </classBean>
>>>             <classBean>
>>>               <id>O82</id>
>>>               <fullId>http://purl.bioontology.org/ontology/ICD10/O82</fullId>
>>>               <label>Single delivery by caesarean section</label>
>>>               <type>Class</type>
>>> 
>>>               <relations>
>>>                 <entry>
>>>                   <string>ChildCount</string>
>>>                   <int>5</int>
>>>                 </entry>
>>>               </relations>
>>>             </classBean>
>>>             <classBean>
>>> 
>>>               <id>O81</id>
>>>               <fullId>http://purl.bioontology.org/ontology/ICD10/O81</fullId>
>>>               <label>Single delivery by forceps and vacuum extractor</label>
>>>               <type>Class</type>
>>>               <relations>
>>>                 <entry>
>>>                   <string>ChildCount</string>
>>> 
>>>                   <int>6</int>
>>>                 </entry>
>>>               </relations>
>>>             </classBean>
>>>             <classBean>
>>>               <id>O80</id>
>>>               <fullId>http://purl.bioontology.org/ontology/ICD10/O80</fullId>
>>> 
>>>               <label>Single spontaneous delivery</label>
>>>               <type>Class</type>
>>>               <relations>
>>>                 <entry>
>>>                   <string>ChildCount</string>
>>>                   <int>4</int>
>>>                 </entry>
>>> 
>>>               </relations>
>>>             </classBean>
>>>           </list>
>>>         </entry>
>>>         <entry>
>>>           <string>PAR</string>
>>>           <list>
>>>             <classBean>
>>> 
>>>               <id>O00-O99.9</id>
>>>               <fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
>>>               <label>Pregnancy, childbirth and the puerperium</label>
>>>               <type>Class</type>
>>>               <relations>
>>>                 <entry>
>>>                   <string>ChildCount</string>
>>> 
>>>                   <int>8</int>
>>>                 </entry>
>>>               </relations>
>>>             </classBean>
>>>           </list>
>>>         </entry>
>>>         <entry>
>>>           <string>ChildCount</string>
>>> 
>>>           <int>5</int>
>>>         </entry>
>>>         <entry>
>>>           <string>Semantic_Type</string>
>>>           <list>
>>>             <string>Therapeutic or Preventive Procedure</string>
>>>           </list>
>>> 
>>>         </entry>
>>>         <entry>
>>>           <string>TUI</string>
>>>           <list>
>>>             <string>T061</string>
>>>           </list>
>>>         </entry>
>>>         <entry>
>>> 
>>>           <string>UMLS_CUI</string>
>>>           <list>
>>>             <string>C0011209</string>
>>>           </list>
>>>         </entry>
>>>         <entry>
>>>           <string>SuperClass</string>
>>> 
>>>           <list>
>>>             <classBean>
>>>               <id>O00-O99.9</id>
>>>               <fullId>http://purl.bioontology.org/ontology/ICD10/O00-O99.9</fullId>
>>>               <label>Pregnancy, childbirth and the puerperium</label>
>>>               <type>Class</type>
>>>               <relations>
>>> 
>>>                 <entry>
>>>                   <string>ChildCount</string>
>>>                   <int>8</int>
>>>                 </entry>
>>>               </relations>
>>>             </classBean>
>>>           </list>
>>>         </entry>
>>> 
>>>       </relations>
>>>     </classBean>
>>>   </data>
>>> </success>
>>> 
>>> Here we have for example relation entries like SubClass, SuperClass, PAR, TUI... What is the semantic behind them, and are there some full URIs? For some of them I guess it is clear, so SubClass is maybe equal to rdfs:subClassOf, but what about others like PAR, TUI.
>>> 
>>> Kind regards,
>>> Lorenz
>>> 
>>> On 05.12.2012 20:11, Paul R Alexander wrote:
>>> > Lorenz,
>>> 
>>>                 >
>>> 
>>>                 > You can see information about the property ids
>>>                 found in the relation element by making a separate call
>>>                 using the ontology version id:
>>> 
>>>                 >
>>>                 http://rest.bioontology.org/bioportal/ontologies/properties/38801?apikey=YourAPIKey
>>> 
>>>                 >
>>> 
>>>                 > If this isn't what you are looking for, please let
>>>                 me know.
>>> 
>>>                 >
>>> 
>>>                 > Paul
>>> 
>>>                 >
>>> 
>>>                 >
>>> 
>>>                 > On Dec 5, 2012, at 6:43 AM, Lorenz Bühmann <buehmann at informatik.uni-leipzig.de
>>>                 <mailto:buehmann at informatik.uni-leipzig.de>>
>>>                 wrote:
>>> 
>>>                 >
>>> 
>>>                 >> Hello BioPortal developers,
>>> 
>>>                 >>
>>> 
>>>                 >> I'm currently playing around with the BioPortal
>>>                 REST services, and now I'm just wondering how it is
>>>                 possible to get the URIs for the relations which are
>>>                 contained in the relations part, when I for example use
>>>                 the term service. Is there a preferred namespace for the
>>>                 relations you provide via the REST service? Or is there
>>>                 somewhere a full list of possible relations?
>>> 
>>>                 >>
>>> 
>>>                 >> Kind regards,
>>> 
>>>                 >> Lorenz Bühmann
>>> 
>>>                 >> -- 
>>> 
>>>                 >> M.Sc. Inf. Lorenz Bühmann
>>> 
>>>                 >> Institute of Computer Science, University of
>>>                 Leipzig
>>> 
>>>                 >> Research Group: Agile Knowledge Engineering and
>>>                 Semantic Web (AKSW) <http://aksw.org/>
>>> 
>>>                 >> Workpage: http://bis.informatik.uni-leipzig.de/LorenzBuehmann
>>> 
>>>                 >> _______________________________________________
>>> 
>>>                 >> bioontology-support mailing list
>>> 
>>>                 >> bioontology-support at lists.stanford.edu
>>>                 <mailto:bioontology-support at lists.stanford.edu>
>>> 
>>>                 >> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>>>                 >
>>> 
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>>> 
>> 
> 
> -- 
> M.Sc. Inf. Lorenz Bühmann
> Institute of Computer Science, University of Leipzig
> Research Group: Agile Knowledge Engineering and Semantic Web (AKSW)
> Workpage: http://bis.informatik.uni-leipzig.de/LorenzBuehmann

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