[MOBY-dev] Strange inconsistence (bug?) in MobyCentral

Dmitry Repchevsky dmitry.repchevski at bsc.es
Wed Jul 8 02:25:03 UTC 2009


Hello,

Trying to optimize a little bit my MobyCentral API I found a strange a 
thing:

According the "specification"
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/XMLPayloads.html#retrieveObjectDefinition

There are two ways to get the relationships for an object:

first way is to get Relationships directly (through "Relationships" 
operation):

Output:

        <Relationships>
           <Relationship relationshipType="RelationshipOntologyTerm1" 
	   lsid='urn:lsid:authority.uri:namespace:id'>
                [ <objecctType lsid='...' articleName='foo'>OntologyTerm</objectType> | 
		<serviceType lsid='...'>OntologyTerm</serviceType> ]
                       ...
           </Relationship>
           ...
        </Relationships>

This one I used to use...

But there is another way using "retrieveObjectDefinition" method:

Output:

        <retrieveObjectDefinition>
            <objectType lsid='urn:lsid:authority.uri:namespace:id'>ObjectClassName</objectType>
            <Description><![CDATA[
                    human readable description
                    of data type]]>
            </Description>
            <Relationship relationshipType="RelationshipOntologyTerm" 
	    lsid='urn:lsid:authority.uri:namespace:id'>
               <objectType articleName="SomeName" lsid='urn:lsid:authority.uri:namespace:id'>ExistingObjectType</objectType>
            </Relationship>
            ...
            <authURI>your.URI.here <http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Authorities.html></authURI>
            <contactEmail>owner at their.address.com</contactEmail>
        </retrieveObjectDefinition>


The problem is that instead of [relationshipType="RelationshipOntologyTerm"] it returns lsid!!!

Here is the output:

<retrieveObjectDefinition>
  <objectType lsid='urn:lsid:biomoby.org:objectclass:Zip_Encoded:2007-11-16T11-34-07Z'>Zip_Encoded</objectType>
  <Description><![CDATA[A Zip file encoded in Base-64.]]></Description>
  <authURI>inb.bsc.es</authURI>
  <contactEmail>romina.royo at bsc.es</contactEmail>

  <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:isa'>
    <objectType articleName='' lsid='urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z'>Object</objectType>
  </Relationship>
  <Relationship relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'>
    <objectType articleName='rawdata' lsid='urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z'>String</objectType>
    <objectType articleName='mimeTypte' lsid='urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z'>String</objectType>
  </Relationship>
</retrieveObjectDefinition>

As far as I understand from the specification it should be:

<Relationship relationshipType='ISA' lsid='urn:lsid:biomoby.org:objectrelation:isa'>

Could someone clarify please... 

Dmitry




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