[MOBY-dev] case-sensitivity

[Martin Senger]

Mark,
   Today Rebecca pointed me out that there are problems with the Moby
Graphs. And, indeed, there are. Not only for her Moby server - but also
for the main Moby server.
   I am looking into it now - but the first thing which seems to be
obviously wrong (they may be others) is about case-sensitivity of entity
names. I will tell you what I see and you wil tell me if it is normal,
strange or wrong.
   Let's talk about data types (I assume that the same can be seen by
other entities as well but I have not checked):
   If I ask for all data types names ('retrieveObjectNames') I am getting
(for example for a string data type):

<Object name='String'>
<Description><![CDATA[a string]]></Description>
</Object>

   So far, so good.
   If I ask for its definition ('retrieveObjectDefinition') I am getting:

<retrieveObjectDefinition>
        <objectType>urn:lsid:biomoby.org:objectclass:String</objectType>
        <Description><![CDATA[a string]]></Description>
        ....
</retrieveObjectDefinition>

   Which seems okay because both methods returned 'String' (one as the
whole name, the second one as a last part of an LSID). But if I do the
same thing with the Rebecca's server, I get first 'String' but the
'retrieveObjectDefinition' returns:

   <objectType>urn:lsid:biomoby.org:objectclass:string</objectType>

   Notice that now the last part of the LSID is 'string' with lower-case.

   The LSID specification explicitly says that starting from the
'namespace' field it is case-sensitive. However, perhaps BioMoby does not
care and treats LSID as case-insensitive (meaning actually that it
recognizes the same object under many different LSIDs - differing by the
cases). Is this the case? Or does Rebecca's server do something wrong?

   When this is answered and discussed I will look further why graphs are
not being created properly...

   Thanks,
   Martin

-- 
Martin Senger

EMBL Outstation - Hinxton                Senger at EBI.ac.uk     
European Bioinformatics Institute        Phone: (+44) 1223 494636      
Wellcome Trust Genome Campus             (Switchboard:     494444)
Hinxton                                  Fax  : (+44) 1223 494468
Cambridge CB10 1SD
United Kingdom                           http://industry.ebi.ac.uk/~senger