[MOBY-dev] [moby] Articlenames

[Mark Wilkinson]

Hi all, 

If you have any objections to this, please flame me, not Eddie.  He
asked me, and I told him to go ahead without properly thinking about it;
however now I am having second thoughts.  MOBY Central is still using
the old codebase, so no worries there.

For data-types, it is clear that we have to follow the rules for data-
typing that XML places on us.  Since data-types in MOBY become XML tags,
those rules are pretty restrictive, but generally speaking there aren't
any troublesome ones in the registry right now.  We do have a problem
with some of the Gene Ontology-created namespaces having a second ":"
character in them, but I am going to talk to Midori about this ASAP!
Hopefully we can get rid of those. 

However, for articleNames, the XML rules are a lot looser, since these
are represented in MOBY as XML attribute values.  There are already some
articleNames in the object ontology that contain spaces, and those don't
particularly concern me (are they causing problems for anyone else?);
however other unusual characters might cause problems if the code isn't
expecting them.

It would be a change in the API if we were to impose limitations on the
articleName character-set at this point, but it wont affect most (any?)
existing objects or services.  Does anyone object to putting a
restriction on the characters that can be used in articleNames?  Either
way, we should probably make an explicit note in the API about what
characters are acceptable, even if we simply say "any".

M




On Thu, 2006-09-07 at 15:22 -0700, Edward Kawas wrote:
> Hi,
> 
> I have just committed code that prohibits the registry from registering services
> and datatypes that have articlenames that contain spaces or special characters
> `~!@#$%^&*()=+;:'"<,>./?\|.
> 
> I did this because having those characters prohibits us from expressing the
> Datatype ontology in OWL.
> 
> There are a few offending datatypes that currently make use of these characters
> and hopefully I can track down the people who registered them and ask them to
> re-register the datatypes.
> 
> If you know offhand that you may have done this, could you fix your datatypes.
> 
> Thanks,
> 
> Eddie
> 
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-- 
Mark Wilkinson
Asst. Professor, Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics, iCAPTURE Centre
St. Paul's Hospital, Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274

"Since the point of a definition is to explain the meaning of a term to
   someone who is unfamiliar with its proper application, the use of
language that doesn't help such a person learn how to apply the term is
 pointless. Thus, "happiness is a warm puppy" may be a lovely thought,
                     but it is a lousy definition."
                                                                Köhler et al, 2006