[moby] Re: [MOBY-dev] Migration of database to new API

[Mark Wilkinson]

As you have noticed, the change has already happened at the code level
just to prevent any more registrations of what will soon be illegal
objects.  I have a script that will update the database records of the
ontologies and deprecate the old nodes, but we haven't yet run it on the
public registry.  Eddie is going to make a couple of changes to it over
the next day or two, and then will send out a heads-up that the
ontologies are changing forever, and a tutorial on how to do the update
for service providers.  We'll give a reasonable amount of time for
people to update their services (say, 6 weeks) and then we will delete
the old nodes from the ontology completely.  The script is in the CVS so
anyone running a registry can do the same thing.

When I went to update my own services it took me less than 5 minutes to
do so, so 6 weeks should be more than enough time for anyone who is
actively concerned about their service :-)

Cheers!

M



On Thu, 2005-10-06 at 17:32 +0200, Pieter Neerincx wrote:
> On 27-Aug-2005, at 12:20 AM, Mark Wilkinson wrote:
> 
> > Hi all,
> >
> > As we move toward deploying the new API, there are some serious
> > consequences on the underlying databases.
> >
> > Let me first re-cap the new API features that I am discussing and what
> > effects they have on the databases:
> >
> > 1)  Inheritence from primitives through ISA relationships is no longer
> > allowed.  e.g. plain-text ISA String  is no longer allowed.  To  
> > achieve
> > the same result, you now create an object that inherits from Object  
> > and
> > contains the primitive.  e.g. plain-text ISA Object; plain-text HASA
> > String.
> 
> Hi Mark et al.,
> 
> Any idea when this change will happen? If I look in the Central that  
> is running the latest and greatest codebase, the forbidden ISA [some  
> primitive] relationships are still in place :(. What is even worse is  
> that the primitive DateTime ISA String. As a result I can not get one  
> of my Objects (that plays by the rules of the latest specs)  
> registered. At least I suspect this to be the problem. I don't get an  
> error message when register my object, but it has amongst others a  
> HASA DataTime and that relationship is not getting registered...
> 
> Cheers,
> 
> Pi
> 
> 
> 
> 
> Wageningen University and Research centre (WUR)
> Laboratory of Bioinformatics
> Transitorium (building 312) room 1034
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
> phone: 0317-483 060
> fax: 0317-483 584
> mobile: 06-143 66 783
> pieter.neerincx at wur.nl
> 
> 
> 
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-- 
"Ontologists do it with the edges!"

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