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

[Edward Kawas]

Hi,

I am working on this script right now as we speak, but I
just wanted to get feedback (for a second time).

>From what I understand, I am going to go through the
ontology, and deprecate any data type that inherits from a
primitive. Any object that I deprecate will be duplicated
and have an _2 appended to its name as well as having its
ISA relationship set to object and adding a HASA primitive
relationship. So far so good.

In six weeks, I am going to go through the ontology and
remove all objects that inherit from a primitive, leaving
those that were duplicated with an _2 alone. Therefore, in 6
weeks, we will have objects like text-plain_2, text-xml_2,
etc.

I know that some people are fine with this and others are
not. Some might not even care. However, what I want to know
is what MOBYers think and if anyone has any other
comments/suggestions. So please let me know.

Just to get this started, I am still pretty iffy about
leaving x_2 data types in the ontology. I do see Marks point
on how services that are not updated choking since they
expect the data type to inherit from a primitive. Any ideas?

Thanks,

Eddie

> -----Original Message-----
> From: Mark Wilkinson [mailto:markw at illuminae.com]
> Sent: Thursday, October 06, 2005 9:08 AM
> To: Core developer announcements
> Cc: Eddie Kawas
> Subject: Re: [moby] Re: [MOBY-dev] Migration of database
> to new API
> 
> 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
> >
> >
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at biomoby.org
> > http://www.biomoby.org/mailman/listinfo/moby-dev
> --
> "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