[moby] [MOBY-dev] Reserved word... perhaps unnecessary...

[Mark Wilkinson]

Okay, I have thought about this now, and discussed it with Eddie and Ben
for a while.  I can see the way Martin is thinking, and it is certainly
different from how I have always "seen" MOBY Objects.

Here's how the argument goes:

Martin:  MOBY Objects are just syntax, so there is no such thing as a
"core" data-type for MOBY objects.  They don't have an "essense"!
Objects are just "stuff"

Mark:  Yes they do!  The ISA hierarchy implies that an object has an
"essense".  There are two ways to construct an AnnotatedFASTA object:
It can either inherit from FASTA, and add an Annotation, or it can
inherit from Annotation and add a FASTA.  Under the new object creation
system, the syntactic outcome of these paths is identical, but they are
"qualitatively" different.... it is nonsensical to "FASTA an
Annotation", but it is sensible to "Annotate a FASTA".  The "essense" of
the object is the FASTA sequence it contains, based on its ISA
hierarchy.  The problem we have now is that, without querying the
ontology and traversing back to the most primitive object, I cannot know
which contained object represents the "essense" of my in-hand object
(i.e. the thing that I would MOST want to represent if I had to
represent that object in a hurry).

It also causes a problem with rendering... a FASTA sequence and a
Genbank record are formatted strings.  What happens now that we have
contained primitives is that you have to ask the parent tag about its
type before you know how to render the child tag. I can't render a
string containing a genbank record without paying attention to its
formatting, but I don't know that a String is a formatted string until I
ask the parent GenBankFlatfile object what it is...  :-/

  >>sigh<<

I dunno... the world just got much harder.

M




On Wed, 2005-11-02 at 17:51 -0800, Mark Wilkinson wrote:
> Hi Martin,
> 
> I love using you as the bellweather for my own thoughts :-)  You are 
> seldom wrong, and delight in telling me when I am! ;-)
> 
> I think I am starting to see your point - I had not been thinking of the 
> object ontology in quite that way, but you've got me reconsidering now.  
> I'm going to bring it up for discussion at my lab meeting tomorrow and 
> try to hash-out with the local guys exactly why I feel the way I do, and 
> whether or not there are any serious adverse effects to thinking about 
> it your way.  It certainly makes things easier to do it your way, though 
> I wish now that we had had this discussion while Eddie was writing the 
> database update script because I would have changed the way we 
> approached it...
> 
> Oh well...  I guess that's why MOBY is still considered a research 
> project ;-)
> 
> Thanks for being so forthright in your opinons - you are an extremely 
> valuable asset to the project!
> 
> M
> 
> 
> 
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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