On Jul 20, 2007, at 3:52 AM, Eric Jain wrote:
Alan Ruttenberg wrote:
Who's mission? Remember that one of the reasons this came up was
the claim that the Uniprot URI identified the protein in the real
world.
Who claimed that?
If we wanted to identify each protein in the real world we'd have
to assign zillions of URIs just for the protein molecules in my
body, impractical :-)
My bad. I mean to say:
"Remember that one of the reasons this came up was the claim that the
Uniprot URI should be used to identify a set of real things."
What I'm trying to get at is that when we talk about a "protein",
it's just a useful abstraction for us and our users, and it's the
same for all other databases I'm aware of (except that their
"proteins" may differ from ours).
I get confused when I read statements that sound like "x means the
same thing in in all databases, except it might mean something
different in a database that isn't Uniprot". I'm sure this isn't what
you mean. What do you mean?
Since a "protein" is always a (more or less) artificial set of real
things, I don't see the need for URIs for both the "record" and the
"real thing"?
I will read "protein" as "protein class", so as not to confuse the
set with the individual member of the set, OK?
When someone makes a statement, such as the ones about the BAG-1
isoforms I cite in another message to Phil, I don't think that we
should say this is an artificial set of real things. While it may be
the case that there is a certain amount of ambiguity in exactly which
set of proteins "BAG-1 p33" identifies, we know some things that I
think would be profitable to be conveyed in OWL.
For example:
a) There is no protein that is both a member of the set "BAG-1 p33"
identifies and also a member of the set "BAG-1 p33" identifies.
b) If it turns out at a later date that the properties (e.g. being
able to inhibit apoptosis) ascribed to proteins in the set identified
by "BAG-1 p33" only were true when the protein was phosphorylated,
and some different, conflicting properties(e.g. not being able to
inhibit apoptosis) became known of the unphosphorylated ones, then we
would have to say that our original statements about "BAG-1 p33"
needed to be modified to be statements about the set of proteins
identified as e.g. "phospho BAG-1 p33". I.e. we would name a new set
of things: "phospho BAG-1 p33", know it was a subset of the set of
things identified as "BAG-1 p33", that it was also disjoint from the
set of things identified by "BAG-1 p29". We would be able to answer
the question: If we cause "BAG-1 p33" proteins to be overexpressed,
but knock out the kinase that phosphorylates such proteins, do we
expect(or do we have any evidence to support believing) apoptosis to
be inhibited?
-Alan
