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Re: blog: semantic dissonance in uniprot

From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sat, 21 Mar 2009 15:02:08 +0100
Message-ID: <6aeb064b0903210702g2bc74e9cnd1d406c4df854b2b@mail.gmail.com>
To: eric neumann <ekneumann@gmail.com>
Cc: marshall@science.uva.nl, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
On Sat, Mar 21, 2009 at 5:01 AM, eric neumann <ekneumann@gmail.com> wrote:
> There is no such thing as a referenceble instance of a specific instantiated
> molecule ("that specific molecule"); all gene, protein, and chemical records
> are about the category or group of exemplar molecules:
> SAME molecular structure, NOT SAME atoms (so we already aren't really things
> in the real world ;-) ); all molecular databases are based on this asserted
> fact.

Even worse. Since there are >10^20 molecules in most used materials,
many 'molecular' properties are really material properties. A melting
point is not a molecular property, but often even reported as
elemental property.

> Most users of molecular information aren't ignorant about the difference
> between a protein and a record of a protein; it's just that they don't want
> to deal with all the extra CS mechanics (that prevent getting their job
> done). And so an instance of a protein record in a database (or a reference
> to it from another database) is the closest thing to saying: "here's the
> protein".

Chemists are not interested in single molecules (well, most are not,
but with increasing nanotechnology...). I was told recently that upper
ontologies have proper mechanisms to point out the difference between
(in Java terminology) objects and classes, or instances and concepts.

> Different records exist for the same protein, which indeed has been a
> historic point of complication; but this is really a social issue, not a
> semantic one, and the key data authorities have already for years
> coordinated on this point by supplying cross-references to each
> other.

There is another level to this: that of a measurement or observation,
and the identity we assign to it. The sequence of a protein, or
molecular structure of a drug of the model that people assigned to
some measurement. Measurements that point to the same measurable, may
actually be assigned different identities...


Post-doc @ Uppsala University
Received on Saturday, 21 March 2009 14:02:47 UTC

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