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From: piugwikimaster_at_gmail.com [mailto:piugwikimaster_at_gmail.com]
Sent: Tuesday, December 16, 2008 11:49 AM
To: piugwikimaster_at_gmail.com
Subject: [PIUG] PIUG Space > Gene Sequence
Gene Sequence <http://wiki.piug.org/display/PIUG/Gene+Sequence>
Added by Robert W. March <http://wiki.piug.org/display/~robertmarch> , last
edited by Robert W. March <http://wiki.piug.org/display/~robertmarch> on
Dec 15, 2008 22:44
Can anyone give me an example of a recent (2003 to present) gene sequence
claimed by name in a patent (US preferably) but not indexed by its genetic
sequence? In other words, a gene sequence search alone, would not retrieve
the reference. If this is not possible, please let me know why.
Thanks,
Bob March
DuPont
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Gene
<http://wiki.piug.org/display/PIUG/Gene+Sequence?focusedCommentId=4981657#co
mment-4981657> Sequence
Page commented by Kristine H. Atkinson
<http://wiki.piug.org/display/~khatkinson>
I'm thinking that this is the type of thing I see now and again as a trivial
name---an example would be patent 6,107,080 (a biosensor) where a sequence
listing is part of the specification, but because it isn't a separate
section of the patent and not in the claims, the sequence probably would not
be indexed. The claims specify several generic gene products like
streptavidin complex, and are characterized by their function (binding). I
pulled this one at random, but see sequences often enough that have to do
with diagnostic devices. The spec says in part:
...the ligand in the biosensor is anchored to biosensor surface, i.e.,
embedded within the hydrocarbon-chain monolayer, by a coiled-coil
heterodimer complex formed of two subunit peptides. The heterodimer-subunit
peptides employed in the biosensor invention are two non-identical,
preferably oppositely charged polypeptide chains, typically each about 21 to
about 70 residues in length, having an amino acid sequence compatible with
their formation into two-stranded .alpha.-helical heterodimeric
coiled-coils. They are designated herein as HSP1 (heterodimer-subunit
peptide 1), and HSP2 (heterodimer-subunit peptide 2). In the discussion
below, HSP1 will refer to the peptide attached to the biosensor surface in
the biosensor, and HSP2, to the peptide having an attached ligand. It will
be understood that these designations refer to the functional role played by
the subunit peptide, not the actual peptide sequence.I pulled this patent at
random, but see partial sequences often enough that have to do with
diagnostic devices. The device world aims at getting the most generic
identification possible---so if a competitor wants a rapamycin effect, my
patent claiming antibiotics trumps. In the above patent, the sequence is
given in order to enable, not to claim it. You often see "kitchen sink"
listings of common chemical names in order to teach, so that your
competitors can't design around you with an obvious substitute.
There are changes on the horizon on indexing protocols, but for now I'm
assuming if a separate document/ attachment exists for a sequence listing,
or of course if it's been deposited in a public database, that's how it's
done; they aren't searching for little pieces of sequences within patent
specifications. I went to one semantic search seminar in Napa where the guy
proposed using noun-verb-noun phrases to parse claims---he looked a little
stunned when I told him a claim didn't need a verb.
Is this the kind of thing you were driving at? For a test, take your
compound common names and look for them under the umbrella of usage
platform---diagnostics, treatment are huge areas that can de mined.
Let's hope Rob Austin or other expert will enlighten us further on whether
"collateral" sequences get collected in indexing.
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Received on Fri Dec 26 2008 - 12:12:52
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