On Mon, Dec 14, 2009 at 4:02 AM, qinghua xu <xy0702cy at="" yahoo.com.cn="">
wrote:
> Dear all,
>
> I would like to know?is there any patent related concern when try?
to publish a microarray study using different classification
algorithms, like KNNs, Random Forest, Support Vector Machine and so
on?
>
> I would appreciate any advice, or pointers to any references for
this!
A couple of places to look:
In the DESCRIPTION of each package available for R, there is a license
line that may be useful for determining the license under which the
software is released. More importantly, though, is probably the
citation() entry, which gives the citations for the package that
should be cited if the package is used in a publication.
As for patents, I'm not sure how important that is from a user
perspective; perhaps others want to comment here.
Sean
Dear Qinghua,
I don't think you should concern yourself too much with patents on
most
classification methods.
Yes, there might be lots of SVM patents in a biomedical field, but the
basic method for SVM is not patented and the same is true for almost
all
other methods.
Unless something malicious was going on, the license field should tell
you if there is anything you should worry about. For example, the
siggenes packages says that a paid license is needed for non-academic
users.
But as I said, I don't think any of the basic classification methods
in
R (including in e0171) are patented and I would not worry about it in
a
publication.
If you were planning on commercializing a test, it could be worth
checking more heavily about it. I would expect those patents are of
the
sort, using genes X,Y,Z with this algorithm with these parameters to
solve this problem. Just using the same algorithm would probably not
be
covered by those patents. Still, if there is money at stake, you would
be better off contacting someone specialized in the field.
Francois
On 12/14/2009 10:49 PM, qinghua xu wrote:
> Dear Sean,
>
> Thanks a lot for your prompt reply!
>
> I think the main concern? is not the citation issue.? That should be
OK. I have rapidly checked the "GNU GENERAL PUBLIC LICENSE" under
which? R packages are released. If I understand correctly, it is more
about COPYING, DISTRIBUTION? and MODIFICATION program itself, rather
than the outputs from? using program.
>
> Take? the famous package (e0171) as an example. Without doubt,? it
is under the licence GPL-2, however, I? also find massive patents? of
SVM application in the biomedical field.? Maybe, it is rather a
question for intellectual property protection specialists.
>
> Thanks again!
>
> Qinghua
>
>
>
> ________________________________
> ???????????? Sean Davis<seandavi at="" gmail.com="">
>
> ??? ?????? bioconductor at stat.math.ethz.ch; qinghua.xu at
as.biomerieux.com
> ??????????????? 2009/12/14 (??????) 8:38:58 ??????
> ??? ?????? Re: [BioC] Patent issues of classification algorithms
>
>
>> Dear all,
>>
>> I would like to know is there any patent related concern when try
to publish a microarray study using different classification
algorithms, like KNNs, Random Forest, Support Vector Machine and so
on?
>>
> [[elided Yahoo spam]]
>
> A couple of places to look:
>
> In the DESCRIPTION of each package available for R, there is a
license
> line that may be useful for determining the license under which the
> software is released.? More importantly, though, is probably the
> citation() entry, which gives the citations for the package that
> should be cited if the package is used in a publication.
>
> As for patents, I'm not sure how important that is from a user
> perspective; perhaps others want to comment here.
>
> Sean
>
> ________________________________
> ????????????????? ?????????????????????????????????
>
>
> ___________________________________________________________
> ????????????????? ?????????????????????????????????
>
> [[alternative HTML version deleted]]
>
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
Hi Francois,
just one little correction: siggenes is now available under LGPL
(>=2).
Best,
Holger
-------- Original-Nachricht --------
> Datum: Tue, 15 Dec 2009 14:00:41 -0500
> Von: Francois Pepin <fpepin at="" cs.mcgill.ca="">
> An: qinghua xu <xy0702cy at="" yahoo.com.cn="">
> CC: qinghua.xu at as.biomerieux.com, bioconductor at
stat.math.ethz.ch
> Betreff: Re: [BioC] : Patent issues of classification algorithms
> Dear Qinghua,
>
> I don't think you should concern yourself too much with patents on
most
> classification methods.
>
> Yes, there might be lots of SVM patents in a biomedical field, but
the
> basic method for SVM is not patented and the same is true for almost
all
> other methods.
>
> Unless something malicious was going on, the license field should
tell
> you if there is anything you should worry about. For example, the
> siggenes packages says that a paid license is needed for non-
academic
> users.
>
> But as I said, I don't think any of the basic classification methods
in
> R (including in e0171) are patented and I would not worry about it
in a
> publication.
>
> If you were planning on commercializing a test, it could be worth
> checking more heavily about it. I would expect those patents are of
the
> sort, using genes X,Y,Z with this algorithm with these parameters to
> solve this problem. Just using the same algorithm would probably not
be
> covered by those patents. Still, if there is money at stake, you
would
> be better off contacting someone specialized in the field.
>
> Francois
>
> On 12/14/2009 10:49 PM, qinghua xu wrote:
> > Dear Sean,
> >
> > Thanks a lot for your prompt reply!
> >
> > I think the main concern? is not the citation issue.? That should
be
> OK. I have rapidly checked the "GNU GENERAL PUBLIC LICENSE" under
which? R
> packages are released. If I understand correctly, it is more about
COPYING,
> DISTRIBUTION? and MODIFICATION program itself, rather than the
outputs
> from? using program.
> >
> > Take? the famous package (e0171) as an example. Without doubt,? it
is
> under the licence GPL-2, however, I? also find massive patents? of
SVM
> application in the biomedical field.? Maybe, it is rather a
question for
> intellectual property protection specialists.
> >
> > Thanks again!
> >
> > Qinghua
> >
> >
> >
> > ________________________________
> > ???????????? Sean Davis<seandavi at="" gmail.com="">
> >
> > ??? ?????? bioconductor at stat.math.ethz.ch;
> qinghua.xu at as.biomerieux.com
> > ??????????????? 2009/12/14 (??????) 8:38:58
> ??????
> > ??? ?????? Re: [BioC] Patent issues of classification
> algorithms
> >
> >
> >> Dear all,
> >>
> >> I would like to know is there any patent related concern when try
to
> publish a microarray study using different classification
algorithms, like
> KNNs, Random Forest, Support Vector Machine and so on?
> >>
> > [[elided Yahoo spam]]
> >
> > A couple of places to look:
> >
> > In the DESCRIPTION of each package available for R, there is a
license
> > line that may be useful for determining the license under which
the
> > software is released.? More importantly, though, is probably the
> > citation() entry, which gives the citations for the package that
> > should be cited if the package is used in a publication.
> >
> > As for patents, I'm not sure how important that is from a user
> > perspective; perhaps others want to comment here.
> >
> > Sean
> >
> > ________________________________
> > ?????????????????
> ?????????????????????????????????
> >
> >
> > ___________________________________________________________
> > ?????????????????
> ?????????????????????????????????
> >
> > [[alternative HTML version deleted]]
> >
> >
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
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