Re: Licensing terms for data derived from ARB/SILVA data
On 28/11/14 15:48, Frank Oliver Glöckner wrote:
> Dear Sascha Steinbiss,
Dear Prof. Dr. Gloeckner,
> thanks for the information.
> We discussed it and in general we agree that the HMM profiles derived
> from LSURef_115_tax_silva_full_align_trunc.fasta can be distributed.
Thanks for getting back to me about that. I am glad to hear that.
> But we would like to ask you to clearly indicate that the profiles are
> only free for non-commercial usage, commercial users need a licence.
> The easiest approach is to add a reference to the SILVA terms of license
> assigned to the software/profile.
Agreed. I have added the SILVA license terms to the mandatory copyright
description file which goes with every Debian package. This was the last
missing step and the package is now ready in principle.
Unfortunately, due to the non-commercial use restriction we can not make
the barrnap software available via the main Debian software repository.
For inclusion into this repository, all components of a package are
required to be free for all users, under a respective license
(https://wiki.debian.org/DFSGLicenses). This includes the HMMs of
course. Hence this package in its current state will need to go into a
separate 'non-free' repository, which could limit its impact and
usefulness to end-users as its contents will not be usable to them 'out
of the box'.
In this light I would like to kindly ask you to reconsider the licensing
terms for this particular set of models.
> Have a nice weekend
> Frank Oliver Glöckner
Many thanks and best regards
Sascha Steinbiss
> Am 26.11.2014 20:28, schrieb Sascha Steinbiss:
>> On 26/11/2014 17:56, Frank Oliver Glöckner wrote:
>>> >Dear Sascha Steinbeiss,
>> Dear Prof. Gloeckner,
>>
>> thanks for your prompt reply.
>>
>>> >Before we can answer your question may I ask you to provide us with
>>> some
>>> >more information about the:
>>> >1. name of the tool
>> The software in question is barrnap
>> (http://www.vicbioinformatics.com/software.barrnap.shtml) written by
>> Torsten Seemann.
>>
>>> >2. functionality of the tool, e.g. does it just detect rRNAs, and/or
>>> >does it classify sequences?
>> The main functionality is to detect rRNAs and to output their locations
>> in an input sequence as GFF3 features. As far as classification goes, it
>> does distinguish between the individual rRNAs for a given kingdom
>> (5S,23S,16S for bacteria; 5S,5.8S,28S,18S for eukaryotes, etc.) but does
>> not taxonomically classify them as being close to a particular
>> species. You can see example output on the web page given above.
>>
>> It is basically a wrapper around nhmmer searching for a relatively
>> general rRNA pHMM, meant for de novo annotation.
>>
>>> >All the best
>>> >Frank Oliver Glöckner
>> Best wishes from a former 'Nordlicht' (I think we met once when I still
>> was at the ZBH Hamburg)
>> Sascha Steinbiss
>>
>>> >
>>> >Am 26.11.2014 12:34, schrieb Sascha Steinbiss:
>>>> >>Dear ARB/SILVA team,
>>>> >>
>>>> >>I am writing to inquire about a special case regarding your data
>>>> >>licensing terms.
>>>> >>I am involved with the Debian Med project
>>>> >>(https://www.debian.org/devel/debian-med/), whose goal it is to
>>>> provide
>>>> >>software from the medical and bioinformatics fields to users of the
>>>> >>Debian Linux distribution. Currently I am working on packaging a
>>>> piece
>>>> >>of free (GPL) software for prediction of rRNA genes in sequences.
>>>> This
>>>> >>software requires (and would be bundled with) a set of nucleotide
>>>> >>profile HMMs (built with HMMER) based on several individual data
>>>> >>sources. One of the data sources used to build these HMMs was the
>>>> file
>>>> >>LSURef_115_tax_silva_full_align_trunc.fasta, available from your
>>>> >>database.
>>>> >>Since your licensing terms
>>>> >>(http://www.arb-silva.de/silva-license-information/) are not clear
>>>> about
>>>> >>how derivatives of your data are to be licensed, I would like to ask
>>>> >>whether it would be OK for us to package and redistribute these HMMs
>>>> >>under a free license, for both academic and non-academic users. I
>>>> wish
>>>> >>to make it clear here that the original file
>>>> >>LSURef_115_tax_silva_full_align_trunc.fasta will NOT be included
>>>> in the
>>>> >>package, only HMMs built from it (and other free sources).
>>>> >>
>>>> >>I am looking forward to your response.
>>>> >>
>>>> >>Best regards
>>>> >>Sascha Steinbiss
>
Reply to: