Re: Licensing terms for data derived from ARB/SILVA data
On 11/28/2014 04:48 PM, Frank Oliver Glöckner wrote:
> Dear Sascha Steinbiss,
> 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.
> 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.
Argghh! this will prevent from being in free section. And I suppose
those profiles are mandary for software usage ?
>
> Have a nice weekend
>
> Frank Oliver Glöckner
>
> 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
>
>
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