Tag: closed rRNA databases

Well, this is annoying. I started to look at the sharing policies for data from various ribosomal RNA databases. And boy was I surprised. One database, the RDP, run out of Michigan State University has a page with information about their policies. The page says the following:

By downloading data (“Data”) from the Ribosomal Database Project (“RDP”), you agree as follows:

Data are copyrighted by the Michigan State University Board of Trustees. 

You may use the Data for your own non-commercial research purposes, and may make derivatives from the Data for your own non-commercial research purposes. All other rights are reserved by Michigan State University. 

You may not sell the Data or any derivatives you prepare from the Data, nor may you provide the Data or derivatives you prepare to any third party for commercial purposes. 

MSU makes no warranty, express or implied, to you or to any other person or entity, including without limitation the implied warranties of merchantability or fitness for a particular purpose of the data. MSU will not be liable for special, incidental, consequential, indirect or other similar damages, even if MSU or its employees have been advised of the possibility of such damages. 

You will only distribute the Data or derivatives with copyright notices. 

If you publish from the Data, you will acknowledge the contribution of Michigan State University and the Ribosomal Database Project 

This cannot be right? Most of the data came from Genbank so certainly they cannot Copyright it. Now it may be that they are referring to sequence alignments and other derivatives of the raw data but this implies that all the data in the RDP is Copyrighted.

Mind you, I do not like the policy even if it is just for the derivatives of the data (e.g., alignments) since this will certainly make some things very difficult in terms of publishing.  For example, if I use an alignment from RDP, how do I provide the alignment when I publish a paper? If I provide it, do I only provide it to non commercial entities? Does that mean, in essence, commercial entities would not be allowed to see alignment figures?

I get that people do not want people to download and then redisplay all of their content, thereby in essence possibly killing the original database.  But Copyrighting all the data in the database?  Even data that is not theirs?  Is this just a scare tactic of some sort?  A mistake? I cannot tell.  There must be better ways to prevent someone from redisplaying the entire database structure and content without such severe tactics. 

So – is this an issue just with RDP? Turns out – no. The SILVA database in Europe has some restrictions too:

Though thankfully they do not seem to be trying to Copyright or reserve rights for other people’s data. They simply refer to downloads from their database and what one can do with such downloads. They never say they own in any way the data itself.

Fortunately greengenes seems to have no restrictions on the use of data or anything downloaded from there.  Though I am still looking into this.

I think it is time for rRNA researchers to think carefully about using data/alignments/etc from databases like Silva and RDP.  If one uses an alignment from one of these databases it is possible one would be violating the DB policies if one released the alignment as part of a paper.  Yet, if one uses the alignment in the paper, one should release it.  So seems better to seek out and used fully open datasets and alignments and other results.

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Below are some discussions relating to some tweets I posted about this issue yesterday: