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Re: Assigning DOIs to dictionaries


Greetings,

There are archival resources that are specifically tasked to manage diffraction data sets such as

https://proteindiffraction.org/, https://www.cxidb.org/, and  https://data.sbgrid.org/data/.

Before promoting the notion of storing data in Zenodo, please support these resources which

provide curation and integration with other data resources. 

John

On 6/10/20 9:11 AM, James Hester via comcifs wrote:
CAM+dB2daWP7sX3mmQWJrGbXK2FjLFHCx6o3gMDJjAEWJQKj79Q@mail.gmail.com">
Glad you approve Herbert. There is I think an attribute for the DOI in the dictionary but I didn't manage the Github - Zenodo dance as well as I could have this time and so didn't edit in the Zenodo-assigned DOI before publishing.  Hopefully we'll be able to iterate to a point where inter-dictionary references via DOIs are machine-actionable - the insistence on DOIs pointing to landing pages instead of files throws a bit of a spanner in the works.

On Wed, 10 Jun 2020 at 19:40, Herbert J. Bernstein <yayahjb@gmail.com> wrote:
Working through Zenodo make sense.  While it is not a COMCIFS issue, IUCr should also consider
formalizing use of Zenodo for posting DOIs for raw data behind journal publications, and then back to
COMCIFS --adding a uniform DOI tag category _in_ all our dictionaries for all raw data, dictionaries
and other relevant permanent links in CIF documents, so it is easy to build permanent document networks.  -- Herbert

On Mon, Apr 27, 2020 at 3:14 AM James Hester via comcifs <comcifs@iucr.org> wrote:
Dear COMCIFS,

In the past we have discussed assigning DOIs to our CIF dictionaries via the mechanism used by the IUCr for their publications. So far this discussion has not yielded much fruit.  A DOI is quite useful as it allows us to refer to other dictionaries via DOIs and URLs that are pretty much guaranteed to not become outdated and are machine-actionable.

Instead of the IUCr publication mechanism it occurred to me that we might use an outside service like Zenodo to deposit canonical dictionary versions. How this would work is as follows:

(1) A new dictionary version would be approved using the current mechanisms
(2) The dictionary would be deposited at Zenodo using a COMCIFS or IUCr official account and a DOI reserved (ie document is not yet published)
(3) This DOI would be edited into the dictionary if necessary
(4) Further technical editing would be undertaken as needed
(5) The final dictionary is published on the IUCr website and the 'Publish' button pushed on Zenodo

Ideally the 'author' for Zenodo and citation purposes would be either 'COMCIFS' or 'IUCr'. The authentication password could reside with the COMCIFS secretary(s). I have chosen Zenodo because it is not affiliated or funded by a commercial entity and I have some experience publishing there, but alternative suggestions are welcome.

The minor downsides I see with this scheme are that (1) the DOI would contain the string 'zenodo', which is sort of against the spirit of the underlying object being able to move locations (2) a data DOI such as that delivered by Zenodo points to a 'landing page', not to the object itself. The resources are instead linked from the landing page; as far as I can tell these links are predictable (DOI URL + '/files/<filename>').  I'd prefer an even simpler way to point a program at a DOI and get back the file I wanted, but I digress.

Thoughts?

James.
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M +61 (04) 0249 4148

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John Westbrook
RCSB, Protein Data Bank
Rutgers, The State University of New Jersey
Institute for Quantitative Biomedicine at Rutgers
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e-mail: john.westbrook@rcsb.org
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