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April 05, 2011

Dryad and DSpace

It seems everyone has their own data management solution these days. Dryad is an example of a larger system designed to serve as data repository for data from peer-reviewed articles. It is built on an open source platform called DSpace. Sure would be nice if they had a sandbox available.





Sure, there's the DSpace demo site.

See below the fold for more of my IRC chat.

< kbk1> Hi there. Is DSpace completely custom code or is it built on top of existing code? I just watched a preview video and the theme of the demo site recalled wordpress.
< kbk1> From what I am seeing so far, it looks as if it is built from the ground-up.
< tdonohue> Hi kbk1. DSpace is completely custom code. It was initially built by MIT and Hewlett Packard back in 2002, and since then was open sourced and is community maintained code.
< td> (so, it actually pre-dates WordPress, by about a year, I believe)
< kbk1> I don't suppose there is a sandbox available? I've worked with a few field stations to build an information management system on Drupal and am curious about what other solutions look like.
< td> There is a sandbox/demo site. It's at http://demo.dspace.org
< kompewter> [ DSpace 1.7.0 Demonstration Repository ] - http://demo.dspace.org
< kbk1> Awesome!
< td> From there, you'd want to visit *either* the XMLUI (XML-based UI) or JSPUI (JSP-based UI). Those are the two offered UIs for DSpace.
< td> If you visit one of those UIs, there are actual sample logins provided on the homepage (e.g. read the intro text of the XMLUI, which provides you with sample logins to the demo system: http://demo.dspace.org/xmlui )
< kompewter> [ Community List ] - http://demo.dspace.org/xmlui
< kbk1> I will take a look. I found out about DSpace while reading a paper which mentioned Dryad - which is built on DSpace. Dryad claims the ability to assign DOI's to datasets. Is this functionality within DSpace?
< td> kbk1: DSpace does not specifically assign DOIs by default. But, it will assign Handles (http://handle.net/), which are a part of the DOI system -- see: http://en.wikipedia.org/wiki/Digital_object_identifier
< kompewter> [ Digital object identifier - Wikipedia, the free encyclopedia ] - http://en.wikipedia.org/wiki/Digital_object_identifier
< td> PeterDietz -- That's fine. A GSoC project need not cover all UIs, to be honest. It could be specific to one UI. As of 1.7, we no longer have complete "UI parity", so it doesn't matter if we scoped around XMLUI (as long as the project didn't do anything that would "break" another UI)
< td> PeterDietz -- that being said, if we still had concerns about the project, or no interested mentors, we could 'pull' the project and suggest the student look at other GSoC projects.
< td> kbk1: also if you have specific questions about the Dryad project, one of it's repository programmers, ks, is currently "lurking" in this chat channel. So you might want to ask him, if he's got time.
< ksclarke> yep, I'm around
< ks> DOI assignment takes place through a module Dryad has developed and we're working to make it work within the identity services module atmire is developing (maybe moving our code into that, eventually, if it sees uptake in the dspace community)
< ks> our DOIs have a particular form (meaning embedded in them, unfortunately (imo), related to our modeling of data packages and data files) so are not completely generic like a regular dspace module should be
< kbk1> Thanks ks. If I could add one feature to our IMS it would be DOI assignment. I think it would really encourage researcher buy-in.
< kbk1> I like the workflow for item submission on the demo site.
< ks> I did notice recently that the ezid service (that CDL provides and that we use to register) allows minting now in addition to registering... it might not be much work to build something over that for data-centric DOI registration
< ks> yes, we chose DOIs over other schemes because we though the buy-in would be more significant for that reason
< ks> we thought
< kbk1> Did you think correctly?
< ks> we are seeing uptake in our submissions; we're also working with journals though who are now requiring deposition in a data repository like dryad -- so we can't (I don't think) tease apart what's contributing to our growth
< ks> and I'm not front lines (interacting with folks) so I don't have much ancedotal evidence
< ks> I could ask our curator though so see if she's had feedback about the assignment of DOIs
< ks> I know our workflow passes the DOI back to the submittor so that it can be included in their article
< ks> so we're definitely presenting it as a selling point ("here is your DOI for your data package so people can reference you")
< kbk1> Right, the paper by Vision (BioScience 2010) was the only one I've found thus far that explicitly advocated a DOI for datasets. I work with a lot graduate students and would like to tell them to add Contributed Datasets to their CV's.
< ks> Yeah, that would be great! My believe is having a DOI will do more to encourage that... I'll ask our curator
< ks> my belief
< ks> arg, can't type today
< kbk1> But I can't tell them to do that if it is not a more widely applied practice.
< ks> Yes, I understand... we're definitely hoping to encourage people in that direction but it's not a widely applied practice yet
< kbk1> Either way, if we do move in this direction it may be helpful to talk with someone who has been there. Is IRC your preferred forum?
< ks> IRC works for me but I'll only be with the project for about another month (moving on to something else); you could join the Dryad mailing list... it's low volume and questions, etc. are welcome there: https://lists.nescent.org/mailman/listinfo/wg-digitaldata
< kompewter> [ Wg-digitaldata Info Page ] - https://lists.nescent.org/mailman/listinfo/wg-digitaldata
< ks> I believe that's the open list
< kbk1> Thanks. I just joined. If you are interested, here is the Drupal-based IMS I have built: http://umbs.lsa.umich.edu/research/
< kompewter> [ University of Michigan Biological Station ] - http://umbs.lsa.umich.edu/research/
< ks> there is also a dryad-dev list that's intended to be for dev-focused discussion: http://groups.google.com/group/dryad-dev?pli=1 (also low volume... though we're trying to use it more)
< kompewter> [ dryad-dev | Google Groups ] - http://groups.google.com/group/dryad-dev?pli=1
* ks goes to take a look
< ks> nice, my last place of work was moving towards drupal
< ks> this looks like a nice example of what can be done with it
< ks> btw, just had a colleague tell me the dryad-dev list is intended to be the open public list for discussions, etc.
< kbk1> So favor that over the nescent list?
< ks> yes, I guess so
< ks> I'm surprised you were able to join if the other is not intended to be open but perhaps they were hoping for security through obscurity
< ks> which I've now foiled
< kbk1> Oops. Let the spamming commence.
< kbk1> I'm off to lunch but I appreciate the chance to chat. Looks like you guys are up to good.

Posted by kkwaiser at April 5, 2011 10:47 AM

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