Comments on: A Digital chemical repository – is it being used?

By: Digital repositories. An update. « Henry Rzepa

Digital repositories. An update. « Henry Rzepa — Sat, 21 Jul 2012 17:25:15 +0000

[...] blogged about this two years ago and thought a brief update might be in order now. To support the discussions here, I often perform [...]

By: Henry Rzepa

Henry Rzepa — Wed, 05 May 2010 09:41:39 +0000

Picking up on another phrase you used Tobias: “having a HANDLE or DOI number for each experimental set or spectrum as an eternal and citable entity is really cool“

This leads to the question of how eternal any individual instance of a DSpace server actually is. Our server was, and still is, real tin. We will however be virtualizing it over the summer so that it does not depend on a specific server box for its function. But taking the eternity metaphor one step further, I have just tried to archive an individual entry from our digital repository into WebCite. This provided the following (hopefully a bit more eternal) link: http://www.webcitation.org/5pUnKxCOM. The individual files in the repository all work! I dont know if it would be acceptable to automatically archive each entry in our DSpace using Webcite though. But this does look promising!

By: Henry Rzepa

Henry Rzepa — Wed, 05 May 2010 09:29:54 +0000

It proved a challenge to find information on how to control a (Google) search. Thus this page is a useful summary of the syntax, but its a trial to find it. There is also this site which is rather more generic and this page provides the best summary of the syntax, including discussion of stemming, Boolean operators, etc. One that was of interest to me was the field filetype: which might allow searches for files of specific content, ie filetype:cml.

By: Henry Rzepa

Henry Rzepa — Wed, 05 May 2010 09:16:17 +0000

Hi Tobias, If one tries a Google search with the string site:spectradspace.lib.imperial.ac.uk the first 50 or so hits are all to entries in the repository. Google uses these field qualifiers internally, but they are rather poorly documented (a few minutes search did not reveal the complete list, another is for example author:name). Last time I checked, there were several thousand DSpace servers out there (but not many in chemistry!). Quite why they are so difficult to find is a mystery.

By: Tobias Kind

Tobias Kind — Wed, 05 May 2010 08:04:09 +0000

Hi Henry,
interesting access statistics, but I usually don’t trust those URLs
with port numbers, for fear they are like the GeoCities of the internets:
soon to be extinct. (I have to disclose we offer similar bad URLs).

https://spectradspace.lib.imperial.ac.uk:8443/dspace/

spectradspace.lib.ic.ac.uk:8443 uses an invalid security certificate.
The certificate is only valid for spectradspace.lib.imperial.ac.uk
(Error code: ssl_error_bad_cert_domain)

Now to your question, is it being used??
I knew the concept and I cited the paper in our publication
“How large is the metabolome? A critical analysis of data exchange practices in chemistry”
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673031/

The funny part is, I did not know that the website
https://spectradspace.lib.imperial.ac.uk:8443/dspace/
exists and that is actually functional, because it could be nowhere found.
IF you do a Google Search for the URL it returns:
Results 1 – 7 of 7 for “spectradspace.lib.imperial.ac.uk:8443. (0.23 seconds)

I agree having a HANDLE or DOI number for each experimental set or spectrum as an eternal
and citable entity is really cool.

I *love* the idea of having access to Gaussian log files, spectra results etc,
because it preserves our earth, I am not kidding, by preventing the 1000ths
recalculation of the lowest energy conformer of methane with MP2, B3LYP and others.
It simply saves CPU cycles.

So I guess its not only about making a nice case, but really about advertisement and
promotion and making the hopefully new URL known to many researchers (if thats intended).
Maybe a cloud-like approach can be built with such a setup, because Amazon offers free
storage for open data sets. Well what happens when Amazon does not exist anymore?

How about spectra.imperial.ac.uk or spectra.ic.ac.uk?

Cheers
Tobias

PS: not sure about the funny bold and normal font settings in my post
I didn’t do it…