[Cod-bugs] "crystal structure alarm" / feature suggestion

[Saulius Gražulis]

Dear Behrnd,

thank you for your e-mail and for the feature suggestion!

Indeed, COD is updated frequently (in fact daily :), so you can use it
to get the hottest info regarding solved crystal structures.

The closest functionality of what you describe are the RSS feeds for the
deposited COD structures, to which yo can subscribe using your favourite
RSS client:

http://www.crystallography.net/cod/structures.rss

(I've noticed that we do not have a link to this feed on our front page;
we'll fix that).

As for a more detailed filtering, there are so many possibilities to
select and filter the data that we can hardly come up with the "one size
fits all" solution. What is interesting to me will be off-topic for you
and possibly vice-versa. So the idea is that on top of the *open*
database like COD anyone can (and some people do;) implement multiple
filters, serving different parts of community.

Also, please note that adding new features to COD need human work
(design, coding, testing, integration, support), and that plainly costs
money :). Since the COD web site does not generate any revenue directly,
we have limited resources to implement new functionality, and therefore
we are primarily focused on data quality and making all data available
freely (as in "free speech", not as in "free beer") ;)

Sincerely yours,
Saulius

On 2018-01-30 17:26, Behrnd Norwid wrote:
>         Dear developers and maintainers of COD,
> 
>     the other day I set an alarm in Thomson-Reuter's / Clarivate's
> literature data base /Web of Science/, i.e. periodically, the data base
> will check if an article interesting for me was cited by an other
> publication, and inform me -- even if the result shall be ``none'' (when
> the data base is not aware about a recent additional citation of this work).
> 
>     From this experience, on one side, and remembering that at least a
> considerable fraction of the data deposited in the COD may be retrieved
> by pattern comparison of Smiles which in turn may be automated, the
> thought occured to me that something similar might be implemented in the
> COD's portfolio.  There are two kind of alerts I am aware of:
> 
> + The COD user wants to stay abreast about the discovery of new
> polymorphs of organic molecules, with models already curated in the
> COD.  This may be of interest for pharmacological relevant ingredients
> since at least some of the exhibit different physicochemical /
> pharmacocinetical properties and are patented / deplyed as "polymorph A"
> rather than "polymorph B".
> 
> + To the astonishment of a COD user, there is a gap -- a crystalline
> compound was not yet characterized by diffraction analysis, or at least,
> COD is not (yet) aware of such a data set.  Beside the option to perform
> this characterization by himself / herself, s/he might be interested to
> learn /when/ this characterization was done by someone else; and
> subsequently access the original publication COD points to.
> 
>     While I do not assume, that this list of reasons for such an alert
> is exhaustive, the two perspectives are appealing enough to suggest such
> an implementation in crystallographic data bases, too.  Provided COD is
> updated much more frequently than CCDC's CSD file, /perhaps/ the
> implementation shows of benefits earlier, than at CCDC to which I wrote,
> too.  From which specialty within chemistry COD receives the most data
> per unit of time?  This likely different ratio might contribute to
> determine if such crawling across the newly curated data shall be
> performed monthly, quarterly, once a year.  On the other hand, maybe the
> task is facilitated because COD is backed by subversion; and the
> repeatitive crawling "just" has to be told to go back in history to the
> date of the last crawl per profile (in other words, commit #212121),
> instead of digesting /all/ folder and data again.
> 
>     With kind regards,
> 
> Norwid Behrnd, PhD
> 
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-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366