We would like to include NMR spectra in a chemical database. Is this possible with instantjchem?
No, IJC does not currently support this, but we do hope to support various types of analytical data in the longer term. (e.g LCMS, NMR, IR...).
The key issues are which formats to support - there are lots of instrument vendors and lots of formats. Please suggest any particular ones that you would like to be supported.
We use Bruker and Varian instruments but we could convert to a common format such as JCAMP-DX. I was thinking of 1D spectra at this stage but we would also have use for storing 2D spectra.
Do you have an idea how long 'longer term' might be?
We currently don't have this on the development plans, so it probably wouldn't hapen until 2008.
That said however, the development plans are defined by user demand, so if this was a common request then we would likely try to do it sooner. So far this is the first request for this feature, but I suspect it might have a wider demand.
Would you expect the NMR data to reside in the IJC database (in which case some mechanism is needed for importing this data), or, for instance, as files that were accessible (e.g. via HTTP) based on an ID or the name of the file (which would probably be simpler to implement and would be more generic)?
I'm not sure of the merits of each approach at this stage. This is a new project so I don't have experience in this area. I can see that including (particularly 2D) spectral data within the database might generate large databases very quickly.
If IJC does not handle spectral data directly, is there a mechanism to pass data contained within the database to a 3rd party program? In other words, can I store say 1D spectra within the database and pass the files to a display package?
Yes, storing the spectra in the database is probably not the best option as it would be inflexible, the DB would rapidly grow in size, and you need to deal with importing all the spectra into the DB in the first place.
I think the best appoach is to make the files available to IJC from a web server and add the information about each spectra's location to the IJC DB by either using a naming convention for the files based on the compound's ID (or any other field associated with the compound).
That way IJC would be able to generate the spectra's location based on the ID and could then display it.
As for methods for displaying the spectra, we could fairly easily launch an external application to view the data (just as IJC can launch a web browser).
A better approach would be to integrate a spectral viewer into IJC so that they can be displayed within an IJC form. See http://jspecview.sourceforge.net/
for an obvious candiate to use for viewing JCAM-DX format data.
The new IJC forms view opens up a huge number of new opportunities like this. We should have a preview of this around then end of this month. Providing custom viewers for data like this is just one such possibility.