APIs seem to be very popular with scientific data in the modern realm of science. If I wanted to provide a service within an electronic lab notebook where chemicals that were logged in entries had multiple attached identifier types would it be better to use an online web API for conversion as described in the module or install a back end service like open babel?
This would most likely be in the form of the user providing an identifier in one form and the server retrieving or generating the other forms.
How would one convert from boiling point to any of the other information? Is there an API that allows one to get a list of molecules with a specified BP?
Alex,
the JCAMP-DX standard was originally intended for X,Y data where the x values were all the same distance apart and so the compression into the various "flavours" SQZ, DIF, DIFDUP then came about to end up with text files that were about the same size as a ZIP but were not binary and so could move across early data networks without loss of integrity.
Many Mass Spec files were in the form of Tables where only a relatively small number of intensities were reported often less than 20 peaks. These can not be readily converted to equally spaced XY pairs so compression was not used.
I'm not sure what type of Mass Spec file you are opening but you should be able to check if it is a PEAK TABLE type file or an XYDATA type file with a simple text editor like Notepad etc.
The Peak Table type will be just a set of X,Y pairs but with a number across a line separated by tab or space.
Pretty easy to move to a spreadsheet for plotting etc.
If the file does contain XYDATA and you are unable to convert to XY then that would seem to be a bug.
Why is JSpecView unable to export the data from a Mass Spec into XY formats? I would have thought that the data would have just been arranged in a X:Mass/Charge Y:Intensity format.
Why do some of these web services require tokens? Do they use them in a way to stem from mass downloading of chemical data, or is it simply just a foresight on bandwidth usage?
I am interested in using the Cactus API to pull SMILES from a given molecule name, what would be the best approach to do this in a java environment? I have used XML parsing for other portions of my project, but I am not entirely sure the same thing would work in an HTML document to grab the name.
When I click the link gChem-CDK,
<a href="https://docs.google.com/spreadsheets/d/1YqDxTF2B2D-jlevY1NVcFdP5-UoHAISHKcI1tIRyPcU&newcopy=true">https://docs.google.com/spreadsheets/d/1YqDxTF2B2D-jlevY1NVcFdP5-UoHAISHKcI1tIRyPcU&newcopy=true</a>
It says "Google Drive, page not found". Is the link correct?
Thanks,
When plotting the HNMR data, excel seems to be multiplying the data by a thousand once put into the graph. So instead of integrating for 5 hydrogens, its reads 5000. So is the case for the chemical shift.
What type of graph within excell 2013 should I use for plotting the mass spectra data? The clustered collum graph fails when adding additional data sets.
Kourtnei,
need more details. You say you downloaded the spectra in JCAMP-DX format and could view them. What did you use to view them?
When you exported them what filename extension did you give? It probably needs to be .JDX and if you are using Windows with the default setting whereby the extension is hidden then you may have a file called xylene.jdx.txt or some variation of this and the JSpecView viewer is ignoring it.
If you are using Linux or Windows there is a JAVA standalone application that you can download to run and display files. It is available from Sourceforge http://sourceforge.net/p/jspecview/svn/HEAD/tree/dev2/JSpecView/build/JS...
I tried p-xylene and downloaded the file and then dropped it onto a page with JSV running and it opened without issue
Best way to provide multiple identifiers?
Activity 2 Question
JCAMP-DX files
Alex,
the JCAMP-DX standard was originally intended for X,Y data where the x values were all the same distance apart and so the compression into the various "flavours" SQZ, DIF, DIFDUP then came about to end up with text files that were about the same size as a ZIP but were not binary and so could move across early data networks without loss of integrity.
Many Mass Spec files were in the form of Tables where only a relatively small number of intensities were reported often less than 20 peaks. These can not be readily converted to equally spaced XY pairs so compression was not used.
I'm not sure what type of Mass Spec file you are opening but you should be able to check if it is a PEAK TABLE type file or an XYDATA type file with a simple text editor like Notepad etc.
The Peak Table type will be just a set of X,Y pairs but with a number across a line separated by tab or space.
Pretty easy to move to a spreadsheet for plotting etc.
If the file does contain XYDATA and you are unable to convert to XY then that would seem to be a bug.
Robert
Mass Spec Data
Confirmed
API Tokens
Pulling data from Cactus
gChem-CDK and finger prints
Graphing questions
NMR spectra
Kourtnei,
need more details. You say you downloaded the spectra in JCAMP-DX format and could view them. What did you use to view them?
When you exported them what filename extension did you give? It probably needs to be .JDX and if you are using Windows with the default setting whereby the extension is hidden then you may have a file called xylene.jdx.txt or some variation of this and the JSpecView viewer is ignoring it.
If you are using Linux or Windows there is a JAVA standalone application that you can download to run and display files. It is available from Sourceforge
http://sourceforge.net/p/jspecview/svn/HEAD/tree/dev2/JSpecView/build/JS...
I tried p-xylene and downloaded the file and then dropped it onto a page with JSV running and it opened without issue
Robert