AutomationInterfaces

nmrshiftdb2 has a number of interfaces which can be used for automation purposes. They are listed here. Note that if possible they should be called using the www.nmrshiftdb.org URL in order to have a stable URL (the "real" URL might change, not constantly, but perhaps in 5 or 20 years). This is possible in all cases where www.nmrshiftdb.org is used on this page (technically, the redirection does not keep query parameters in the URL, so anything needing them must go via the real URL).

These are possibilities to get data for automatic processing, typically in CML format:

• The most flexible approach is using the REST interface https://nmrshiftdb.nmr.uni-koeln.de/api-docs/#/. The old web service interface at https://www.nmrshiftdb.org/axis/NMRShiftDB.wsdl is being retired.

Some other services available follow. They are partly in the REST api as well. Generally, these were written before REST became popular as direct calls to URLs:

• You can get a structure and all its spectra (if it is in nmrshiftdb2) via an InChI like this: https://www.nmrshiftdb.org/NmrshiftdbServlet/nmrshiftdbaction/exportcmlbyinchi/inchi/InChI%253D1%252FC6H6%252Fc1-2-4-6-5-3-1%252Fh1-6H/spectrumtype/13C Alternatively, JCAMP-DX is possible as format, just append /format/jcamp at the end (the action name xportcmlbyinchi stays, even if it is a bit wrong). Note there is a fallback, if no structure is found with this InChI and the InChI contains a stereo layer, the search is done without the stereo information.
• You can get a spectrum for a structure with a link like this https://www.nmrshiftdb.org/NmrshiftdbServlet/nmrshiftdbaction/searchorpredict/smiles/CCCC/spectrumtype/13C (CML format) or https://www.nmrshiftdb.org/NmrshiftdbServlet/nmrshiftdbaction/searchorpredict/smiles/CCCC/spectrumtype/13C/format/jcamp (jcamp format). This gives a measured spectrum if it exists and a predicted if not (measured have an nmrshiftdb2 ids, predicted not), so you will always get a result. In case of a prediction, the CML contains a lot of additional data in peaks. These are as follows:
  • XValue: The prediction (actually the mean of the matching shifts)
  • XMin: The minimum of the matching shifts
  • XMax: The maximum of the matching shifts
  • XWidth: The median of the matching shifts
  • YMin: Number of HOSE code spheres used for prediction
  • YMax: Number of matching shifts
• An rss feed of the latest structures is available at https://www.nmrshiftdb.org/NmrshiftdbServlet/nmrshiftdbaction/rss/numbertoexport/4 (numbertoexpot is optional, default is 10). A personalized feed as available at https://www.nmrshiftdb.org/NmrshiftdbServlet/nmrshiftdbaction/rssmine/numbertoexport/4/user/XXX - the username is the login name. https://www.nmrshiftdb.org/NmrshiftdbServlet/nmrshiftdbaction/exportlastinputs/numbertoexport/4/username/XXX gives the latest submits of a user as images.
• https://www.nmrshiftdb.org/NmrshiftdbServlet/nmrshiftdbaction/assignspectrum/cml/XXX does an assignment. In XXX there must be a cml document with a <cml> root element as described in the NMRShiftDB CML convention. The peaks in the spectrum will get atomrefs for the most likely assignment according to the nmrshiftdb2 prediction.
• From http://nmrshiftdb2.svn.sourceforge.net/viewvc/nmrshiftdb2/trunk/snapshots/ you can downlaod a stand-alone prediction tool (preditorc.jar for carbon shifts, predictorh.jar for hydrogen shifts). See [PredictorJars] for details.
• The quickcheck can be used with a POST request like this:

curl --header "Content-Type: application/json" --request POST --data '{"inputs":[{"id":1,"type":"nmr;13C;1d","shifts":"117;123;103","solvent":"Chloroform-D1 (CDCl3)"},{"id":2,"type":"ms","shifts":"1;2;3"},{"id":3,"type":"nmr;hsqc;2d","shifts":"7.11,117; 7.32,123; 6.46,103 ","solvent":"Chloroform-D1 (CDCl3)"}],"moltxt":"62-53-3\n\n\n  7  7  0  0  0  0  0  0  0  0999 V2000\n   -0.1116    1.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8260    0.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.8260    0.1454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1116   -0.2670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.6028    0.1454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.6028    0.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1116   -1.0920    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  1  1  0  0  0  0\n  4  7  1  0  0  0  0\nM  END"}'  https://nmrshiftdb.nmr.uni-koeln.de/NmrshiftdbServlet/nmrshiftdbaction/quickcheck

The following links go directly to certain pages in the web application and can be used to link to nmrshiftdb2:

• Each record is accessible by its molecule id like this: https://www.nmrshiftdb.org/portal/js_pane/P-Results/nmrshiftdbaction/showDetailsFromHome/molNumber/XXXXXXX. Alternatively, https://www.nmrshiftdb.org/molecule/XXXXXX can be used (nicer link, this does a redirect)
• You can also link to an atom by https://www.nmrshiftdb.org/atom/XXXXXX - the atom ids are mostly internal, but may be published e. g. in more technical papers, these links can then be used to look them up.
• You can link to a prediction page for any structure like this: https://www.nmrshiftdb.org/portal/js_pane/P-Predict/nmrshiftdbaction/predict/smiles/XXXXX/spectrumType/1/applet/applet For spectrumType, the key is like this: 1=13C,2=1H,3=15N,4=31P,5=19F,6=11B,7=29Si,8=17O,9=73Ge,10=195Pt,1=33S
• You can link to a spectrum by id with a a link like this: https://www.nmrshiftdb.org/portal/js_pane/P-Results/eventSubmit_doGeneralsearch/eventSubmit_doGeneralsearch/searchfield/spectrum+id/searchaction/exact/searchstring/20197084#spectrum20197084 The #spectrumId at the end just just to the particular spectrum on the page, since all spectra of the molecule are displayed. If you know the molecule id the specrum is in, you can also use https://www.nmrshiftdb.org/portal/js_pane/P-Results/nmrshiftdbaction/showDetailsFromHome/molNumber/7901#spectrum20197084 (nicer link). Alternatively, https://www.nmrshiftdb.org/spectrum/20197084 can be used (nicest link, does a redirect, only spectrum id needed, same as https://www.nmrshiftdb.org/portal/js_pane/P-Results/nmrshiftdbaction/generalsearch/searchfield/spectrum+id/searchaction/exact/searchstring/20197084#spectrum20197084).
• You can linke directly to a search for all spectra with a certain keyword with a link like nmrshiftdb.nmr.uni-koeln.de/collection/ChiuZ, again using www.nmrshiftdb.org/collection/ChiuZ is better and redirects.
• nmrshiftdb.nmr.uni-koeln.de/collections/ChiuZ|NIC searches for several spectra keywords, again https://www.nmrshiftdb.org/collections/ChiuZ|NIC is possible.