I have found an article about "Open Data in Science" written by Peter Murray-Rust (Article can be downloaded from http://www.dspace.cam.ac.uk/handle/1810/194890 ), where 'OSCAR-3' (a tool for extracting data from the chemical literature) in the context of C-NMR spectroscopy has been mentioned.
I am now surprised, that the NMRShiftDB-collection ( http://nmrshiftdb.org/ ) increased only by 8 structures within 7 weeks ( from Nov 18th, 2007 to Jan 6th, 2008 ), when OSCAR-3 is around, which allows automatic extraction of NMR-data from articles ?! For legal reasons only the automatic extraction of data from OA-journals seems to be possible, which reduces the number of available data. Therefore I simply want to see ONE, SINGLE FULLY ASSIGNED C-NMR spectrum. which has been AUTOMATICALLY EXTRACTED by OSCAR-3 from the chemical literature.
A corresponding question has been deposited at Peter Murray-Rust's Weblog - I hope to get an answer. Check back, I'll keep you up-to-date.
My questions can be found on
http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=916#comments
Just for your comparison:
The increase of spectra within CSEARCH can be found here - without OSCAR-3 support ;-))
Showing posts with label data. Show all posts
Showing posts with label data. Show all posts
Sunday, January 6, 2008
CSEARCH Data and InChIKeys
InChIKeys are an excellent tool for identical structure searches on the web using the usual search-engines like google, yahoo, msn, etc. The architecture of the InChIKeys allows searching for two-dimensional topologies when using only the first 14 characters, whereas using the full InChIKey allows the inclusion of all additional features like stereochemistry.
Within the CSEARCH-environment all structures have been converted into InChIKeys and together with my data-exchange protocols dating back into the late '80s a collection of links has been built. Each page summarizes for a specific two-dimensional molecular topology all systems, where the corresponding C13/O17/N15/F19/P31/B11/Si29-spectrum is available.
The following systems have indexed:
CSEARCH including upcoming data
SPECINFO
CHEMGATE
NMRPredict
NMRPredict ONLINE
KnowItAll
KnowItAll Anywhere
NMRShiftDB
University of Mainz, In-house database
A total number of nearly half a million spectra from approx. 350,000 different structures has been indexed in a systematic way. The pages have already been crawled by the most important search engines.
How to make use of this 'portal of existing NMR-spectral information' ?
Generate the InchiKey for your query structure, e.g. this is "ABCDEFGHIJKLMN-ABCDEFGHIJ"; now take the first 14 characters (before the hyphen!) and construct the follwoing URL:
http://nmrpredict.orc.univie.ac.at/inchikey/ABCDEFGHIJKLMN.html
Request the corresponding page; in case this particular 'structure family' (=two-dimensional molecular topology) has C/O/N/F/P/B/Si NMR-data available in one of the above listed systems, you will get a list of links to them. In case there is no NMR-spectral information available, your http-request will be answered by a 'Page not found (404)' - error.
Within the CSEARCH-environment all structures have been converted into InChIKeys and together with my data-exchange protocols dating back into the late '80s a collection of links has been built. Each page summarizes for a specific two-dimensional molecular topology all systems, where the corresponding C13/O17/N15/F19/P31/B11/Si29-spectrum is available.
The following systems have indexed:
CSEARCH including upcoming data
SPECINFO
CHEMGATE
NMRPredict
NMRPredict ONLINE
KnowItAll
KnowItAll Anywhere
NMRShiftDB
University of Mainz, In-house database
A total number of nearly half a million spectra from approx. 350,000 different structures has been indexed in a systematic way. The pages have already been crawled by the most important search engines.
How to make use of this 'portal of existing NMR-spectral information' ?
Generate the InchiKey for your query structure, e.g. this is "ABCDEFGHIJKLMN-ABCDEFGHIJ"; now take the first 14 characters (before the hyphen!) and construct the follwoing URL:
http://nmrpredict.orc.univie.ac.at/inchikey/ABCDEFGHIJKLMN.html
Request the corresponding page; in case this particular 'structure family' (=two-dimensional molecular topology) has C/O/N/F/P/B/Si NMR-data available in one of the above listed systems, you will get a list of links to them. In case there is no NMR-spectral information available, your http-request will be answered by a 'Page not found (404)' - error.
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