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Preview: Comments on: Further Comments on the Quality of NMRShiftDB and NMR Prediction Algorithm Validation

Comments on: Further Comments on the Quality of NMRShiftDB and NMR Prediction Algorithm Validation

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By: Ryan Sasaki

Wed, 06 Jun 2007 12:46:45 +0000

Before anyone takes Robien's results about the NMR prediction comparisons AS FACT...please read my latest post about the details of the comparison. There are still some remaining questions about how Modgraph came to an average deviation of 1.40 ppm. So before we can make a final decision on performance, I think Modgraph needs to make very clear the following: 1. What is the overlap between NMRShiftDB and Modgraph’s NMR prediction databases? Further, with several different database sources how much duplication of data exists across the databases and within the entire package? 2. Once that overlap is removed from the dataset, what is the final deviation produced by NMRPredict? I think this information needs to be made very clear from Modgraph before they can claim to be, “the most accurate carbon 13 NMR predictor in an independent evaluation?”

By: Wolfgang Robien

Wed, 06 Jun 2007 08:24:46 +0000

NMRShiftDB Debate CSEARCH performs at 2.22ppm/2.19ppm before/after correction with a certain network and a certain parameter setting. ACD's CNMR-Predictor performs at 1.59 as can be seen from the table above. MODGRAPH's NMRPredict performs at 1.40ppm as can be seen from their website. That's the facts, which came out from the discussion now .... I think, it's good to know that, verified on the same dataset. I initiated this discussion, therefore I want to recall the starting point of this discussion: The central question of my webpage at was: (Statements copied from: "Is there a visible improvement when you spent a few hours on data-correction, both on a statistical basis and also with a few specific examples?" The answer was: "This small improvement - which is far away from being perfect and/or complete - without the use of one, single literature citation improves the assignment quality by ca. 6,200 ppm !" "My finding was, that spending less than an afternoon you can improve a collection of some 20,000 NMR-spectra having more than 200,000 shiftvalues by 0.03ppm or ca. 6,200ppm in total." My summary was: "That's an amazing result ! NMRShiftDB has been online for about 5 years, the 20 most important contributors are mentioned on their homepage by name and I think many other people have contributed into this project. All these people together were unable to spend less than an afternoon on data-correction within 5 years! That's exactly the point nobody seems to (be willing to) understand !" Peter Murray-Rust stated on his blog with respect to NMRShiftDB-data: "...... It contains mechanisms for assessing data quality automatically. For example software can be run that will indicate whether values are seriously in error........." My answer was: "That's really a great idea AFTER being 5 years on the web ! ....... let me know which data-correction protocol has been applied to the NMRShiftDB-data leading to deviations of about 130ppm (= 2/3 of the usual C-NMR shift range) BEFORE you put them on the web ! ......" Final remarks: Only 4 main-contributors are involved in this discussion: That's me - I have started this 'avalanche' Antony Williams and Ryan Sasaki from ACD Peter Murray-Rust from Cambridge I couldn't find any comment by NMRShiftDB people including Christoph Steinbeck. In order to improve science with a project like NMRShiftDB, the first step should be to look around what is already there ("State-of-the-art"), the second step should be to avoid the errors other people have already paid for ("Avoid starting from scratch") and the third step should be avoiding hacking the same numbers/strings into a computer ("share resources") The community needs chemical data, THEY SHOULD BE VALIDATED ACCORDING TO THE STATE-OF-THE-ART (when you cite me, please use both parts of this sentence!) - I have shown by spending a few minutes CPU-time, that the second part of this sentence was not true for NMRShiftDB as downloaded on March 10th, 2007. What's the result of this discussion: a) We know how accurate 3 programs perform on the same dataset b) There was severe error-correction performed on NMRShiftDB after my analysis Both items are valuable contributions for the scientific community. At the end a personal remark to Christoph Steinbeck: Copied from: Start citation ---- ..... We also feel that this makes a strong case for our open access, open source policy, which gave our reviewer the chance to access our full material and run this test. As Eric Raymond puts it: "Given enough eyeballs, all [...]

By: Ryan's Blog on NMR Software

Thu, 31 May 2007 18:13:41 +0000

More Dialogue on NMRShiftDB Debate Peter Murray-Rust and Tony Williams have added their two cents to this debate on their respective blogs. Peter provides a great justification on providing open access to scientific information:In the case of NMRShiftDB I am firmly of the opinion that