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Bioclipse, RDF and defeasible reasoning
Well, I have yet to read the paper in detail, but my new student Samuel is going to work for 20 weeks on defeasible reasoning with DrProlog in Bioclipse.
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Open Chemical Data #1: NMRShiftDB
As I reported earlier, progress is only possible of you can modify and redistribute. This is why Open Data, Open Source, and Open Standards are so important to us Blue Obelisk members. For data, proper licensing makes these two requirements possible, but more importantly, make those rights explicit. Rich is running the nice Zusammen blog, but most of his entries are not Open Data. Even larger chemistry data repositories can be vague and have seemingly contradicting statements.
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The Art of Programming: do not leak implementation details
At the JChemPaint workshop here in Uppsala, where we have Mark from Chris’ group as our guest, we encountered an inconsistency in CDK 1.2, where the bond stereochemistry did not yet follow the pattern recently adopted of having Class fields, to allow using null to have the semantics of undefined. Previously, the defaults for native values were confounded with set values. For example, the formal charge unset and 0 would be have a field value int = 0.
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NMRShiftDB RDF #2: Some statistics
This morning I had some more fun, and since the statistics view on the NMRShiftDB server is down, I though I could recalculate the statistics myself. Because the current RDF version of the data does not include all information yet, I cannot reproduce all of them. On the other hand, I can determine some other interesting statistics.
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NMRShiftDB RDF #1: Spectra by InChI
Originally, I wanted to include a SPARQL query in my yesterdays blog showing how to retrieve NMRShiftDB spectra based on an InChIKey, but it horribly failed. I have yet to discover why. This morning I discovered that it is specific for that field, and that using the same thing with InChI is no problem:
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NMRShiftDB enters rdf.openmolecules.net #2: SPARQL end point with Virtuoso
About 6 months ago I reported about my efforts to RDF-ize the data from the NMRShiftDB. Since then, time was consumed by many other things, but now that Bioclipse can query SPARQL end points, that I want to contribute the triple set (it is GNU FDL-licensed) to Bio2RDF, that a student started working in my group (now larger than just me :) on reasoning on life sciences data, and that I recently contributed my 1000th NMR spectrum to the database, I thought it was time to finally reinstall Virtuoso.
