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Validating MDL SD files and Symyx molfiles with the CDK
Bioclipse 2.0 introduced a new, powerful molecular table support, and we have been eager to test that on large SD files. A recent ChEBI SD file failed to open, and eyes were immediately at the CDK, which is the cheminformatics library used in Bioclipse.
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CDK 1.2.5: the changes
Mostly license statement fixes (thanx to Andrew for caring about it!), and a bug fix in the
UniversalIsomorphismTester: -
Semantic Web features in Bioclipse 2.2
Ola is releasing Bioclipse 2.2.0 today, and asked me to show case the semantic web functionality in Bioclipse. I realized that I do not have a nice page showing the semantic web overview. But I did blog a lot about RDF functionality, so here’s a list of pointers:
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Semantic Chemistry with the Resource Description Framework
First Call for Papers
Semantic Chemistry with the Resource Description Framework
240th ACS National Meeting & Exposition
Boston, Massachusetts, August 22-26, 2010
CINF Division -
Extracting RDF from Chem4Word documents
Joe has released the first Chem4Word demo file, and has written about how to extract the CML with Java and with C#.