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ChEMBL 09 as RDF
Update 2021-02: this post is still the second-most read post in my blog. Welcome! Some updates: -
"Fill in the #Wikipedia Survey and Help Our Community"
Fulfilling a request by Daniel, following Antony’s title, and adding a random link to a Wikipedia molecule just to see it show up in Chemical blogspace now that I fixed the InChI detection, I hereby invite every scientist to fill out this questionnaire, surveying how scientists use and do not use Wikipedia to spread knowledge. -
Bioclipse upgraded to CDK 1.3.8 and CDK-JChemPaint 17: builds broken
Yesterday I did some boring plumbing: I upgraded our GC/MS machines with new hardware. Well, the cheminformatics equivalent of it anyway. I upgraded the Bioclipse bundles in org.openscience.cdk for CDK 1.3.8 and CDK-JChemPaint 17. This is typically a painful process, and now even more because a lot is changing with how Bioclipse is build, which is with Buckminster on Bioclipse’ Hudson server. I am happy that Arvid is doing the digging into Buckminster, as automatic building of Eclipse-RCP tools is straightforward. Each part is describes by, seemingly, at least five configurations files. For each plugin we have plugin dependencies, plugins are wrapped into features, where you can get dependencies wrong too, and update sites, which need to be in shape too. And on the Buckminster-side there are .rmap and .cquery files pointing to the right git repositories, each of which you can get wrong too. -
Chemical data curation: yes, it is that bad.
The readers of Antony’s blog know enough about the problem. And many in the QSAR community know it too (and many other do not). Chemical structure data is noisy. I haven’t recently created a new local data set for analysis, so I have not taken time to blog about it much, but the ambiguity in chemical databases is enormous. Just yesterday, Antony and I had a good discussion about tautomers and in particular how things are linked together.
