chem-bla-ics: September 2013

Urgent Open Science needs for Drug Discovery: pKa and logP

There is quite some discussion right now on Open Source Drug Discovery, and questions about what is Open Source and what is not. But as I made clear yesterday, I do not think that a project that requires the assigbment of specific rights independent from Open licenses is not the way forward, and in many cases not even possible. In my humble opinion, an #openscience approach is critical. Hiding data pending a (open) patent does not work for me; I'm sorry. Not that I am against patents in general (primarily, the patent system is broken and misused, but the idea has merits)...

Instead, I very much prefer to focus on solutions. Like the CDK, Bioclipse, BODR, CML, and many other Blue Obelisk tools.

Sep

Why do databases make sharing Open Data difficult?

I tend to feel quite isolated in these matters, but they matter to me: licenses, agreements, etc. Because I try to be a friendly guy and respect the wishes expressed by others.

However, this puts me in a situation where I cannot join many otherwise interesting initiatives. There are many examples, but I will isolate one, for no particular reason other than that they just published an interesting paper about DMSO solubility modeling (doi:10.1021/ci400213d): the Online Chemical Database.

Sep

Changes in CDK 1.6 #1: some removed classes

Because John is doing great work in shaping up CDK master, we're heading towards a new stable release. Time to start writing up all the API changes.

Removal of the nonotify interface implementation

The NoNotificationChemObjectBuilder and the matching implementation classes are removed. Please use the SilentChemObjectBuilder instead.

Removal of IMolecule and IMoleculeSet

The IMolecule interface and all implementing classes have been removed.

Sep

First WD of "Encoding units and unit types in RDF using QUDT"

While the editors draft has been online for a while, I have added some more Unit Ontology - QUDT mappings and updated the matching jQUDT library, and now put the first Working Draft (WD) version online on the Open PHACTS specifications website, ready to accept comments (it's primarily informative, rather than normative):

A big thanks to Ralph Hodgson and the other QUDT authors for developing this ontology and in particularly to have it include a framework and the needed information to interconv

Sep

Why I still prefer CML (was: #ACSIndy formats session)

At the #ACSIndy meeting there was a session one chemical formats (I hope the slides will all come online). Some key tweets (thanx to Tony for the coverage):

But I am still fan of the Chemical Markup Language. In fact, I started using this when XML was not even standardized yet. Even CML has a SGML background. Well, fairly, only months before XML made it into a recommendation, and CML followed.

Sep

Next Bioclipse-OpenTox Workshop gig: Mainz, September 30

Ola and I will be giving a Bioclipse-OpenTox workshop in Mainz on Monday 30 September, during the OpenTox EU 2013 meeting. Places are filling up quickly (really :), so sign up now if you like to learn your way around in interactively accessing chemical liabilities.