Samuel's Project Blog - planet bioclipse : New Google+ communities: Bioclipse, Cheminformatics, Semantic MediaWiki
After spending countless hours on Google+, I have realized how useful their new group feature is, for sharing/finding interesting stuff happening around different technologies. It's nice handling of previews of movies, images, webpages etc makes it so much easier to spot interesting stuff. IMO it works FAR better than e.g. twitter, for this.
E.g. by subscribing to groups for the topics you are interested in (I have over 50...), I get tons of interesting stuff on your Google+ home page all the time.
While Google+ groups definitely don't replace mailing lists and IRC, which are superior for discussions, it is a great complement for sharing interesting stuff happening around a technology.
With this in mind, during the last week or so, I've tried to make sure that a few of my favourite softwares and topics have groups, which resulted in a few new ones:
... so make sure to join those of these that you like, and post some interesting stuff there! :)
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. CML is flexible, which to some is a downside; to me it is a big advantage, as it allows me to easily extend it. It support ontologies to do this, and is therefore one of the most machine readable chemical formats.
Of course, a lot depends on the libraries that you are using. For reading, there are various approaches I have taken. Originally, I wrote a library (Willighagen2011) that supported the convention idea in CML, which is a pain to many. This feature is still actively used in Bioclipse and the CDK! Of course, many cheminformaticians do not care too much about explicit semantics, and the community standard is MDL molfile V2000 (someone has exact numbers?), even though the improved V3000 update is already 30 years old (see the first tweet!).
Of course, browsing through all tweets, I think the session nicely showed some of the newer requirements, many required the extensions presented in this session. These extension may have been part of the original specification (is there an overview of specification documents of all industry standards?), but in many cases these will also be conventions. E.g. a common convention used by cheminformaticians is to use the bond order type 4 in MDL V2000 molfiles to reflect aromaticity, even though the specification defines it differently.
I hope all specifications of these updates and conventions will find their way to the web, with at least the rights to redistribute, allowing independent tools to properly implement these standards. (The right of modification is debatable for standards.)
Willighagen, E. L., 2001. Processing CML conventions in java. Internet Journal of Chemistry 4, 4+.
The focus will likely be on the graphical user decision support interface, so here's what you would be able to do with scripting:
Bioclipse-OpenTox demo from Egon Willighagen
This workshop would also be great if you like to learn on how we use RDF for all of thise!
It doesn't change so often, but just has seen its 10th release. Actually, it was the first release in more than three years. But, fortunately, core chemical facts do not change often, nor much. So, this release has a number of data fixes, a few recent experimental isotope measurements, and also includes the new official names of the livermorium and flerovium elements. There is a full overview of changes.
BODR 10 is brought to you by Jean Brefort, Daniel Leidert, and I did some small bits too. Also big thanks to all project that keep using BODR and contribute by providing high quality feedback reports!
Oh, and if you use BODR isotope or element data, you are kindly invited to cite the one of the Blue Obelisk papers.
O'Boyle, N. et al. Open data, open source and open standards in chemistry: The blue obelisk five years on. Journal of Cheminformatics 3, 37+ (2011). URL http://www.jcheminf.com/content/3/1/37. Guha, R. et al. The blue obelisk - interoperability in chemical informatics. Journal of Chemical Information and Modeling 46, 991-998 (2006). URL http://dx.doi.org/10.1021/ci050400b.