This blog chronicles the research of the UsefulChem project in the Bradley lab at Drexel University. The main project currently involves the synthesis of novel anti-malarial compounds. The work is done under Open Notebook Science conditions with the actual detailed lab notebook located at usefulchem.wikispaces.com. More general comments posted here relate to Open Science, especially when associated with chemistry.
Tuesday, October 20, 2009
Fourth Cheminfo Retrieval class: ChemSpider and Beilstein Databases
Peggy Dominy, our chemistry librarian at Drexel, was kind enough to teach my third class while I was at NERM. She demonstrated RefWorks - including how to copy and paste the proper formats to Wikispaces - and how to use our ILL (Inter-Library Loan) process.
I'm including a recording of the fourth class on Chemical Information Retrieval on Oct 15, 2009 at Drexel University. It starts with some tips on removing formatting from Wikispaces pages, the Drexel Cisco VPN client for accessing paid subscriptions off campus and how to link to a DOI. The first two assignments for the class are then described. The first involves summarizing each paragraph of an article and an option to use AcaWiki is demonstrated. The second involves filling in an FAQ for publishing in chemistry. FriendFeed is then presented as a resource to help answer questions followed by an extensive overview of available information on ChemSpider, covering SMILES, InChIs, InChIKeys, experimental and predicted properties, linked databases and contributed spectra. Finally a demonstration of Beilstein Crossfire/DiscoveryGate is presented with an emphasis on doing substructure searching.
I gave my first lecture yesterday (Sept 24, 2009) for my Chemical Information Retrieval course at Drexel. One of my main objectives for the course is to provide the most current information about how to best find and review chemical information.
To this end, I set up a wiki (http://getcheminfo.wikispaces.com) which should become considerably enriched over the course of the term. I invited students to help contribute useful links to the resource page - and even before I finished giving the first lecture they added several really good ones. I also invite any chemists or librarians to add links to resources we may have missed. Just request to join the wiki to contribute.
The wiki will also be used for students to write a report on a chemical topic making use of cheminfo resources. Right after the lecture I made sure the students joined the wiki and created two pages: one for their report and one for a "research log". The idea is that students will report significant steps in conceptualizing their projects and how they are searching databases. I can then comment directly on their log pages for quick guidance. I suppose anyone with helpful suggestions that I missed could also comment - again just request an account on the wiki.
This class has traditionally required a written report. This term I'm adding a twist: the minimum number of words can be reduced somewhat if students elect to incorporate a multimedia or other creative component. To provide examples of what that might look like I visited Drexel Island on Second Life and demonstrated 3D molecules, interactive NMR spectra and a chemistry museum (from Sandy Adam). There is a lot of chemistry possible on Second Life (see Lang & Bradley) At the end of the tour on the island we visited a wildlife area recently built by Robert Brulle for a project related to environmental science (more on this in a later post). I got a hug from a panda and got sprayed when I tried to pet a skunk - just to give a taste of what kind of fun things can be constructed in a virtual world. Other projects could involve screencasts, Jmol, games, Facebook, etc. As long as it requires students to access chemical information, I am pretty open to ideas. Students will work through their ideas on their log page and the final product will also be available on the wiki. These projects could provide interesting examples for others interested in the topic of chemical information.
At the end of my lecture I provided a brief overview of the NaH oxidation controversy. There really could not be a better example of the importance of staying on top of new communication channels to follow and participate in chemical research. This year the most important of these new tools are probably blogs, wikis and FriendFeed. Next year it might be something else - Google Wave?
Barry Bunin from Collaborative Drug Discovery (CDD) has just given me word that UsefulChem now has an account on their database free of charge. Their current business model involves charging data contributors so I appreciate the invitation.
Our account can be accessed at http://www.collaborativedrug.com/ (user: usefulchemistry, password: cdd). There is currently a set of compounds from our molecules blog. One of the features that I think will be useful for us is a way to record assay results. This comes in at a good time, since we just received the first results from the National Cancer Institute on the screening of one our compounds against tumor cell lines.
It will be interesting to compare CDD with other services like ChemSpider, as they evolve. One current limitation with CDD is that it is not possible to create links to molecules or assays that are truly public and indexable.
However, they are making some data pseudo-public by providing a public username and password (UsefulChem is not yet part of this beta):
Collaborative Drug Discovery (CDD, Inc) is pleased to announce the introduction of its next generation database technology. Collaborative Drug Discovery's Web-based database enables scientists to collaborate in novel, global efforts to more effectively develop new drug candidates for commercial and humanitarian markets. The technology enables novel community-based research efforts that become more and more useful as additional participants contribute data. Publicly available data sets currently in the system include the FDA orphan and approved drugs and small molecule drug discovery data dating back over half a century. These data sets pertain to a diverse group of neglected diseases, including malaria, tuberculosis, African Sleeping Sickness, Chagas Disease and Leishmania.
