Well said, Rajarshi and PMR. I was surprised to see Amber mentioned as being funded by the NIH. Isn't this commercial and proprietary?
- Noel 2009/5/19 Rajarshi Guha <[email protected]>: > > > Begin forwarded message: > > From: "Vivien Marx" <[email protected]> > Date: May 18, 2009 8:33:41 PM GMT-04:00 > To: <[email protected]> > Subject: the story for you > Hi Rajarshi, > > Thanks so much, here is the story for you. > > All best, > Vivien > > -- > > http://www.genomeweb.com/informatics/royal-society-chemistry-buys-chemspider-open-access-chem-resources-gain-momentum?page=show > > > > ________________________________ > > Royal Society of Chemistry Buys ChemSpider as Open Access Chem Resources > Gain Momentum > > May 15, 2009 > Newsletter: > BioInform > > This week, the Royal Society of Chemistry acquired ChemSpider, an open > access chemistry search engine and repository holding over 20 million > chemical structures from 200 data resources. > > Antony Williams, president of consulting firm ChemZoo and the lead developer > of ChemSpider, told BioInform via e-mail that ChemSpider has been "free > access with no price barriers to access and that is intended to continue." > Williams will serve as vice president of strategic development for > ChemSpider at the RSC. > > The RSC noted that it has acquired ChemSpider to "fulfill its strategic > objective of disseminating knowledge to the chemical community." The > ChemSpider development team will continue to be located in the US and there > are plans to re-launch an improved version of the ChemSpider website later > this year on RSC servers, but the present version will remain active for the > time being. > > Financial terms of the acquisition were not disclosed. > > ChemSpider intends to become a "bigger and better" community resource from > this point forward, Williams said. The plan is to continue to provide > "access to integrated diverse resources for chemists via ChemSpider as a > centralized hub and have it form one of the foundations of the semantic web > for chemistry. At no charge." > > Williams said there will be fees for some of the web services set to be > created in the future, "but this is already that way that ChemSpider > operates." > > Williams noted on the ChemSpider blog that he believes the acquisition is > "absolutely … a good thing" because it means he and his team no longer need > to deal with "very significant resource limitations." > > He added that since ChemSpider was launched in 2007, "we have been > approached by a number of organizations to merge/acquire/consume," but in > all those cases, "things didn't feel quite right." In discussions with RSC, > however, "it was clear that we are like-minded. Our want is to have a > positive impact on the flow of data, knowledge, and information in the > domain of chemistry," he said. > > The news of the ChemSpider buyout by the RSC is "great news, not only for > ChemSpider but the chemistry community in general," Rajarshi Guha, > co-founder of the open source cheminformatics group Blue Obelisk, told > BioInform this week. > > RSC's backing should eliminate worries about the future of the services, he > said. "It's also great to see the RSC supporting the open access vision of > ChemSpider and I'm sure that the combination of ChemSpider and the RSC > semantic web technologies will result in many innovations in the near > future," Guha said. > > Liberate the Data > > RSC's validation of ChemSpider's open access model is in line with a growing > trend in the cheminformatics community toward freely available resources. > > At the recent Bio-IT World conference in Boston, University of Cambridge > chemistry professor and open source advocate Peter Murray-Rust pointed out > that he and like-minded chemists are devoted to "liberating data" for > chemists through resources like ChemSpider as well as PubChem, a free > database of chemical structures housed at the National Center for > Biotechnology Information; NMRShiftDB, an open access database of chemical > structures hosted at the Max-Planck Institute for Chemical Ecology; and > CrystalEye, a resource that Murray-Rust and his colleagues have developed > that aggregates crystallography data from web resources. > > Murray-Rust recommended in his talk that chemical data should be converted > to a semantic format using tools such as the Chemical Markup Language, which > he developed, and the chemistry ontology ChemAxiom, so that it can be linked > and made openly available to the research community. > > In a conversation with BioInform Murray-Rust said that chemistry is a > "mature" subject with practices that have not changed for a long time, > information sources that have developed over decades, and a "large chemical > information industry" that is accustomed to selling data under a model that > has been stable "until recently." > > Pharma has been inward-looking, he said, with each company seeking to be > self-sufficient for its information needs. These factors have all > contributed to chemistry having "missed the boat" in terms of the open > access model that the bioinformatics community, by contrast, has adopted > wholeheartedly. But that is all beginning to change, he said. > > "The chemical information industry is about 10 years behind bioinformatics," > he said. If bio-scientists are envious of certain aspects of data-sharing in > physics, he said, then "we as chemists look enviously at bioscientists." > > Biotech companies know they need to be multidisciplinary, he said. In > chemistry, "there is not enough pain in the system for people to see open > source, or open access, or open anything else as a driving force," he said. > > A Reactive Discipline > > Chemistry is one of the "most reactive disciplines" and is "conservative," > said Murray-Rust. Unlike biology, where researchers often need to tweak > tools to work with new instruments and embrace open workflow platforms such > as Taverna, no comparable culture exists in chemistry, he said. > > In biomedical research, it is common for studies to take place in the public > domain, and the community has long encouraged rapid public release of all > experimental data. Even pharmas are beginning to embrace data sharing, as > evidenced by the non-profit organization Sage founded by Merck researchers > Eric Schadt and Stephen Friend, and the Pistoia Alliance, a new organization > founded to share pre-competitive information across pharma companies. > > Murray-Rust said that these new developments are being pushed along by the > difficulties in the industry to create new drugs. > > However, although there is an abundance of open source software for > bioinformatics, open-source software in chemistry is scarce, partially due > to cultural reasons. "The IT people believe, the biologists believe, the > chemists don't," Murray-Rust said. > > One challenge, he said, is that chemists have a difficult time getting > funding to develop open source tools. "You can get funding for that in > bioscience to a much greater degree," he said. > > Nevertheless, he said that the broader open source culture is finding its > way into chemistry. In particular, he said that as more biology tools are > integrated with chemistry tools, that will draw the open-source culture into > chemical research. "The biologists will come in and eat the chemist's > lunch," he said. > > In his talk, Murray-Rust praised Blue Obelisk, an organization founded in > 2002 by a group of chemists and software programmers who advocate open > source software and open standards for cheminformatics. > > Among other projects, Blue Obelisk is propelling OpenSMILES, a project to > develop an open standard for the SMILES (Simplified Molecular Input Line > Entry System) grammar used to represent chemical structures as text strings. > > At Bio-IT World, Blue Obelisk co-founder Guha, a visiting professor at > Indiana University's School of Informatics, explained that the ecosystem of > open source cheminformatics is relatively small but vibrant and includes the > Chemistry Development Kit, or CDK, a cheminformatics software suite > developed at Notre Dame; OpenBabel, a chemical toolbox for data conversion; > and RDKit, a suite of tools for cheminformatics, computational chemistry and > predictive modeling. > > Guha agreed with Murray-Rust that chemists display "a lot of disinterest" > when it comes to open source cheminformatics. That is either because the > tools don't apply to their problems, or due to "inertia because they don't > want to go and see what they could do with these things," he told BioInform > after the conference. > > A "vicious cycle" comes into play because chemists with programming skills > would like to help develop computational tools for experimental chemists but > the "bulk of chemists don't see value" in this activity, he said. > > Guha has just landed a cheminformatics position at the National Institutes > of Health as a staff scientist mainly focused on informatics aspects > connected to RNAi screening within NIH's Center for Chemical Genomics. There > is "a strong group of people doing cheminformatics" there, he said. > > Part of his job is to develop open-source software for assays as well as > computational support for screening projects, he said. > > Guha also agreed with Murray-Rust's view that funding is scarce for > cheminformatics development. While NIH has a software maintenance funding > program that has financed software such as the Amber molecular dynamics > package, that is the exception. "Just trying to get money for software on > its own is difficult," Guha said, though there is a better likelihood of > funding for projects focused on a scientific question that may require > software development as "a side effect." > > Overall, though, he believes that the momentum for open source chemistry is > building. One driver for this, he said, is the NIH's Molecular Libraries > Probe Production Centers Network, a nationwide network of small molecule > screening centers, which has triggered a need among academics for tools and > methods as scientists. > > But progress will likely be slow. As part of the molecular libraries > program, in 2005 NIH awarded six exploratory centers for cheminformatics > research. Guha said that he and his colleagues hoped that these centers > would spawn interest in cheminformatics and lead to further funds, but NIH > did not renew the grant last summer, he said. "That was a big blow," > especially compared to the "strong" funding that NIH makes available for > bioinformatics, Guha said. > > ________________________________ > > > ------------------------------------------------------------------- > > Rajarshi Guha <[email protected]> > > GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 > > ------------------------------------------------------------------- > > Q: What's polite and works for the phone company? > > A: A deferential operator. > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables > unlimited royalty-free distribution of the report engine > for externally facing server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Blueobelisk-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > > ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
