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.
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Rajarshi Guha <[email protected]>
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A: A deferential operator.
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