Chemistry Central Blog

arXiv celebrates 20th birthday

It is 20 years this month since the launch of arXiv – a preprint server that hosts publications in physics, mathematics and computer science. arXiv can be regarded as the first major step towards open access, as for the first time scientists could publish their findings online without any financial barriers for readers to access them.

The success of arXiv can be seen in the number of articles it has handled over the past 20 years. The database now contains close to 700,000 preprints and is growing at a rate of 75,000 articles per year. This popularity has led to open access becoming an established publishing model amongst many researchers, particularly those working in high energy physics.

The success of arXiv has not been mirrored in chemistry publishing. A preprint server operated by ChemWeb was launched in July 2000, but closed four years later due to a lack of cross-publisher support. More recently, Nature Precedings was set up to report pre-publication research and preliminary findings across biology, medicine, chemistry and earth sciences, but although it has seen steady growth, chemistry continues to be underrepresented.

The Study of Open Access Publishing that was carried out last year showed that chemists were less supportive of open access than researchers in medicine and biological sciences. However, popularity amongst chemists is growing, and initiatives such as the EPSRC introducing an open access mandate should help to increase the adoption of open access within chemistry.

Posted by Bailey Fallon at 10:17    Comments (0)

EPSRC announces new policy on access to research outputs

The UK Engineering and Physical Sciences Research Council (EPSRC) has announced a new policy on access to research outputs that it funds.

From September 1st, all EPSRC-funded research articles that are submitted for publication will need to be made available on an open access basis. This policy is being introduced to ensure that this research is made as widely and freely available as practicable, in line with the Research Councils UK position statement on access to research outputs.

The policy ‘requires authors to... ensure that all published research articles arising from EPSRC-sponsored research, and which are submitted for publication on or after 1st September 2011, must become available on an Open Access basis through any appropriate route’.

Authors will be able to choose between ‘Green’ open access publishing, where research is published in a subscription journal, with the peer reviewed papers being archived in an online repository (typically following an embargo period), or the ‘Gold’ option, where peer reviewed papers are published in open access journals which do not charge subscription fees. The EPSRC will cover publication costs associated with ‘Gold’ open access publishing, either as 'directly incurred costs' (if incurred before the end date of the relevant research project) or as indirect costs (and hence factored into the fEC indirect cost rate for the relevant research organisation)’.

This policy mirrors those of other funders such as the Wellcome Trust and the National Institutes of Health, and should provide UK-based researchers with the opportunity to make their work as widely and easily accessible as possible.

Posted by Bailey Fallon at 15:10    Comments (0)

Open access in chemistry education

A new commentary published in Chemistry Central Journal delivers a compelling argument for using open access articles as an educational tool.

The article by Harry Pence and Barbara Losoff, “Going beyond the textbook: The need to integrate open access primary literature into the Chemistry curriculum”, explains that chemical educators can use open access articles to develop research-related skills and cultivate the next generation of scientists.

There is already some support for educators who develop science curricula incorporating research-like experiences into undergraduate teaching, but while conventional journal subscriptions can be a financial burden for small colleges and high schools, peer-reviewed papers from open access publications are freely available, and they can expand the potential for enriching scientific education.

The authors explain that “Open access peer-reviewed journals provide the means for chemistry educators, regardless of institutional resources, to introduce undergraduate students to the primary literature and to promote higher level cognitive skills by integrating primary scientific literature into the curriculum.”

Posted by Bailey Fallon at 11:44    Comments (0)

EMBL-EBI launches OA drug discovery database

The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) this week announced the launch of an online database - ChEMBLdb - containing information on the properties and activities of drugs and drug-like small molecules and their targets.

The database contains information on over half a million compounds.  The number of small molecules covered is over 520,000, with over 2.4 million records of their effects on biological systems.  The data includes information about how small molecules bind to their targets, how these compounds affect cells and organisms, and information on the molecules' absorption, distribution, metabolism, excretion and toxicity.

Dr John Overington, leader of the ChEMBL team at EMBL-EBI, commented that large and small pharmaceutical companies and academic institutions will all benefit from free access to the data, in their development of innovative drug therapies.

More details are available in the press release.

Posted by Jan Kuras at 15:07    Comments (0)

Nobel Laureates support open access

41 Nobel prize winning scientists, including 16 chemists, have sent an open letter to the US Congress to express their strong support for the Federal Research Public Access Act to enhance access to federally funded published research.

They state that broad dissemination of research is fundamental to the advancement of knowledge and its open availability in open online archives supports accelerated discovery and innovation, and encourages greater participation by providing equal access to all researchers.  Additionally, open availability expands the global visibility of research conducted in the US.

The signatories of the letter include the following Chemistry Central Editorial Board Members: Robert F. Curl and Kary B. Mullis (Chemistry Central Journal), and Jack W. Szostak (Journal of Systems Chemistry).

Posted by Jan Kuras at 16:13    Comments (0)

ChemSpider Journal of Chemistry

Tony Williams at ChemZoo Inc. has announced the launch of ChemSpider Journal of Chemistry with the publication of 8 articles.  It is intended that the journal demonstrates how web technologies can be used to enhance the information that can be communicated using web-based tools over standard online publishing approaches.

The plan is to host chemistry-related materials including synthesis, analytical chemistry, solid-state chemistry, chemical biology, cheminformatics, and molecular modeling, and publish original research, review articles, commentaries, methodologies, blog pages, and book and software reviews.  All papers published in ChemSpider Journal of Chemistry will be made freely accessible online immediately upon publication; and will use a mixed review process of peer and public review.

The launch issue includes articles marked-up using ChemMantis technology from ChemZoo.  The articles were sourced, with permission, from two Open Access journals - Chemistry Central Journal and MDPI’s Molbank.

The articles sourced from Chemistry Central Journal are: Isolation, purification, and full NMR assignments of cyclopamine from Veratrum californicum by Cooper et al. and Solvent effect on the spectral properties of Neutral Red by Rauf et al.

Posted by Jan Kuras at 15:31    Comments (0)

NIGMS funds new structure-activity database

The National Institute of General Medical Sciences (NIGMS), which is one of the National Institutes of Health, has announced funding of a project to enhance computer-aided drug design.  

The University of Michigan will lead the project to expand and enhance the molecular data needed to develop computer programs that more accurately predict potential drug candidates. The data will be presented in a free access online database.  The project is estimated to receive up to US$5 million over 5 years from the NIGMS.

Chemist Heather Carlson of the University of Michigan will oversee the creation and operation of the new Community Structure-Activity Resource.

To build it, Carlson and her co-investigators at the University of Michigan will gather molecular data from existing resources as well as generating new data. A major activity will be the collection of unpublished data from pharmaceutical company scientists, who emphasized both the need for this information and a willingness to share it.

The team also will draw from published literature as well as from Carlson’s Binding MOAD (“Mother of All Databases”), which contains more than 11,000 protein-ligand complexes, and the PDBbind database, which was developed by co-investigator Shaomeng Wang, and provides experimentally measured binding data. The team will conduct experiments to address any gaps in the data and sponsor community-wide events to facilitate collaboration among scientists.

Posted by Jan Kuras at 12:54    Comments (0)

Open source organic dictionary created

An open source dictionary of organic chemistry has recently been compiled for word processors.

The dictionary, hosted by ChemSpy, was put together by Adam Azman - student in the chemistry department at the University of North Carolina at Chapel Hill - who decided to create his own because of the lack availability of free chemical dictionaries.

The dictionary, which can be downloaded on the ChemSpy site, is in a standard “.dic” format, and so can be opened in NotePad to view - and if desired, edit - the entire content. Instructions for installing it on Microsoft Word OpenOffice can be found in the download together with licensing information - the dictionary is covered by a Creative Commons Attribution License.

As Azman concedes, further improvements will be needed to the 18,000-word resource, such as in eliminating some misspellings and including UK spellings. To help expand the dictionary's content, ChemSpider has also provided 'many hundreds of thousands of chemical names and terms' that can be harvested from. The project highlights yet another interesting open source avenue that scientists are pursuing. 

Posted by Gino D'Oca at 16:21    Comments (1)

eChemistry project gets Microsoft funding

It was recently announced that Microsoft is to fund the two year eChemistry pilot project, whose aim will be to explore digital library technology in the hope of demonstrating the benefits to chemists of online, open access data. The work is a collaborative effort comprising chemists and computer scientists from eight bodies: Microsoft Research, PubChem, the Los Alamos National Laboratory, and the universities of Cambridge, Southampton (UK), Cornell, Indiana, and Penn state (USA).

Posted by Gino D'Oca at 12:15    Comments (0)

NIST's new free (and cool) on-line solid materials database

The National Institute of Standards and Technology (NIST) has recently published a free on-line database of the properties of solid materials at temperatures ranging from cryogenic (around 4 K/ -269 C) to room temperature. The publication of the database - which is officially known as the NIST Standard Reference Data Database #152 - is said to have been prompted by 'numerous inquiries from academia, industry, and other government labs', many of whose research and development concerns the stresses imposed on materials by the effect of cryogenic temperatures.

Posted by Gino D'Oca at 11:28    Comments (0)

DrugBank continues to offer open access drug information

The DrugBank database is a freely available, bioinformatics and cheminformatics resource that combines chemical, pharmacological and pharmaceutical drug data with comprehensive drug target (i.e. protein) information.

The database, designed and created by Dr David Wishart of Alberta University, Canada, presently contains around "4300 drug entries including [over] 1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and [over] 3,000 experimental drugs. [In addition]... more than 6,000 protein (i.e. drug target) sequences are linked to these drug entries."

The entry cards for each drug, or DrugCards, contain around 80 data fields. The drug or compound information includes details on mechanism of action, pharmacology, and related metabolising enzymes; whilst the information held related to the drug target or receptor includes details on target pathways, the location of the target chromosome and the DNA sequence of the target. A table listing the principal entry card data fields can viewed here.

The database can be queried using a number of search options: "[t]he PharmaBrowse button allows users to browse through drugs as grouped by their indication... useful for pharmacists and physicians, but also for pharmaceutical researchers looking for potential drug leads. The ChemQuery button allows users to draw (using a ChemSketch applet) or write (SMILES string) a chemical compound and to search DrugBank for chemicals similar or identical to the query compound. The TextQuery button supports a more sophisticated text search (partial word matches, case sensitive, misspellings, etc) of the text portion of DrugBank. The SeqSearch button allows users to conduct BLASTP (protein) sequence searches of the 15,000 sequences contained in DrugBank. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported. The Data Extractor button opens an easy-to-use relational query search tool that allows users to select or search over various combinations of subfields." In addition, there is also a 'download option' that allows users to download selected text components and sequence data from the database, and also track the latest DrugBank statistics.

A more detailed summation of DrugBank, written by its architects, can be found here.

Posted by Gino D'Oca at 14:51    Comments (1)

'SciVee' to help take science the way of the YouTube generation

The Public Library of Science (PLoS), the National Science Foundation and the San Diego Supercomputer Center (SDSC) are set to launch SciVee in September, an internet source aimed at "free and widespread dissemination and comprehension of science" by using video and podcasts to supplement traditional peer-reviewed articles.

Posted by Gino D'Oca at 12:53    Comments (0)

Interview with Bryan Vickery, Editorial Director for Chemistry Central, is published in Reactive Reports

Bryan Vickery, Editorial Director for Chemistry Central, was recently interviewed by science writer David Bradley. The following interview was published in the July-August issue of Reactive Reports.

Bryan Vickery did his BSc in chemistry at Liverpool University, and then studied electrochemistry there for his PhD. He has never regretted his choice of university or city, but having ruined too many pairs of jeans and a laboratory fume cupboard opted for a desk instead of a bench job. He is currently Publisher at BioMed Central with special interest in Chemistry Central.

What's your chemistry background?

They say you always remember a good teacher. And I do. My chemistry GCSE/A-level teacher, Mr. Metcalfe, was a complete inspiration to me. His love of the subject was infectious; several of my class went on to do chemistry degrees.

I chose Liverpool University, and was there for 7 years taking BSc Chemistry and then studying Electrochemistry for a PhD. I've never regretted my choice of university or city, but I couldn't stay at the bench—I ruined too many pairs of jeans, and a fume cupboard!

How did you make the sideways step online?

During my PhD studies I was one of dozens of students in about nine European locations working on an EU funded project. Some were synthesizing crown ethers and porphyrins, we were using the complexation behavior of these molecules in an attempt to transfer metal ions across immiscible interfaces; others were developing micro-interfaces with photoablation techniques or membrane technologies. It was complex!

It was at this point I heard about email and the World-wide Web. I started to communicate with my peers this way, and we shared information faster and faster, and built web pages displaying our work. I was really excited about this, and concentrated more on the Internet side and less on the chemistry. At Liverpool we created WWW Links for Chemists as one of the first ways to catalogue the chemistry web, and Michael Barker did a phenomenal job of keeping that going. I decided a career in online development was where I wanted to be, but my dad would have throttled me if I'd not used my training. At that point I saw a job ad for ChemWeb.com, and the fit was perfect. My first role there was in managing a more sophisticated version of Mark Winter's ChemDex.

ChemWeb pioneered a lot of the things chemists now take for granted, such as online chemistry news, preprints, literature database searching; what were the highlights for you?

That's a very difficult question to answer because, looking back, we were so far ahead of our time—possibly too far. The biggest highlight for me has to be the friends I made, and the opportunity to work with some talented people in ChemWeb, MDL and Elsevier. It was a creative environment for us to gain publishing experience, a lot like it is here at BioMed Central.

The most exciting projects for me were:

Virtual Conferences/Virtual Lectures. This was truly groundbreaking stuff! We started in 1999, streaming audio and video, with slides and transcripts and 300 delegates. You'd think we were mad. In fact, on occasion the technology did creek and the bandwidth issues could get quite tricky, but we managed to broadcast real conferences LIVE and use a whiteboard for presenters to show molecules and software demos! The archive was very popular, and a lot less prone to traffic issues. My favorite was Breakfast with Wendy—we created a small studio in a hotel room at an ACS National Meeting, and Wendy Warr was our anchor. We broadcast news from the previous day's conference/expo and carried out interviews with important figures in the chemical information world. We also streamed the IgNobel awards ceremony live twice, which was huge fun.

The Alchemist. This was ChemWeb.com's magazine, and I loved the style of the articles we published, and pace of work when we moved to daily news. It was good to give Chemical & Engineering News a run for its money— even if the ACS did ban us from the press room at its conferences!

And that leads me on to "simply being controversial"! In that, I mean challenging the status quo and also the perceptions of Elsevier. Building services like free abstract searching, and the Chemistry Preprint Server didn't go down very well with all publishing houses! We were a community-driven service, and had over 400,000 members, but without the support of large amounts of advertising revenue, our lack of commerciality told.

It's a shame that Web 2.0 and the surge in advertising dollars came a little too late for ChemWeb, because it would have been well placed to benefit from all that is happening now—who knows, given its community drive it could even have been an open access publishing option for Elsevier. The site still exists now, and is run by ChemIndustry.com, but I haven't heard how things are going under its new ownership.

How is the chemistry wing of BioMedCentral fulfilling the promise of a chemical web?

It isn't down to us to fulfill that promise alone, but to facilitate it. Groups of motivated researchers around the world are already demonstrating what can be done with today's technology. Our job is to make the literature and data available freely, for datamining, etc., in a useful and meaningful way, and to employ linking technologies to make finding your way seamless. One of the main benefits of open access is that anyone can download the article, figures, schemes and data for reuse. We're looking at much more in the way of improved tools for authoring manuscripts, how articles are displayed and where data is deposited.

When, if ever, will we reach the crossing point, as traditional journals fade and open journals succeed?

Estimates suggest that 10% of journals and the same amount of research articles are now open access. That's a significant number! Open access is starting to enter the mainstream. What we need to do now is create a level playing field for authors, and there's an important role for libraries, research managers and funders to play here. Some question the sustainability of open access journals, but there are no new costs introduced by this model and traditional subscription-based journals do not make their revenues or cover their costs from thin air. Subscription journals are supported by vast library budgets.

We're seeing movement on this issue. Funders, such as the UK PubMed Central partners are mandating open access for research output they fund, and are providing funds for open access publication charges. The University of Nottingham recently announced a central fund to cover open access publishing charges. The tipping point is certainly coming, and it will accelerate as funders offer the money to cover publishing charges, institutions put in place mechanisms to centralize these funds, and authors continue to see the benefits of free access and reuse of the literature.

Why is it taking so long for researchers to fully engage with open journals?

Researchers have, for too long, been kept in the dark when it comes to the cost of publishing their research. It's strange to think that "publications" are a "library thing", especially as research output is increasing and library budgets are static. Researchers also put up with terrible customer service and delays in publication, sometimes to fit a particular journal's volume/issue structure. Authors generally think "but why should I pay?" but never consider that the librarian is being held to ransom, and paying huge sums on their behalf. In fact, library budgets are, in part, funded through the indirect costs from research grants so researchers are paying without knowing it.

We strongly believe that publication is part of the research process, and should be funded as such. By making our costs visible and transparent we want authors to know how much it costs. As more and more publishers move to open access, we can fix this dysfunctional market and authors and their institutions can choose where to publish based on quality, service, prestige and price.

In what areas of chemistry does Chemistry Central accept papers? What submission trends if any are emerging?

Chemistry Central is a publishing platform the same way that BioMed Central is. It will launch further chemistry related journals in the coming months and years, some we will run ourselves and some will be run by communities. Chemistry Central Journal, our first Chemistry Central launch (though not BMC's first chemistry journal), is broad ranging and covers all of chemistry and related/outlying disciplines. We've deliberately built it as that because of the huge overlap in current research areas.

There are 3 areas where we are understandably seeing good levels of submissions: Computational & Theoretical Chemistry/Chemical Information, as these groups of researchers are leading the charge to open access and open data; Biochemistry/biotech, because of our already strong reach into these communities; and Physical chemistry/chemical physics, because of the history of preprinting and use of arXiv.

Can anyone mirror freely the archive of Chemistry Central papers?

Absolutely, anyone can set up their own mirror and we encourage this. We take this part of our role very seriously, and are working with 2 new mirrors in China right now. BioMed Central deposits the open access articles that it publishes in multiple digital archives around the world to guarantee long-term digital preservation. These archives include: INIST (France), Koninklijke Bibliotheek (The Netherlands), Potsdam University (Germany), PubMed Central (United States), UK PubMed Central (UK). BioMed Central is also participating in the British Library's e-journals pilot project, and plans to deposit copies of all articles with the British Library.

We make article metadata available in compliance with Open Archives Initiative protocols, enabling automated 'harvesting' of our research articles for inclusion in any other digital archives. We support non-exclusive digital archiving of research articles by as many international archives as possible, to ensure the security and permanent accessibility of that research. BioMed Central is a participant in the LOCKSS (Lots of Copies Keep Stuff Safe) initiative. LOCKSS will enable any library to maintain their own archive of content from BioMed Central and other publishers, with minimal technical effort and using cheaply available hardware. To facilitate datamining research, the fulltext XML of all BioMed Central open access research articles is available for FTP download as a ZIP archive. See our datamining research pages.

In the wake of Nature Precedings, which in turn simply reinvented the ChemWeb Preprints wheel, might we see Chemistry Central papers "published" as preprints to be reviewed live?

We'll be doing just that with PhysMath Central in fact. Our new launch into physics, mathematics and computer science allows authors to upload their files directly from arXiv, and upon acceptance PhysMath Central will deposit, immediately, the final version back into arXiv. What is more, any article submitted directly to us will also be deposited in arXiv. Having worked closely with him at ChemWeb and at Elsevier, I'm delighted that Chris Leonard has joined us in this venture.

Time is running short for traditional peer review, what new models might take its place?

There is still a lot of value in peer review, as it stands today, but you are right in that people are starting to experiment. Our medical journals offer open peer review, making the full prepublication history available to readers for example. Biology Direct is already providing a unique service to authors and readers of research articles, with a novel system of peer review, making the author responsible for obtaining three reviewers' reports, via the journal's Editorial Board. The process of peer review is open, rather than anonymous, eliminating the principal source of abuse in the refereeing process and increasing the responsibility of the referees. The reviewer can prepare comments for the author but also, if they wish, to prepare 'public' comments, however critical, that will appear alongside the final version of the article when it is published.

PLoS has also launched PLoS One, which leaves the community to decide on the quality of the work published and offers excellent comment/annotation facilities. There's a lot happening right now, certainly in the social networking and collaborative authoring areas—Wikipedia has certainly demonstrated what can be done with living documents offering version control, and this is where PLoS One is headed.

Why does Chemistry Central offer groups the opportunity to start their own Open journal?

There are several reasons why people might want to launch or transfer a journal to us. There are still niche/multidisciplinary/emerging areas which are not covered by a journal and we can quickly give the research output from these areas a home. Also, groups of researchers may want to create an open access journal to compete with expensive subscription based titles. More and more we are seeing societies come to us to transfer the journal(s) to an open access model whilst retaining editorial control, and we provide the platform to enable them to do this.

What limitations do you foresee in the open approach that must be addressed before it is more fully adopted? 

Right now, the most important thing is making the funds available to smooth the transition. Once the funds are in the right place we will see a quick realignment of the market. The second most important thing is a move away from the reliance on Impact Factors for journals. The rules governing how and when an Impact Factor is given to a journal is a minefield for publishers, and the IF itself can, obviously, be distorted. Many open journals are relatively new, and a three-year wait for an IF can be very limiting. We have the technology to be able to use better metrics for judging the value of an article or an author; isn't it about time we started to use them?

Posted by Gino D'Oca at 10:34    Comments (0)

ChemXSeer: an integrated digital library and database for chemical kinetic data

Posted by Gino D'Oca at 17:02    Comments (0)

A New "Preprint Server" From Nature

Just over 7 years ago I was working on the launch of the Chemistry Preprint Server (CPS), while at ChemWeb.com. Alongside me at Elsevier was Chris Leonard, who's now working with me again at BioMed Central launching PhysMath Central.

We launched the service as an experiment in communication, and it was not unsuccessful. There were some 8-900 submissions in the course of 3 years. The CPS was closed down when Elsevier sold ChemWeb.com in 2004, but the articles are still available via ScienceDirect.

During the American Chemical Society (ACS) National Meeting in August of 2000, The Chronicle Daily (As Experts Call for a Chemistry Preprint Server, Elsevier Unveils Its Own. 22 August, 2000) reported that chemists were calling for such a service. It was lucky for us that we launched the CPS that very day to the shock of many. After all, what was Elsevier doing launching a free publishing service? It's interesting looking back at this short article now. R Stephen Berry, who recently joined the Editorial Advisory Board of Chemistry Central Journal was one of the supporting voices then, urging chemists to "try everything".

The ACS was one of just a few Publishers who refused to accept submissions which had previously appeared on the CPS.

In response to a recent blog posting by Derek Lowe (In the Pipeline: Exalted Paper) "yagwara" (comment #26) asked "what forces prevent the existence of an arXiv for chemistry," and  suggested "If it didn't already exist and was invented today, Elsevier and Springer would be introducing draconian measures against authors who posted papers there." As you can imagine, I felt I needed to jump to Elsevier's defence (comment #27).

So why am I telling you all this?

Because, interestingly, Nature has recently launched a preprint server called Nature Preceedings, which aims to cover biology, medicine, chemistry and earth sciences. Just like the CPS, submissions will be screened for appropriateness, but no judgement will be made by the internal editors about the quality of the work. This, is the job of the community.

The next step is, obviously, to allow authors of research articles posted to Nature Preceedings, to be able to submit these directly to a peer reviewed journal and for that journal to be able to link directly back to previous versions of the manuscript.

PhysMath Central, from BioMed Central, does exactly that. Authors can upload their arXiv manuscript directly to the online system. See Chris' recent blog posting "How to submit your arXiv manuscript to PMC Phys A."

Nature is certainly taking what Web 2.0 has to offer, and making it reality. I wish them luck.

Posted by Bryan Vickery at 11:21    Comments (2)