Depth-First: Tag openaccess

Building a Unique Chemistry Journal: Responses to Questions from Nature Chemistry

Rich Apodaca — Thu, 08 May 2008 14:48:00 -0400

Neil Withers of the soon-to-be-launched chemistry journal Nature Chemistry has asked for feedback to some questions about the best ways to display chemistry research papers on the Web. Here are some responses:

(1) HTML vs PDF: does anyone read the HTML articles? Do you read the PDF on-screen or print it out?

I've used PDFs both for offline archiving and sharing of especially important articles as well as one-off printing of a paper I'm interested in. I rarely read a paper on-screen if I can avoid it.

Typical workflow: (1) download PDF; (2) print it out; (3); let paper sit while I go do something in the lab that can't wait (or bring it with me); (4) put paper onto a rather large stack of papers just like it; (5) pull paper out of stack from time to time as needed; (6) (optional) file paper in an increasingly chaotic system of folders or recycle it.

This system is bad, and I cursed it weekly during my time as a research chemist. Most of my colleagues had similar experiences.

There are plenty of opportunities to address pain points with the Web. Some ideas:

Make it very easy to find papers on the Nature Chemistry site. If I know a paper is trivial to find, I'm less likely to print it out in the first place. Good search may not be enough (see question 3).
Make the online version as readable as it can be. Minimize fluff like menus, ads and general clutter. Maximize things that promote readability like reasonable column-widths, appropriate fonts, and attractive and readable images.
Add conveniences that make it easier to read the paper online such as hover-popups that display 2D chemical structures for trivial names and IUPAC nomenclature (see below).

Paper is portable but Web documents are alive. Both can be readable - for example, I never print out a blog posting to read it.

(2) Big vs little graphics: what does everyone else think about the tiny size of the graphics in ACS html articles?

Graphics should be sized appropriately. ACS HTML articles are a good example of failing to design the obvious. You'd never read a blog post that looked like those articles, so it's not surprising everyone prints out the PDF.

Another problem is over-wide columns. It's puzzling why journal publishers would ignore all of their hard-won design experience just because a document appears as a Web page. If the ACS used a narrower column width, the Web version would be more readable. For example, check out this article from Beilstein Journal of Organic Chemistry. The only thing I'd change is to make the font larger.

Both problems are correctable using the right software and techniques.

(3) Tagging/’semantic web’: what do you think about the toys on the RSC’s Project Prospect? What kind of things would you like to see tagged/linked to other content in Nature Chemistry? For instance, Steve would love to do something with named reactions.

If by tagging, you mean giving users the ability to tag articles like Flickr allows photos to be tagged, and for other users to make use of those tags while searching, I think it's long overdue and could be a game-changer. It would clearly play to the strength of the Web as a medium.

I must confess that I'm not a fan of the implementation of Project Prospect, although the idea has a lot going for it. There's too much bling and a lot of it fails on my Linux/Firefox 2 system.

The one Prospect feature well worth adapting would be the one that lets you get a 2D structure by clicking on a trivial name or IUPAC name. But there's a much better way to implement it:

Turn it on by default and get rid of the floating right-hand menu.
Make the structure appear, without clicking, by simply hovering the mouse over the trivial name or IUPAC nomenclature. Be sure the delay is set right so that it's not popping up unintentionally.

That's all there is to it. It needn't be complex, just usable.

Another possibility: harvest all of the 2D molecular structures appearing in articles over a given period of time to be displayed in a dense, hyperlinked graphical abstract format ideal for quick browsing.

(4) 3D molecular structures: do these help your understanding of a paper?

Rarely, and in many cases they just add clutter. For almost all small molecules, a properly laid-out and well-drawn 2D chemical structure is more useful. If a central point of discussion in a paper is a 3D structure, then that would be a good use of the technology.

(5) How useful to you are InChIs and SMILES?

Not very. Research chemists rarely care about this kind of technology. They'd much rather have a good-looking 2D chemical structure. InChIs and SMILES, if available, should be hidden away and only brought out when requested. A more basic problem is neither system will be able to encode all of the molecules your journal's authors are likely to discuss.

(6) Forward linking: the RSC and Elsevier/Science Direct offer this – do you use it? Would you use an RSS feed that alerted you to new citations of a particular paper.

It could be useful provided that clutter could be kept to a minimum. It's essentially a form of linkback (see below).

An RSS feed that published linkback activity might be useful, but many of the chemists I know still don't know what RSS is. On the other hand, a page (or email service) that could keep an interested reader updated on linkback activity on all of their papers of interest simultaneously could be very useful.

(7) Would you actually comment on papers if there was a comments box at the end?

Like Egon Willighagen, I'd probably use my blog to do it.

However, most chemists don't maintain blogs or other websites and for them I can see how the ability to post comments would be useful.

Both kinds of users could be accommodated through a combination of comments and linkbacks. Provided that a good spam filtration system were used, this two-pronged approach might be very useful to readers.

Blogs are just the tip of the iceberg, though. Web publication technologies are creating all kinds of opportunities for creating highly focused, constantly evolving, collaborative mini-reviews on special topics. Linkbacks would create value for both readers and authors of these mini-reviews as well as forward-thinking scientific publications that embrace them.

(8) We really like the Biochemical Society’s HTML article style (sample one here) – do you?

No. Frames makes that site very difficult to navigate.

It will be very interesting to see how Nature Publishing Group takes advantage of its opportunity to create something unique among chemistry publications. Asking the kinds of questions they're asking now, and doing so in the way they're doing it, shows they're at least on the right track.

Yet Another Free Chemistry Database: Pherobase

Rich Apodaca — Tue, 15 Apr 2008 18:56:00 -0400

The creation of free chemical databases continues unabated. Today's entry is Pherobase, a service dedicated to documenting the relationship between chemical structures and the insect world.

Users can search Pherobase by text, or browse a large number of precompiled categories: alphabetical by genus; alphabetical by species; and compounds by genus or species. Each compound data sheet contains a wealth of data, all linked to the primary literature: mass spectrum; nmr; synthesis; and behavioral function. There's even an interactive Jmol model for each entry.

Pherobase is clearly designed to be useful to farmers and others involved in agriculture who are interested in using pheromones in pest control. Are insects eating your olive tree? Let pherobase help. Need help with fire ants? Pherobase can help there, too. Wonder what else besides Gypsy Moths might be affected by disparlure? Pherobase has the answer. And nearly all of this information is backed by references to the primary literature.

Pherobase clearly demonstrates the value of building comprehensive, focused chemical databases around a limited subject of high practical utility. After all, chemistry's most enduring contribution is in the production of useful properties, not the production of compounds.

Pherobase is also noteworthy for the way it's being used by its creator, Ashraf El-Sayed. Rather than standing on its own, Pherobase is designed to direct users to suppliers of pheromones and related pest control products by educating them about what might be possible. In this sense, Pherobase's approach offers another intriguing example of an Open Access business model that can actually work.

Open Access: Think Globally, Act Locally

Rich Apodaca — Mon, 24 Mar 2008 09:24:00 -0400

Source: blip.tv via Chemists Without Borders

NIH Hears Publisher Feedback on Open Access Mandate

Rich Apodaca — Fri, 21 Mar 2008 18:17:00 -0400

The NIH heard public comments yesterday on its plans for implementing PL 110-161 Section 218, a new law that grants the agency broad powers to intervene in the scientific publication system.

Scientific publishers were out in force. According to The Scientist, Jack Ochs of the American Chemical Society (ACS) was first in line to offer comments:

He started out by saying that a brief meeting was no substitute for the formal comments on rulemaking process like the one the NIH held when they were implementing the voluntary submission program in 2005. He was the first of several to call a halt to implementing the mandate so the details could be worked out.

A lot is riding on the outcome. The new law requires NIH grant recipients to deposit peer-reviewed manuscripts of their publications into PubMed Central, in apparent opposition to the policies of many leading scientific publishers - including the ACS.

NIH has given its grant recipients until April 7 before compliance will become mandatory. It remains unclear what steps, if any, ACS will take to enable authors to comply.

Unless ACS policy changes, NIH grant recipients face the possibility of losing one of the most prestigious publication options in chemistry.

Also see Peter Suber's comments.

A New Beginning or More of the Same?

Rich Apodaca — Thu, 27 Dec 2007 16:02:00 -0500

As discussed by Peter Suber, Peter Murray-Rust and others, President Bush signed H.R. 2764 into law yesterday. Among the many items in this bill is one that proponents argue could change the nature of the Open Access debate. Does this new law represent a fundamentally changed game, or just the next inning of the old one?

The text of the new law spells out what is now required:

SEC. 218. The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

IANAL, but the provision requiring the policy to be implemented "in a manner consistent with copyright law" offers publishers (and scientists) all the flexibility they need to continue business as usual.

The reason is simple. Transfer of copyright from the author of a scientific paper to the publisher is usually one of the first things to happen "upon acceptance" of a manuscript for publication. And the new law makes it perfectly clear that copyright law takes precedence over deposition into PubMed Central.

Most of the journals in question will be hostile to the idea of having their copyrighted material deposited into PubMed Central and so understandably won't allow it to be done by the authors of papers or anyone else.

Take this hypothetical scenario for example: Professor Gross at California University gets his manuscript approved for publication in the Journal of Nanoscale Devices (JND). Professor Gross is fully aware both of HR 2764 and JND's refusal to deposit manuscripts into PubMed Central - the reasons why Professor Gross would choose JND anyway are interesting, but not relevant here. Along with the acceptance letter, JND requests prompt return of a signed copyright transfer agreement. Professor Gross sends in the signed form and from that point on, all rights to his article belong to JND. As is their policy, JND refuses Professor Gross permission to deposit a copy of his paper into PubMed Central within 12 months after publication.

Unless I'm missing something, neither Professor Gross nor JND have violated any laws. The assumption made by proponents of the new law seems to be that to implement the new policy, the Director of NIH will forbid publication by grant recipients in journals that don't allow deposition of articles into PubMed Central.

How many influential scientist do you know of who would tolerate the government telling them which journals they can and can't publish in? The minute such a misguided policy is put in place, the national scientific outcry would more than overwhelm anything Open Access proponents could muster.

Neither HR 2764 nor any form of government intervention will bring widespread Open Access into being. The only things that will change the status quo are: (1) the availability of tools for making it happen; and (2) the realization by individual investigators that continuing to give away their hard-earned copyright makes them far less competitive than their peers who don't.

Open Access proponents should forget about getting the Federal Government to fix the mess that modern scientific publication has become. Instead, they should focus on making Open Access-like options more attractive to scientists.

Image Credit: mayr

Open Access Business Models That Can Actually Work: Sigma-Aldrich's ChemBlogs

Rich Apodaca — Thu, 11 Oct 2007 12:49:00 -0400

A gem of a chemistry blog has been operating for some time - apparently without much notice. ChemBlogs is Sigma-Aldrich's Web answer to their Aldrichimica Acta print magazine, and it's packed with mini-reviews on synthetic chemistry with links to the primary literature. This approach to scientific marketing has so much potential, I can't imagine why others aren't doing it.

Nevertheless, there are some small things that could be done to make ChemBlogs a lot more effective. Here, in no particular order, are some suggestions:

Submit the RSS feed to Chemical Blogspace. Chemical Blogspace is perhaps the most widely-read aggregator of free chemistry content on the Web. And it's one of the best ways to get your chemistry blog noticed, bookmarked, and linked to.
Make it easier to discover and use a post's permalink. If I see an article I like in ChemBlogs, such as this one on gold catalysis, there's no obvious way for me to link to it in my own blog. Standard practice is that all titles on the front page are hyperlinked to the article's permalink. This article discusses the importance of permalinks.
Don't moderate comments - use reCAPTCHA instead. Nothing stifles online discussion like moderated comments. The Web is about immediacy. Make a change and see it live instantly. Everything else is so 1999. If spam is the concern, reCAPTCHA is a wonderful tool for the job.
Drop the company group when identifying authors. No reader cares whether Sharbil J. Firsan is part of the Marketing Group or not. In fact, it's a bit of a turn-off to have the word "Marketing" appear at all.
Each author should have an online bio that links to their name. Although titles and company divisions are not useful, other information about authors is. In a multi-author blog like ChemBlogs, the byline should hyperlink to a bio of the author, or a collection of their writing. This makes it easier for readers to follow authors they like.
Link to the primary literature via DOI. ChemBlogs cites many articles appearing in journals, which is a great thing. Unfortunately, there's no way for a search engine to know that this is happening. The simple fix is to hyperlink a literature citation to the DOI entry, like this one for Chem. Rev. 1994, 94, 2483-2547.
Include InChIs for all important structures. Free tools like InChIMatic can then be used to quickly find articles dealing with those molecules.
Post more frequently and/or regularly. More content means more eyeballs. When it's regularly posted, readers know when to expect it.
Invite some working scientists to write articles. If recent experience with Wikipedia and Chemistry is any guide, there are plenty of capable scientist more than willing to create free, high-quality compound monographs and other chemical content. Invite some of them to contribute very short articles for ChemBlogs in their area of expertise and see what happens.
Release all content under a Creative Commons License. Information wants to be free - why not make it free? Allowing ChemBlogs' content to spread far and wide just makes it that much more visible. For example, at last count, Depth-First content was reproduced on about a dozen other Web sites, including one in Korean. This matches my goals exactly, and it's all perfectly legal thanks to the way the content is licensed.

With a little tweaking, Sigma-Aldrich's experiment in Permission Marketing could pay off - for everyone. Readers would conveniently get useful bits of information to make them more productive. The Internet would get new, high-quality chemical content - free to use and link to. Who knows - this might even become an Open Access business model that actually works.

And Sigma-Aldrich would have a far more effective marketing tool than anything else they currently use. With the possible exception of the Handbook, but even that could change.

Image Credit: angela7

Yale University Libraries Cancel BioMed Central Membership in the Face of Spiraling Costs

Rich Apodaca — Tue, 07 Aug 2007 08:14:00 -0400

Yale University has ended it's financial support of BioMed Central's Open Access Membership program effective July 27, 2007. Under the program, Yale libraries paid an annual fee to cover the costs of submissions by Yale authors to BioMed Central (BMC) open access journals. Yale authors can continue to submit manuscripts to BMC, but must pay for all charges themselves.

According to the August 3, 2007 statement by Yale,

... Starting with 2005, BioMed Central page charges cost the libraries $4,658, comparable to single biomedicine journal subscription. The cost of page charges for 2006 then jumped to $31,625. The page charges have continued to soar in 2007 with the libraries charged $29,635 through June 2007, with $34,965 in potential additional page charges in submission.

As we deal with unprecedented increases in electronic resources, we have had to make hard choices about which resources to keep. At this point we can no longer afford to support the BioMedCentral model.

Apparently, Yale is not alone in its decision. In a refreshing act of openness, BMC lists both current members and former members. A surprisingly large number of universities have canceled their memberships, including over 80 in the United States alone. In effect, these cancellations represent a version of the journal deadpool, but in reverse.

Cost increases pose a real threat to the viability of scientific publication. Journals rely heavily on network effects to attract readers, authors, citations, and ultimately, subscribers. A journal can remain viable for some time in the face of canceled subscriptions. But each cancellation brings a journal that much closer to destroying its network, its only real value.

Open access by itself doesn't solve scientific publishing's most serious problem - it simply changes the paths through which ever-increasing sums of money flow.

Thanks to Wendy Warr for her alert on this story posted to the CHMINF-L mailing list.

Go West, Young Man: Does Open Access Really Matter in the Long Run?

Rich Apodaca — Mon, 16 Jul 2007 09:31:00 -0400

Making a name for yourself in science is no easy job. Aside from the technical challenge of doing noteworthy science while working under constraints, there's the compounding challenge of making your work known to influential colleagues. Excellent work done in a vacuum is lost to science, only to be "rediscovered" by those more willing or capable of self-promotion. Look around at the most successful scientists in your field, and you'll find that they are both extraordinarily adept at doing noteworthy science and in promoting their work.

Scientists have been using the scientific publication system for hundreds of years as a channel for promoting their work. For a variety of reasons, this system is now breaking down before our eyes. There are many reasons - consider these:

The printed page doesn't matter anymore. Old-guard scientific publishers have been able to prosper by acting as gatekeepers of a precious resource: the printed page. The arrival of immediate, ultra-cheap, ubiquitous, interactive, and persistent communication through the Internet means that printed journals are increasingly viewed as wasteful and irrelevant.
Printed journals have priced themselves out of the marketplace. How many printed journals has your library dropped over the last year? Does your "library" even carry current printed journals anymore?
Electronic Information wants to be free. Few things are more frustrating than knowing the answer to your question exists on a server somewhere, but you are forbidden from accessing it. Yes, you can pay $15-$30 for each article you need or get multiple subscriptions costing thousands per year, but is that any way to spend your budget?
The minimum publishable unit is shrinking. Scientists have legitimate interests in maximizing the number of papers they publish, in minimizing their size, and in decreasing their interval. Submissions to top-tier journals continue to increase. New journals are started to catch the overflow, placing additional strain on the system's ability to find readers and "qualified" reviewers, and driving up production costs in the process.
Too much information. How many scientific papers have you actually read, from start to finish, in the last month? How many important, relevant papers in your field could you have completely read in the last month? How many of them did you find through an automatic notification system? How many papers have you used solely for one specific piece of information they contain? How many of these papers did you find through a database of some kind?

Open Access has become a hot topic, mainly in response to the points above. Although well-intended, the debate assumes that scientific publication in the Internet age will continue to work essentially the same way it always has - with scientists submitting manuscripts to publishers who act as editors, distributors, and in many cases quality-assurance agencies.

But what if it doesn't end up working out that way?

The reason that the existing scientific publication system has flourished for hundreds of years is that it solved the fundamental problems of two key groups: (1) scientists who wanted to be informed of new developments; and (2) scientists who wanted to promote their work and careers.

If you accept this premise, then nothing prevents entirely new publication models from replacing the existing ones - provided that they solve the basic problem scientists face. If anything, the Internet is replete with examples of powerful old-guard gatekeepers of all stripes being first undermined as they denied that their business models were failing, then lashing out at everything but the root cause of their problems, and finally being driven into oblivion.

Why should old-guard scientific publishers be immune to this process?

Some scientists are discovering value in bypassing scientific publishers altogether. In chemistry, the best-known example is Jean-Claude Bradley and his group at Drexel. As Bradley's group is joined by others willing to experiment in this area, they will uncover a variety of problems that need to be addressed. Some of the most significant (at this point) include:

tools to create content
services that host and archive that content indefinitely
peer-review mechanisms that fully leverage the power of collaboration over the Internet
utilities for finding and promoting the work

These are the new high-payoff areas in scientific publication. Like all high-payoff areas, this one starts out looking dangerous or insignificant to most people.

This is not to say that that the Internet eliminates the need for gatekeepers. Instead, it creates tremendous opportunities for new gatekeepers. Google, eBay, and Wikipedia are gatekeepers. Facebook and YouTube are also gatekeepers. By all accounts, these services have done phenomenally well and will continue to flourish for some time. Significantly, each service addresses the basic need of information consumers to be informed and information producers to have their message heard. These systems have found powerful mechanisms for quality control that in many cases put the current practice of scientific peer-review to shame. And in no case will you find a business model requiring pay-per-view.

Google, eBay, Wikipedia, Facebook, YouTube, and hundreds of other gatekeepers thrive because each has found a new precious resource to allocate, not by trying to extract every last drop of value from the old ones. Both scientific publishers and Open Access proponents would be wise to consider their example.

Image Credit: Seamus Murray

We Don't Need No Stinkin' Copyright

Rich Apodaca — Tue, 19 Jun 2007 12:11:00 -0400

I realize that being the U.S. Government has its advantages, but the copyright notice at the bottom of a recent J. Chem. Inf. Model. paper caught my attention:

This article not subject to U.S. Copyright. Published xxxx by the American Chemical Society

As far as I can tell, this article is not part of the ACS AuthorChoice program.

Open Access in Organic Chemistry

Rich Apodaca — Fri, 01 Jun 2007 10:03:00 -0400

In a recent interview, Peter Murray-Rust offers some very interesting comments on Open Access in chemistry. Beilstein Journal of Organic Chemistry remains the only widely-available Open Access option for chemical publication backed by a major publisher. With these thoughts in mind, I offer an update to my previous compilation of their statistics.