open access

No-one knows what Open Access means - not even Open Access advocates.

Andrew Walkingshaw — Sat, 03 May 2008 05:14:24 -0700

Description

There's a bunfight going on right now over what Open Access actually is.

Open access contributions must satisfy two conditions:

1. The author(s) and right holder(s) of such contributions grant(s) to all users a free, irrevocable, worldwide, right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship (community standards, will continue to provide the mechanism for enforcement of proper attribution and responsible use of the published work, as they do now), as well as the right to make small numbers of printed copies for their personal use.

2. A complete version of the work and all supplemental materials, including a copy of the permission as stated above, in an appropriate standard electronic format is deposited (and thus published) in at least one online repository using suitable technical standards (such as the Open Archive definitions) that is supported and maintained by an academic institution, scholarly society, government agency, or other well-established organization that seeks to enable open access, unrestricted distribution, inter operability, and long-term archiving.

Which is pretty unambiguous, you'd have thought.

But Open Access, informally, has been since used to mean "you can read journal articles without paying". People've, unsurprisingly, been confused; resulting in an effort to clarify matters by coining, and within a few days repudiating, of the terms "Strong OA" and "Weak OA" by two prominent Open Access advocates, Stevan Harnad and Peter Suber.

Weak OA means you can read the paper for free online, but not (necessarily) do anything with the content; Strong OA itself is subject to argument, but allows reuse of, and the making of derivative works from, the content of articles beyond fair use. (The argument's over whether requiring that use to be non-commercial stops it being Strong OA - the people coming from the free software community arguing that it should, by analogy with the Open Source Definition).

The upshot is that, in the OA world, no-one knows what anything means right now.

Future of chemistry

Source

http://en.wikipedia.org/wiki/Open_access
http://oa.mpg.de/openaccess-berlin/berlindeclaration.html
http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1071
http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1057
http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=1068#comment-188272
http://www.opensource.org/docs/definition.php

Science bloggers are now, effectively, journal editors too (if they want to be)

Andrew Walkingshaw — Fri, 02 May 2008 12:46:33 -0700

Description

Here's the introduction of a blog post on totallysynthetic.com about the popular total synthesis target, platensimycin:

Antibiotic… blah blah… Merck… Nicolaou… other synthesis covered…

Yep, you all know about platensimycin, and half of you have probably worked on / are working on syntheses of this ‘popular’ target. Eun Lee hasn’t bothered with a full total synthesis, instead satisfying a neat formal of the right-hand ‘cage’ motif. Key to this was the optimisation of a substrate for a rhodium catalysed carbonyl-ylide cycloaddition.

In tone, this is pretty informal; but in content, it's a hybrid of peer review and a review article, produced by a working scientist for the hell of it, for the kudos, and as a byproduct of their own literature review. This isn't new, as such - the same thing's gone on in department tearooms forever - but the Internet gives every scientist, or at least every scientist who's so inclined, a megaphone.

And that can mean, sometimes, "peer-review" by virtual pitchfork-wielding mob, whether justified or not. From The Chem Blog:

Bad news bears (VIP: Total Synthesis and Structure Assignment of (+)-Hexacyclinol). James La Clair’s precious and dubious synthesis of Hexacyclinol, the vaulted controversy detailed here, here, here and here (Update: here) appears to be reheating. Scott D. Rychnovsky’s reassignment of the original structure of Hexacyclinol, which appeared after La Clair’s first ‘synthesis’ of the structure, made waves when it became somewhat obvious that either in La Clair’s solo authorship of his Angew paper he totally made up the already improbable synthesis (he had the help of the Bionic Bros) or Rychnovsky was simply wrong. It now appears that John Porco’s group made the compound to prove his point. I gave James the benefit of the doubt, and this currently being based off a ‘news blip’ I still will not rescind that benefit but I’m growing much more concerned as Rychnovsky’s reputation is as credible as one can get. (Porco too, of course)...

Serious, referenced, semi-permanent archives of arguments at Internet speed!

Future of chemistry

Source

http://totallysynthetic.com/blog/?p=976
http://www.thechemblog.com/?p=108

Automatic recognition of chemical terms in free text

Andrew Walkingshaw — Fri, 02 May 2008 12:07:50 -0700

Description

Recently, ClearForest (a division of Reuters) launched OpenCalais - a web service which reads the news for you:

The Calais web service automatically attaches rich semantic metadata to the content you submit – in well under a second. Using natural language processing, machine learning and other methods, Calais categorizes and links your document with entities (people, places, organizations, etc.), facts (person ‘x’ works for company ‘y’), and events (person ‘z’ was appointed chairman of company ‘y’ on date ‘x’).

In other words, it annotates text and marks up four of the journalistic 5 Ws - who, what, where and when, hopefully making it easier for journalists to join the dots and supply the why and how.

This seems only tangentially relevant to chemistry, at first glance, but chemistry's in a sense just a special case - we want to pull the whats (chemicals) and the hows (experimental methods) out of free text - papers, theses, and journal articles. That means chemical named entity recognition, and conveniently:

Oscar3 is a system for chemical natural language processing, focussing on chemical named entity recognition.

The Royal Society of Chemistry use OSCAR3 to annotate journals as part of Project Prospect; it lets them build, automatically, a searchable index of molecular structures (and substructures) published in their journals.

So, in that, there's some overlap with what the service the Chemical Abstracts Service provides; but the CAS model is based on a small army of editors indexing papers by hand, and as such can only scale up so far. On the other hand, there's no reason OSCAR-like robot annotators, even if less accurate than the humans, can't be turned loose on much more - patent applications, university thesis repositories, scientific blogs, mainstream scientific journalism, or anywhere there's chemical text to be read. That has the potential to open up a lot of 'hidden', informal or otherwise unpublished research to chemically-meaningful indexing and search.

Future of chemistry

Source

http://opencalais.com/
http://en.wikipedia.org/wiki/5_Ws
http://oscar3-chem.sourceforge.net/
http://www.rsc.org/Publishing/Journals/ProjectProspect/
http://www.cas.org/
http://cb.openmolecules.net/

Aggregating crystallography: overlay journals and new databases

Andrew Walkingshaw — Thu, 01 May 2008 17:17:38 -0700

Description

A lot of science is published every year, and much of it is only available by subscription. That's inflated one of the favourite political footballs among scientists - the whole Open Access debate . It mostly concentrates on the copyright/access status of the journal articles themselves, because they're often perceived to be the major part of scientific output. But that neglects the data which gives rise to the articles, which is often as valuable. In crystallography, this is usually posted on journal websites alongside the papers, but unlike the papers the raw data's uncopyrightable; it's "just" a collection of facts. So it's not subject to the same restrictions as the articles, and you can build new databases by aggregating it.

One example of this kind of thing is CrystalEye, which brings together the latest small-molecule crystallography data, converts it to CML, and puts it up on the web in a more searchable and browsable form. But what it also does is give us a resource we can mine; it exports its data using the Atom protocol, making it easier for informaticists to write new tools to perform analyses over these streams of crystallographic data. In other words, it makes the data more amenable to programming - whether that's machine learning techniques, visualization, social filtering or something new.

The big noise in the Web world, when it comes to open data and the Semantic Web, is the Linking Open Data project. It uses RDF to make very large open datasets - and, as importantly, the links between them - accessible. Through the links, each dataset builds on the previous one, and resources like CrystalEye can be pulled into the cloud; that lets us begin to build new analyses and visualizations of that data, like this map of the global distribution of crystallography papers. As we get more data, and more connected data, then more subtle and complex relationships will be thrown up; and through that we'll get to new science.

Future of chemistry

Source

http://www.prismcoalition.org/
http://en.wikipedia.org/wiki/Open_access
http://wwmm.ch.cam.ac.uk/CrystalEye/
http://inkdroid.org/journal/2007/08/27/linking-open-data/
http://wwmm.ch.cam.ac.uk/blogs/walkingshaw/?p=53

XML and Open Scientific Publishing

Alex Soojung-Kim Pang — Thu, 03 Apr 2008 00:19:49 -0700

Description

Philip E. Bourne1, J. Lynn Fink, and Mark Gerstein make the argument for the wider use of XML in open publishing systems (over PDF or HMTL), and the need to create virtuous circles between XML adoption and the creation of tools-- e.g., visualizations to create high-level views of literatures, mashups that blur "the distinction between databases and journals," and editing tools to add semantic information to content early on. As they put it, open publishing has mainly been about cost containment to date, and not about exploiting the opportunities that open semantic frameworks offer:

For most of you, open access may imply free access to read the journals, but nothing more. There is a far greater potential, but, up to now, little to point to that highlights its tangible benefits. We would argue that, as yet, the full promise of open access has not been realized.

Plausible Accuracy comments,

the authors echo the call of Science Commons to work on creating applications which can leverage open scientific content. They describe some of the benefits and current shortcomings of producing manuscripts with XML markup (which provides for more facile machine reading and data extraction). They then go on to argue that the only way to convince people to go through the trouble of creating the machine-readable file is to demonstrate what can be done with the current level of markup and then drawing a picture of what expanding this would do.

Source

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000037
http://www.plausibleaccuracy.com/2008/03/31/leveraging-scientific-data-using-the-power-of-the-semantic-web-who-wants-to-start/

Growth of Open-Access Scientific Publishing

Alex Soojung-Kim Pang — Tue, 23 Oct 2007 11:10:30 -0700

Description

Open access promises to replace the current scientific publishing establishment.

Open-access scientific publishing has been gaining ground in recent years alongside steep increases in the cost of scientific journals and a growing perception among scientists that business interests are impeding scientific discovery. For one journal subscription, scientists could pay nearly six figures per year In the next decade, the open-access model, whereby the producers of journal content pay, rather than the consumers. While this could simply result in traditional publishers adopting different business models, access to research papers will open, if slowly, and these papers will be free for all to read, distribute, reference, and copy as they see fit. The public will have the same access to the scientific and clinical literature as the "experts" potentially raising issues about "patient power".

This change in model reflects new power dynamics in the scientific publishing market: with the low cost of publishing, power has shifted back toward scientists and university libraries, many of whom have a strong interest in free and open access to science. These groups, along with certain scientific societies, have been aligning recently to start new journals and standardise archival methods. The US National Institutes of Health encourages its grantees to deposit their papers in PubMed Central, an online database for open-access papers, along with submitting them to commercial publishers. Starting in September 2005, the US National Institutes of Health will grant additional funds to researchers who plan to publish in pay-for-publication, open-access journals such as PLoS Biology. RCUK is considering similar measures under its full economic costing program. In the end, funding for open access will be provided by traditional money sources, including the government, universities, and even industry groups -or those who would have ultimately paid for subscriptions to non-open journals in the past. In the "big" science areas in life sciences and physics, the publishing costs are unlikely to be significant compared to the overall research budget and many open access journals offer preferential rates for papers from scientists working in developing countries. This shift in cost however is likely to affect "low overhead" research areas in developed countries, such as ecology and theoretical physics, where a few thousand pounds to publish a research paper will represent a significant proportion of the research budget.

Commercial journals will likely be forced to change their business models to survive the shift to open access, . but to survive as profitable businesses, these firms will probably need to offer additional value beyond that of their nonprofit competitors. Rather than charge for basic articles, they could differentiate themselves based on value-added services to scientists and readers with higher-quality presentation, editorials, and research synthesis. This is also likely to have a significant affect on learned societies in the UK, many of whom generate their income through their publishing arms and are already considering alternative models of income generation.

Open access still faces questions relating to its own appropriate business model. Critics charge that pay-to-publish open-access journals could compromise quality by accepting too many papers due to economic incentive. The Public Library of Science (PLoS) has sufficient momentum and funding to maintain its journals' quality, but this leaves open the question of whether other, more mid-level scientific journals will be able to survive with open-access business models. Further in the future, these concerns could be mitigated by 'bubble-up' forms of publishing driven by a radical rethinking of the current system of peer and editorial review.

This will be enabled by:

"Development of low marginal cost publishing technologies: the Internet, PDF, peer-to-peer file sharing
Technological and social innovations in paper publishing
New methodologies of peer review based upon ratings systems and 'bubble-up' technologies"

Early indicators include:

"Free archiving, since 1991, of work by physicists online at arxive.org
Dropping in 2004 by the International Society for Computational Biology of its affiliation with a non-open press in favor of PLoS Computational Biology, an open-access journal
Vote by the faculties of Stanford and the University of California in early 2004 to boycott Elsevier journals, even though more than 100 University of California faculty serve as senior editors and more than 1000 serve on editorial boards of Elsevier journals
En masse resignation of several of Elsevier's editorial boards to form new open-access journals, many of which are directly supported by the learned societies in their respective fields
Role played by telescope logs published on the Internet in discovery of the 10th planet"

What to watch:

Downloading of articles from the Public Library of Science's and BMC's online journals increases exponentially.

open access

No-one knows what Open Access means - not even Open Access advocates.

Description

Source

Science bloggers are now, effectively, journal editors too (if they want to be)

Description

Source

Automatic recognition of chemical terms in free text

Description

Source

Aggregating crystallography: overlay journals and new databases

Description

Source

XML and Open Scientific Publishing

Description

Source

Growth of Open-Access Scientific Publishing

Description

Signals