A Blog Around The Clock

New in: Open Access and Science 2.0

The complexity of sharing scientific databases:

Under US law, pretty much anything you write down is copyrighted. Scrawl an original note on a napkin and it’s protected until 70 years after your death. Facts, however, are another matter – they can’t be copyrighted. So while trivial but creative scribblings are copyrighted, unless you choose to release them into the public domain, the information painstakingly discovered about the human genome – DNA sequences, for instance – aren’t. But the containers they’re stored in – the databases they’re held in – can be copyrighted.

Breaking News: Open access to large-scale drug discovery data at EBI:

The Wellcome Trust has awarded £4.7 million to the European Bioinformatics Institute (EBI) to support the transfer of a large collection of information on the properties and activities of drugs and a large set of drug-like small molecules from BioFocus DPI, part of the publicly listed company Galapagos to the public domain.

What scientists are we talking about?:

This discussion seems to have focused on just a small fraction (but an important one) of the number of scientists who would benefit from these tools. These researchers are funded by grants and are in tenure-track positions at 4 year research universities.

More scientists work at non-profits. What sorts of pressures are brought to bear there to prevent open collaboration? How different are these pressures from a research university? Those in business might also benefit from these approaches but have another set of barriers. Can they be surmounted?

This discussion is really important but it also conflates a large number of scientists/engineers who have different needs and pressures. There are 12 million in business who will have different needs than the 1.6 million at research universities.

MedPedia Is Wikifying the Medical Search Space:

The medical industry is one that thrives on innovation and evolution. New procedures, medicines, diseases, and theories are released practically every day. In such an environment, the need for a website to reflect and allow for documentation is apparent.

Open Access to Health and Human Rights:

Here’s another important step forward in the open access movement. Under its new editor Paul Farmer (who is often talked about as a future Nobel laureate), the international journal Health and Human Rights (HHR) has become fully open access.

The entire contents are freely available and are published under a progressive copyright license that allows readers to reuse the materials for any legal non-commercial purpose.

Indexing Institutional Repositories and Authors Self-Archived Collections:

The question then is whether or not ChemSpider can index institutional repositories or authors self-archived collections on their university research group websites. The authors self-archived collections will be very valuable but of course most likely to upset the publishers. We’d like to do both.

I envisage a time when articles are indexed and searchable even before they are published and indexed by others. Why not? If there are changes to the article between pre-and post-publication both can be indexed.

Another Wiki, WikiPathways:

I’ve already made known my “skeptical optimism” for wikis for biological data known in a previous post, reading this later paper, that would still apply here. But right now I’m not going to write beyond that, I’m just going to point you to this paper and wiki. Later (this week, next at the latest) I’ll be critiquing this paper more fully and more generally look at this trend currently to use wikis for community curation and documentation of biological data and databases.

Tracking the openness of databases:

Shirley Fung has launched Molecular Biology Databases, a website to evaluate the openness of databases in molecular biology.


Fung evaluates 34 databases to date, under six criteria: Downloadable, Offers Batch Processing, Offers a Query Interface, No Registration Required, Policy is Available, Public Domain. Her website supports the open-data research of Melanie Dulong de Rosnay, described last week by Ethan Zuckerman (and blogged here).

This is a very time-consuming but useful job. Everyone in molecular biology should be grateful, especially if the project leads to more consistent policies on open data across the field.

Fair game: a grad student’s adventures in fair use and copyright:

For scholars who study media, the internet has broadened research horizons and expanded the reach of teaching and publications. But powerful gatekeepers remain. From academic journals seeking to control our intellectual property to lawyers crying foul when we quote from copyrighted material, we are bombarded with a myriad of confusing and dubious restrictions. In short, the implied threat of legal action creates a chilling effect that impacts us all. Some have pushed back, arguing that our educational activities are protected under the “fair use” statute. But this is a risky game to play. The rules aren’t always clear. And when it comes to fair use, we either use it, or lose it.

Where should we spend our money?:

The lesson here seems to be that the digital environment is inevitably going to change the environment for textbooks as it has for most other kinds of intellectual property, for good or for ill. Georgia seems to feel that the publishers will eventually figure the market out and move to new profit models while supporting open access. But I think there is also an opportunity here for institutions to be more proactive and seek ways to invest in open access textbooks on a campus-wide level.

STM publishers imprisoned in their own walled gardens?:

Journals aggregate interesting science – many scientists still very much like a group of qualified editors and peer reviewers providing a filter on the deluge. Secondly, while knowledge discovery requires unfettered access for machines to content, I don’t see why that necessarily implies unfettered access for humans. You can perfectly well have an API that lets machines mine full-text, while still putting up a paywall for humans. As well, I think the versions issue is very challenging, and we are a long way from reliable automatic disambiguation and identification of authoritative copies. Finally, many conference proceedings already are peer-reviewed, and we can certainly imagine peer review extending to other areas, such as data sets.

History of the Journal Nature:

Nature introduced their formal peer review system in… 1967!

Who comments on scientific papers – and why?:

The quality of comments at BMC is high and the vast majority add value to the paper, though the numbers involved are relatively low (would a larger audience reading higher impact papers be different?).

Perhaps unsurprisingly comments on papers are not like comments on blogs; they’re far more formal (only 8% of comments were of the chatty, supportive variety) and it’s not the same people coming back each time (with the exception of the crazy 2%).


  1. #1 Darrell W. Gunter
    July 23, 2008

    Check out BiomedExperts.com is the world’s first pre-populated professional social network for life science researchers. We have loaded up the research profiles (pub med abstracts) of more than 1.5 million life science researchers with over 20 million connections. The service is free and now has over 30,000 registered users since the launch in January.

    Any questions, comments, suggestions, please let me know.

    best regards,

    Darrell W. Gunter
    Chief Marketing Officer
    Collexis Holdings, Inc.


  2. #2 ChemSpiderMan
    July 27, 2008

    I checked out Biomedexperts.com. Very easy to use and definitely interesting to see all of my recent publications (2 years) come together so quickly into a nice graphic showing my publication network. http://www.chemconnector.com/chemunicating/the-network-of-antony-williams-chemspiderman.html

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