Comments on: Why the Research Works Act Doesn’t Affect Text-mining Research http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/ Sat, 15 Jun 2013 21:49:40 +0000 hourly 1 http://wordpress.com/ By: caseybergman http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/#comment-298 Tue, 08 May 2012 21:50:25 +0000 http://caseybergman.wordpress.com/?p=210#comment-298 Sadly no this is not a technical issue, but a legal/sociological problem. Since there are complex per-journal copyright issues for self-archived manuscripts, PMC has taken a conservative approach to assuming that author-deposited manuscripts are not OA. For this to change it would require each journal to ask PMC to switch author-deposited manuscripts into the OA subset.

Looking at the numbers again today, it appears that 400+ author-deposited manuscripts are now in the the OA subset, all of which are from Nature Publishing Group. So it looks like NPG has been making some inroads into fixing this problem.

]]> By: Britt Holbrook (@jbrittholbrook) http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/#comment-297 Tue, 08 May 2012 21:20:17 +0000 http://caseybergman.wordpress.com/?p=210#comment-297 “while they can be downloaded and read individually, virtually none (<200) are available from the PMC’s Open Access subset that includes all articles that are free (libre) to download in bulk and text/data mine."

Why is this the case? Could there be a technical fix?

]]> By: Comments on the RCUK’s New Draft Policy on Open Access « I wish you'd made me angry earlier http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/#comment-256 Sun, 18 Mar 2012 15:37:34 +0000 http://caseybergman.wordpress.com/?p=210#comment-256 [...] in (UK)PMC are not available for text mining, since the are not in the “OA subset” (see http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-re…).  Thus, for RCUK to mandate libre OA via the green route, RCUK would need to work with [...]

]]> By: Why Are There So Few Efforts to Text Mine the Open Access Subset of PubMed Central? « I wish you'd made me angry earlier http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/#comment-234 Sat, 03 Mar 2012 10:22:44 +0000 http://caseybergman.wordpress.com/?p=210#comment-234 [...] Perhaps it is worth drawing an analogy with another major resource that was released at roughly the same time as PMC — the human genome sequence. According to many, including those in the popular media, the promise of human genome was oversold, perhaps to leverage financial support for this major project. Unfortunately, as Greg Petsko and Jonathan Eisen have argued, overselling the human genome project has had unintended negative consequences for the understanding, and perhaps funding, of basic research. Could the goal of reuse of open access articles likewise represent an overselling of the PMC repository? If so, then the open-access movement runs the risk of failing to deliver on one of the key planks in its platform. Failing to deliver on re-use could ultimately justify funders (if no-one is using it, why should we pay) and publishers (if no-one is using it, why should we make it open) to advocate green over gold open access, which could have a devestating impact on text-mining research, since author-deposited manuscripts in PMC are off-limits for text-mining research. [...]

]]> By: The Open Access Irony Awards: Naming and shaming « O'Really? http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/#comment-209 Wed, 15 Feb 2012 10:24:22 +0000 http://caseybergman.wordpress.com/?p=210#comment-209 [...] of the world’s scientific knowledge remains locked up behind publisher’s paywalls, unavailable for re-use by text-mining software and inaccessible to the tax paying public, who often funded the research through [...]

]]> By: caseybergman http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/#comment-206 Tue, 14 Feb 2012 10:04:31 +0000 http://caseybergman.wordpress.com/?p=210#comment-206 Hi Grace –

This is excellent news. NPG has a very progressive policy on text/data-mining on author-manuscripts, so it is a shame that there are technical barriers to actually using the data. Any progress towards making all NPG author-deposited manucripts available via the PMC OA subset would establish an important precedent, and be welcomed by the text/data-mining community. Many thanks for looking into this issue.

Casey

]]> By: Grace Baynes http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/#comment-205 Mon, 13 Feb 2012 18:54:02 +0000 http://caseybergman.wordpress.com/?p=210#comment-205 Thanks for flagging this. We deposit >1000 manuscripts a year on behalf of authors in PMC (in addition to those which authors deposit themselves), and have been doing so since mid-2008, so I agree there should be more than the 200 your search found in this dataset (which all seem to be from NPG journals as far as I can see).

We’ll look into this with PMC and get back to you with an update. But please be assured there is no change to NPG’s stated policy.

Grace Baynes
Nature Publishing Group

]]> By: Scott Chamberlain http://caseybergman.wordpress.com/2012/02/11/why-the-research-works-act-doesnt-affect-text-mining-research/#comment-200 Sun, 12 Feb 2012 14:52:36 +0000 http://caseybergman.wordpress.com/?p=210#comment-200 Totally agree on this that text mining needs to be possible on open publications. Thanks for the post.

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