Monday, 29 November 2010

Almost 60% of Wellcome-funded papers in PMC are fully open access

The Wellcome Trust's Open Access policy has always made it clear that it considers dissemination costs as legitimate research costs and as such provides grantholders with additional funding, through their institutions, to cover open access charges.

In view of this I thought it would be interesting to see how many papers, attributed to the Wellcome Trust and available through PMC and UKPMC, were "fully" open access papers, in accordance with the Bethesda Principles.

In summary, this means research articles which:
  • were made available in PMC with no embargo
  • deposited by the publisher as "version of record" articles (i.e. excluding Accepted Author Manuscripts (AAMs)
  • included an article-level licence that permitted re-use.
To identify the number of "full" OA articles I ran the following search on PMC (on 29th November 2010)
  1. "wellcome trust" [gr] 14748 articles
    [This finds all articles in which the Wellcome Trust has been identified as a research funder]
  2. Limit #1 to articles published in 2009 = 2483
    [This includes "full" OA articles, as well as author manuscripts, and articles which were made available through PMC because the publisher makes all content available through this repository.]
  3. Limit #2 to "open access" articles = 1436
    [This limits the previous set to full OA articles, as described above.]

    A simple test to validate that the articles are "full OA" is to check that these articles are included in the OA subset, and thus can downloaded in XML format.  The syntax for this is: http://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:2654146 (simply replace the last 7 digits with any open access PMC ID to see the XML
Using the above strategy we can see that around 58% of these articles are fully OA (in accordance with the Bethesda Principles). 

Full figures are shown below:
  • Number of full, Bethesda-compliant, OA articles: 1436 (58%)
  • Number of AAM's: 483 (19%)
  • Number of other Version of Record articles, but had no explicit re-use licence: 564 (23%)

Wednesday, 24 November 2010

Company of Biologists develop full open access option

The Company of Biologists (COB) - publishers of Development and Journal of Cell Science - has developed an open access ("gold") option, which meets the requirements of the UKPMC Funders' Group.

For a fee of £1350, the COB will deposit the final version of the article in PubMed Central (at the time of publication) and allow these articles to be re-used in accordance with the Creative Commons Attribution, non-commercial, share-alike licence.

From January 2011, all content for Disease Models & Mechanisms will be Open Access. The Article Processing Cost (APC) for this title is also £1350 (plus VAT if applicable).

Friday, 12 November 2010

All authors now displayed in UKPMC search results

In response to user feedback, the UKPMC search results page now displays all the authors associated with any published article.

Prior to this change, the search results page had shown just the first seven authors, with the full set of authors only being visible from the abstract and full-text views.

Further feedback on the UKPMC service is welcomed.

Wednesday, 10 November 2010

Article about UKPMC in Nucleic Acids Research (Database Issue)


The January 2011 Nucleic Acids Research Database Issue includes an article by Jo McEntrye and others, that describes the UKPMC service and the developments which have taken place over the last three years.

Key developments include:
  • Single search: Through UKPMC a user can search across some 24 million bibliographic records drawn from PubMed, Patents and recent biomedical theses, as well as the 1.8 million full-text articles held in the UKPMC repository

  • Citation services: UKPMC contains ‘Cited By’ information as an alternative way to navigate the literature.
  • Text mining services. UKPMC has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources.

  • Grantee services. Through UKPMC+ grantees can deposit manuscripts, link papers to grants, publish online portfolios and view citation information on their papers. .
The article also clarifies the relationship between PMC and UKPMC, providing historical context and future directions.

HTML version
PDF version
Screen version

NAR is in fully open access journal.

Tuesday, 2 November 2010

Open access at the Wellcome Trust: 5 years on

In October 2006 the Wellcome Trust become the world’s first research funder to develop an open access policy that required the research outputs, that arose from its funding, to be made freely available.  This presentation, delivered at the recent Berlin 8 meeting, reviews the progress that has been made over the past 5 years – in terms of compliance with the mandate, providing the infrastructure to support open access, and working with publishers to help them develop “Wellcome-compliant” publishing policies – and outlines what additional steps the Trust needs to take to help realise the full potential of its open access mandate.

Looking forward, the presentation also discusses the aspirations of the Wellcome Trust to transform UK PubMed Central into a single, Europe-wide repository for life-sciences research and, more generally, considers how research funders could help to influence innovation in scientific publishing in the open access arena.

View the presentation

Monday, 1 November 2010

UKPMC now offers search RSS

By running a search through UKPMC, then clicking on the RSS feed logo RSS feed logo once your search results have been displayed, you can add a search as feeds in a bookmark to your browser. When new journals are added to UKPMC, the updates will alter your search (remember to refresh your browser rather than used cached contents) - you just click through to the title you want to link through from the feed, accessible from your browser's bookmarks.

Author: Paul Davey

Links to chemical compounds now enabled

As part of the text-mining work being undertaken by European Bioinformatics Institutue [EBI] and The National Centre for Text Mining [NaCTeM], it is now possible to get a list of all chemicals cited in a full-text article at UKPMC and link through to Chemical Entities of Biological Interest (ChEBI) database for further information.

By way of example, on viewing the article at http://ukpmc.ac.uk/abstract/PMC/PMC1828400  - and clicking on the Bioentities Tab - you will see that 11 chemical compounds have been identified. 

In addition to chemical compounds, UKPMC articles are also linked to genes and proteins, protein interactions, species, and diseases.