Scott Edmunds

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<img
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srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/2021-OAW-02-1600x491-Eng-1024x315.png 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/2021-OAW-02-1600x491-Eng-300x92.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/2021-OAW-02-1600x491-Eng-768x236.png 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/2021-OAW-02-1600x491-Eng-1536x472.png 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/2021-OAW-02-1600x491-Eng.png 1601w"
sizes="(max-width: 768px) 100vw, 768px" width="768" height="236"
alt="Open Access Week 2021" />
<figcaption>Banner from Open Access Week 2021, source;
www.openaccessweek.org</figcaption>
</figure>

This week is [International Open Access
Week](http://www.openaccessweek.org/), and with the
[theme](http://www.openaccessweek.org/profiles/blogs/opening-knowledge-and-building-structural-equity-this-week-beyond)
"It Matters How We Open Knowledge: Building Structural Equity". This
aims at highlighting the individual and collective action required
alongside the decisions, actions, and investments in knowledge sharing
to ensure that equity is foundational. Beyond just open licensing of
content (of which is foundational in what we do) there are many other
barriers that we've been trying hard to break to enable more equitable
and open science for all. Since we've launched we worked hard to open
science in many ways, from a technological perspective through many of
the novel editorial practices and integrations we've implemented, to
helping educate and amplify the voices of people working to open
science. Be that through our efforts in [community
genomics](http://gigasciencejournal.com/blog/community-genomes-gigatv/)
and citizen science projects (see [Bauhinia
Genome](http://bauhiniagenome.hk/)) or publishing reviews, commentaries
and guest blogs from open science practitioners.

This Open Access Week seems a good time to look back over these efforts,
and here is a list of 10 of our favourite *GigaScience* papers providing
examples of barriers we've tried to help break for more open science.  

**1. The inclusivity barrier**  
One rare positive of the COVID-19 pandemic has been the potential of
increasing inclusivity of attendance at academic conferences. Yet, the
mere existence of online conferences is no guarantee that everyone can
attend and participate meaningfully. We recently published a
collaboratively written Review from [Open Science Special Interest Group
of the
OHBM](https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3712)
identifying practices that purposefully encourage a diverse community to
attend, participate in, and lead online conferences.

Levitis et al. Centering inclusivity in the design of online
conferences---An OHBM--Open Science perspective, *GigaScience*, 2021,
**10**:8
doi:[10.1093/gigascience/giab051](https://doi.org/10.1093/gigascience/giab051)

**2. The lab barrier**  
You no longer need to be based in a wealthy research laboratory, or have
any laboratory at all, to do cutting edge genomics research. Back in
2018 we published our first example of a study taking DNA sequencing and
genomics to a completely new place: *in situ* genome sequencing in the
jungle. See the [DNA Day
blog](http://gigasciencejournal.com/blog/dnaday2018/) covering this
\#jungleomics.

Pomerantz A et al. Real-time DNA barcoding in a rainforest using
nanopore sequencing: opportunities for rapid biodiversity assessments
and local capacity building. *Gigascience*. 2018, **7**:4.
doi:[10.1093/gigascience/giy033](http://dx.doi.org/10.1093/gigascience/giy033).

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aufgetreten.</h1>
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aktiviere JavaScript, falls es in deinem Browser deaktiviert sein
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</div>
</figure>

**3. The participation barrier**  
In the data driven era, not only in research but in our day-to-day
lives, people are creating more and more personal digitized data that
enables human-participant research in social sciences and personalized
medicine. In 2019 [we
published](https://doi.org/10.1093/gigascience/giz076) an open call from
Open Humans for contributors to their community-based platform for
participant led research from the social sciences to precision medicine
(see the [Q&A for
more](http://gigasciencejournal.com/blog/open-humans-qa/)).

Greshake Tzovaras B, et al. Open Humans: A platform for
participant-centered research and personal data exploration.
*GigaScience*. 2019.
doi:[10.1093/gigascience/giz076](https://doi.org/10.1093/gigascience/giz076)

**4. The transparency barrier**  
One of the most distinctive open science policies carried out by
*GigaScience* since our launch is our open, named peer review and we
have an [editorial](https://doi.org/10.1186/2047-217X-2-1) discussing
the benefits of this policy.

Edmunds SC, Peering into peer-review at *GigaScience*, *GigaScience*,
2:1, 2013,
doi:[10.1186/2047-217X-2-1](https://doi.org/10.1186/2047-217X-2-1)

<figure class="wp-block-image size-large">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/alessandro-fazari-Ngo5FrmF97o-unsplash2.jpg"
class="wp-image-4203" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/alessandro-fazari-Ngo5FrmF97o-unsplash2.jpg 640w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/alessandro-fazari-Ngo5FrmF97o-unsplash2-300x194.jpg 300w"
sizes="(max-width: 640px) 100vw, 640px" width="640" height="413" />
</figure>

**5. The "Data not Available" barrier**  
Publishing sensitive medical data is no longer a barrier to transparent
open peer review, our first example of precious Controlled Access
medical data peer reviewed by named reviewers proving an example of how
'data not available' is no longer justifiable in many of these cases, at
least from the perspective of journals that like ourselves have broken
the "transparency barrier" (see above).

Gabriel AAG et al. A molecular map of lung neuroendocrine neoplasms.
*Gigascience*. 2020 9:11.
doi:[10.1093/gigascience/giaa112](http://dx.doi.org/10.1093/gigascience/giaa112).

**6. The reproducibility barrier**  
*GigaScience* has always been trying to push the boundaries of how we
disseminate reproducible research, and to adapt to the challenges of
dealing with experiments become more data-intensive. [In 2017 we
published our first
example](http://gigasciencejournal.com/blog/data-intensive-software-publishing-sailing-the-code-ocean-qa-with-ruibang-luo/)
showcasing the Code Ocean reproducible research platform that wraps and
encapsulates the data, code, and computation environment in a "Compute
Capsule" that can be interacted with through their platform for testing
and then running via your cloud computing provider if it is of interest.

Luo R, Schatz MC, Salzberg SL. 16GT: a fast and sensitive variant caller
using a 16-genotype probabilistic model. *GigaScience* 2017.
doi:[10.1093/gigascience/gix045](http://dx.doi.org/10.1093/gigascience/gix045)

**7. The collaboration barrier**  
Since our launch, on top of software papers we have seen more and more
complex tools utilizing machine learning approaches. To help with
reproducibility with machine learning-based tools, we recently published
a paper [integrating
Gigantum](http://gigasciencejournal.com/blog/gigantum-joins-giga-reproducibility-machine-learning-toolkit/),
an open source web application that aims for better collaboration,
sharing and making reproducible data science research even easier.
Working these tools into the review and publication process potentially
makes it easier to assess replicability and utility. With a slightly
different and more distributed approach to Code Ocean, via a DOI users
can run the published tool anywhere (laptop, GPU, on premises
infrastructures, and Public Cloud) -- eliminating problems that can
arise when collaborating via multiple infrastructures and contexts are
involved.

Vieira DV, et al, Driftage: a multi-agent system framework for concept
drift detection, *GigaScience*, **10**:6, 2021,
doi:[10.1093/gigascience/giab030](https://doi.org/10.1093/gigascience/giab030).

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<figcaption><em>GigaScience</em>, like our sister GigaByte journal has
experimented with a number of platforms for publishing software in a
more reproducible manner.</figcaption>
</figure>

**8. The "certified reproducibility" barrier**  
While we've worked on methods to make the increasingly complicated
computational research we publish easier to interact with and use, we've
also look at ways of improving their peer-review. Last year we published
the [first published
example](https://doi.org/10.1093/gigascience/giaa026) demonstrating a
new way of peer reviewing software articles: presenting a
[CODECHECK](https://codecheck.org.uk/) certificate. These independently
time-stamped runs are awarded a "certificate of reproducible
computation" and increase availability, discovery and reproducibility of
crucial artifacts for computational sciences.

Piccolo SR. et al., ShinyLearner: A containerized benchmarking tool for
machine-learning classification of tabular data, *GigaScience*,
**9**:40, 2020,
doi:[10.1093/gigascience/giaa026](https://doi.org/10.1093/gigascience/giaa026)

<figure class="wp-block-image size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/CodeCheck2020-1024x726.png"
class="wp-image-4204" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/CodeCheck2020-1024x726.png 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/CodeCheck2020-300x213.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/CodeCheck2020-768x545.png 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/10/CodeCheck2020.png 1368w"
sizes="(max-width: 512px) 100vw, 512px" width="512" height="363" />
</figure>

**9. The methodological comprehension barrier**  
Not just focusing on computation methods easier to scruitinise and
reuse, in 2016 we published [our first
examples](http://gigasciencejournal.com/blog/reproducible-research-resources-researching-parasites/)
where complicated "wet lab" methods for extracting DNA from tiny
parasites where broken down step-by-step and hosted in open access
repository of scientific methods and collaborative protocol-centered
platform protocols.io. Since then, with our team working with authors to
input their methods we have gathered a large collection of protocols in
our [protocols.io
workspace](https://www.protocols.io/workspaces/gigascience-press).

Mofiz E. et al., Genomic resources and draft reference assemblies of the
human and porcine scabies mites, *Sarcoptes scabiei* var. hominis and
var. suis. *GigaScience*. **5**:23. 2016.
doi:[10.1186/s13742-016-0129-](http://dx.doi.org/10.1186/s13742-016-0129-2)

**10. The third dimension barrier**  
To ease access to our published three-dimensional datasets and models we
have gone beyond just describing the data collection and findings by
providing downloadable, interactive files of everything in these study.
For interested citizen scientists out there, we've been doing things
like providing new interactive web-based viewers, video clips and 3D
printable file formats. In 2019 [we published our first
paper](http://gigasciencejournal.com/blog/sketchfab-3d-fossil-seabed/)
showcasing *GigaScience*'s complete integration with the Sketchfab 3D
viewer, which enabling readers to interact with the 3D fossils in the
paper and even view them via virtual reality headsets. Making our
published research far more accessible and interesting to the general
public.

Reid M, et al. A micro X-ray computed tomography dataset of fossil
echinoderms in an ancient obrution bed: a robust method for taphonomic
and palaeoecologic analyses. *Gigascience*. 2019 **8**:3.
doi:[10.1093/gigascience/giy156](http://dx.doi.org/10.1093/gigascience/giy156)

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The post [Open Access Week 2021: GigaScience's 10 Examples of
Open](http://gigasciencejournal.com/blog/gigascience-open-access-week-2021/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


This week is International Open Access Week, and with the theme “It Matters How We Open Knowledge: Building Structural Equity”. This aims at highlighting the individual and collective action required alongside the decisions, actions, and investments in knowledge sharing to ensure that equity is foundational.

Open Access Week 2021: GigaScience’s 10 Examples of Open

Europe PMC Team

::: {dir="ltr" style="text-align: left;"}
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[For Open Access week 2015, we tweeted some number-related  
facts about Europe PMC, reproduced with a little additional context
here.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[1.  #EuropePMC has over 3,447,632 full text  
articles, with over 1,134,397 in the \#openaccess subset
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif; text-indent: -18pt;"}[http://europepmc.org/FtpSite](http://europepmc.org/FtpSite){style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; text-indent: -18pt;"}[
\#OAweek  
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[As well as full text articles, Europe PMC contains all of  
the 25.4M PubMed abstracts, plus additional content comprising a further
5M  
records composed of a number of things, including biological patents.
Find out  
more
[here](http://europepmc.org/Help#whatserachingEPMC).]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[2.  29% of articles published in 2014 are now  
available as full text or \#openacess 
<http://europepmc.org/search?query=%28FIRST_PDATE:%5B2014-01-01+TO+2014-12-31%5D%29&page=1>  
\#OAweek
\#OAinNumbers]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[This compares to less than 7% in 2001. In particular the  
open access subset (which as well as being free to read, is free of
some  
copyright and licensing restrictions) has grown enormously: from less
than 1%  
of articles published in 2001 to over 19% published in
2014.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[3.  #EuropePMC is supported by 27 Europe-based  
research funders, who fund research around the world \#OAweek
\#OAinNumbers]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[See who they are and find links to their open access  
policies
[here](http://europepmc.org/Funders/).]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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| [![](https://4.bp.blogspot.com/-d7P2SvRZmok/Vinm1R65ByI/AAAAAAAAAZ8/puXqMOFsYUI/s320/shutterstock_131784386_Numbers%2Bfalling_megainarmy.jpg){decoding="async" loading="lazy" border="0" height="240" width="320"}](http://4.bp.blogspot.com/-d7P2SvRZmok/Vinm1R65ByI/AAAAAAAAAZ8/puXqMOFsYUI/s1600/shutterstock_131784386_Numbers%2Bfalling_megainarmy.jpg){style="margin-left: auto; margin-right: auto;"} |
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[4.  54,487 -- the number of grants awarded by  
\#EuropePMC funders accessed via the Grant Lookup tool
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif; text-indent: -18pt;"}[http://europepmc.org/GrantLookup/](http://europepmc.org/GrantLookup/){style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif; text-indent: -18pt;"}[  
\#OAweek
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[That's a lot of
funding!]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[5.  UKPMC launched on 8 January 2007, rebranded to  
\#EuropePMC 1 November 2012 \#OAweek
\#OAinNumbers]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[When we launched it was with 8 UK-based funders. Now those  
initial 8 have been joined by a further 19 (more if you count those who
have  
since merged), and include a growing number of funders from across
Europe.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[6.  Since we started 12,279 full text author  
manuscripts have been uploaded -- 2,128 are in the \#openaccess subset
\#OAweek  
\#OAinNumbers]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[Europe PMC is effectively a green and gold repository in  
that both routes to open access are supported for full text content to
get into  
Europe PMC. Most comes via the publisher ('gold') route to PMC from
where it is  
mirrored to Europe PMC. The repositories also have their own
manuscript  
submission systems, which enable authors to use the 'green' route and
archive  
their articles directly, if the work was funded by one of our funders.
Any  
content generated via this route is mirrored back to PMC and vice
versa.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[7.  1,892,647 articles are associated with one or  
more ORCIDs
<http://europepmc.org/search?page=1&query=AUTHORID_TYPE:ORCID&sortby=Relevance>  
\#OAweek
\#OAinNumbers]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[You can use the Europe PMC author-claiming tool to [link your articles
to your ORCID](http://europepmc.org/Help#linktoORCID).  
If you have a common name or have changed your name this is a great way
to make  
sure your articles are easily identified as
yours.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[8.  20 Accession types linked in \#EuropePMC
<http://europepmc.org/Help#databasecitations>  
\#OAweek
\#OAinNumbers]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[Accession types are text-mined so that when they appear in an  
article a link is created directly to the relevant data record in
external  
databases including ArrayExpress, Ensembl, the EU Clinical Trials
Register and  
Treefam.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[9.  #EuropePMC searches abstracts & full text, &  
covers more content. E.g. Alzheimer 100K results Europe PMC vs 80K
PubMed  
\#OAweek
\#OAinNumbers]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[Enough said! But check out tweet 1 if you want a reminder of  
that
content.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[10. 3 ways to create or sign in to a \#EuropePMC  
account: ORCID id, Twitter or Europe PMC-specific login \#OAweek
\#OAinNumbers]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[Don't waste time typing in the same searches each week, save  
your searches instead so that you can easily check what new content has
been  
added to Europe PMC. More great features planned for user accounts
coming
soon!]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[Stay in touch with what's happening at Europe PMC by  
following us on Twitter
[@EuropePMC_News](https://twitter.com/EuropePMC_news){target="_blank"
rel="noopener"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
:::
:::


[For Open Access week 2015, we tweeted some number-related facts about Europe PMC, reproduced with a little additional context here.]{style=“font-family: "helvetica neue" , "arial" , "helvetica" , sans-serif;”}  [ ]{style=“font-family: "helvetica neue" , "arial" , "helvetica" , sans-serif;”}  [1.  #EuropePMC has over 3,447,632 full text articles, with over 1,134,397 in the #openaccess subset ]{style=“font-family: "helvetica neue" , "arial"

#OAweek 2015: Open access in numbers

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[Europe PMC does lots of  
things in the Open Access arena. For Open Access week 2014, we
summarised some of them in a series of tweets over the course of the
week. They  
are gathered together
here:]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

  
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width="480"}](http://4.bp.blogspot.com/-6zRUh2IFT1M/VEn_pxv07tI/AAAAAAAAAVQ/T12oa5jv-vk/s1600/Tweet%2B1.jpg){style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"}
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[2. Articles in ~~\#~~EuropePMC in the ~~\#~~openaccess set:
[http://europepmc.org/search?query=%28OPEN_ACCESS:y%29&page=1
...](http://t.co/u4H735Ljfw "http://europepmc.org/search?query=%28OPEN_ACCESS:y%29&page=1"){expanded-url="http://europepmc.org/search?query=%28OPEN_ACCESS:y%29&page=1"
dir="ltr" rel="nofollow noopener" target="_blank"}
~~\#~~OAfact ~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
3. Textminers: Access the full text ~~\#~~openaccess subset from
~~\#~~EuropePMC via the FTP site [http://europepmc.org/FtpSite
](http://t.co/gd2thkboj3 "http://europepmc.org/FtpSite"){expanded-url="http://europepmc.org/FtpSite"
dir="ltr" rel="nofollow noopener" target="_blank"} ~~\#~~OAfact
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[4. ~~\#~~EuropePMC has 26 European funders with ~~\#~~openaccess
policies [http://europepmc.org/Funders/
](http://t.co/Vsy4m8aPDU "http://europepmc.org/Funders/"){expanded-url="http://europepmc.org/Funders/"
dir="ltr" rel="nofollow noopener" target="_blank"} ~~\#~~OAfact
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

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width="480"}](http://2.bp.blogspot.com/-mUdfPwZf3Yw/VEoBMc2NldI/AAAAAAAAAVc/Z_IKG_uduww/s1600/Tweet%2B5.jpg){style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"}
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[6. Details of Grants awarded by the ~~\#~~EuropePMC Funders are openly
available for download via API: [http://plus.europepmc.org/GristAPI/
](http://t.co/5vpWOV40my "http://plus.europepmc.org/GristAPI/"){expanded-url="http://plus.europepmc.org/GristAPI/"
dir="ltr" rel="nofollow noopener" target="_blank"} ~~\#~~OAfact
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[7. Charities combine to create the Charity Open Access Fund (COAF);
articles published are available from ~~\#~~EuropePMC ~~\#~~OAfact
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[8. ~~\#~~EuropePMC is a green and gold ~~\#~~openaccess repository
[http://EuropePMC.org
](http://t.co/hIZo59XKT0 "http://EuropePMC.org"){expanded-url="http://EuropePMC.org"
dir="ltr" rel="nofollow noopener" target="_blank"} ~~\#~~OAfact
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[9. ~~\#~~openaccess is for life for all, not just for a limited period
or for the lucky few ~~\#~~OAfact ~~\#~~EuropePMC
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[10. ~~\#~~EuropePMC directly links articles to related data we find in
the ~~\#~~openaccess full text ~~\#~~OAfact
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[11. ~~\#~~EuropePMC articles and records are enriched by external links
to other relevant content including PE summaries, data ~~\#~~OAfact
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[12. ~~\#~~openaccess articles about ~~\#~~openaccess on
~~\#~~EuropePMC, e.g. [http://europepmc.org/articles/PMC3226455
...](http://t.co/HYYyZBFT8c "http://europepmc.org/articles/PMC3226455"){expanded-url="http://europepmc.org/articles/PMC3226455"
dir="ltr" rel="nofollow noopener" target="_blank"} \|
[http://europepmc.org/articles/PMC3465200
...](http://t.co/ZtcTqo7109 "http://europepmc.org/articles/PMC3465200"){expanded-url="http://europepmc.org/articles/PMC3465200"
dir="ltr" rel="nofollow noopener" target="_blank"} ~~\#~~OAfact
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

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[![](https://3.bp.blogspot.com/-aL8uxpCAYMM/VEoCv2CgS3I/AAAAAAAAAVk/o5zHLCfjnA8/s1600/Tweet%2B13.jpg){decoding="async"
loading="lazy" border="0" height="172"
width="480"}](http://3.bp.blogspot.com/-aL8uxpCAYMM/VEoCv2CgS3I/AAAAAAAAAVk/o5zHLCfjnA8/s1600/Tweet%2B13.jpg){style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"}
:::

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[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[14. Full text XML, high-res figures and supplemental data of OA
articles via web services: [http://europepmc.org/RestfulWebService
...](http://t.co/FLkFPraCzz "http://europepmc.org/RestfulWebService"){expanded-url="http://europepmc.org/RestfulWebService"
dir="ltr" rel="nofollow noopener" target="_blank"} ~~\#~~OAfact
~~\#~~EuropePMC
~~\#~~OAweek2014]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

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[[![](https://3.bp.blogspot.com/-97l3I9hh2hE/VEoHZWrX2EI/AAAAAAAAAVw/GalsjUBFd30/s1600/Tweet%2B15.jpg){decoding="async"
loading="lazy" border="0" height="106"
width="480"}](http://3.bp.blogspot.com/-97l3I9hh2hE/VEoHZWrX2EI/AAAAAAAAAVw/GalsjUBFd30/s1600/Tweet%2B15.jpg){style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
:::

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[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[16. [Search for articles with a clear CC-BY  
licence:
]{style="text-indent: -18pt;"}[http://europepmc.org/search?scope=fulltext&page=1&query=%28LICENSE%3A%22CC-BY%22%29](http://europepmc.org/search?scope=fulltext&page=1&query=%28LICENSE%3A%22CC-BY%22%29){style="text-indent: -18pt;"}[
]{style="text-indent: -18pt;"}[\#OAfact \#EuropePMC  
\#OAweek2014]{style="text-indent: -18pt;"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="text-indent: -18pt;"}  
[17. [\#EuropePMC now has \#openaccess books as well as articles,
patents, clinical guidelines and more \#OAfact  
\#OAweek2014]{style="text-indent: -18pt;"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="color: red; text-indent: -18pt;"}  
[18. [You saw it here first: \#A2Ucomp launches  
again Nov -- entrants write PE summaries of \#openaccess \#EuropePMC
articles ]{style="text-indent: -18pt;"}[\#OAfact
\#OAweek2014]{style="text-indent: -18pt;"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

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:::

[We'd love to  
hear from you about how these Open Access resources are useful to
you.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[To stay up-to-date with  
Europe PMC news you can  follow us on
Twitter [@EuropePMC_news](https://twitter.com/EuropePMC_news)]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
:::
:::


[Europe PMC does lots of things in the Open Access arena. For Open Access week 2014, we summarised some of them in a series of tweets over the course of the week.

Europe PMC Open Access Facts: a celebration of all things Open Access for #OAweek2014

::: {dir="ltr" style="text-align: left;"}
[*[This post is by our guest,
Dr]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[  
Stephen Pinfield, a Senior Lecturer in the Information School at the
University  
of Sheffield. [[*In this post he introduces us to his recent paper
'Medical research charities and open access' where he reports on a
survey he carried out to assess the Open Access (OA) policies and
activities of medical research charities in the UK, including several of
the Europe PubMed Central (Europe
PMC) funders.*]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}*]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[[[Open]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
access has come a long way in the last decade and the funders of
medical  
research have often been at the forefront of developments. However in
the last  
two years there has been a heightening of the OA debate internationally,
as  
many funders have strengthened their positions on OA and as OA has begun
to  
enter the mainstream of research communication for many disciplines. In
the UK,  
the Finch Review and the Research Councils UK OA policy, and in the USA,
the  
Federal Fair Access to Science and Technology Research bill and the
Office of  
Science and Technology Policy OA policy memorandum, are examples of  
developments that have increased the momentum towards the
'mainstreaming' of  
OA.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}

  

::: {style="margin: 0cm 0cm 0pt;"}
[[In  
this context, and following discussions with Europe PMC and the  
Association of Medical Research Charities, I decided to carry out some
research  
to assess the OA policies and activities of medical research charities
in the  
UK. How are they responding to recent developments? What do they see as
the  
main opportunities and challenges? Where are they taking their
organisational  
policies?]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}
:::

::: {style="margin: 0cm 0cm 0pt;"}
[[I  
asked these and related questions in a survey of UK AMRC and Europe
PMC  
members, and received some very interesting responses. There is clearly
a lot  
going on and some of this is described in an article recently published
(and  
available in open-access form) in the journal *Learned
Publishing*.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}
:::

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loading="lazy" border="0" height="266"
width="400"}](http://3.bp.blogspot.com/-8S08b8JsUeo/UmFZw4we0EI/AAAAAAAAAIk/aE1zoeu5HXU/s1600/shutterstock_128925893.jpg){style="margin-left: 1em; margin-right: 1em;"}
:::

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[[]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif; font-size: xx-small;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}

shutterstock_128925893
:::

::: {style="margin: 0cm 0cm 0pt;"}
[[The  
results presented in the paper show that OA is an important issue for
many  
medical research charities and a large number already have or are
developing  
policies which encourage OA. Some clearly see OA as a really important
way of  
getting the research they fund out there and used. Trends on a wide
range of  
issues from compliance monitoring to licensing are also discussed in the
paper,  
providing a snapshot of the current state of play in the
sector.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}
:::

::: {style="margin: 0cm 0cm 0pt;"}
[[However,  
there are concerns. In particular, there are concerns about costs and
resource  
requirements to support OA. Some of the data presented in the paper
provides  
provisional evidence of the size of the cost challenge for different  
organisations. "Provisional" because what the article illustrates  
amongst other things is the need for more and better data in this area
to help  
create a reliable evidence base to inform policy development. There is
still some  
way to
go.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}
:::

::: {style="margin: 0cm 0cm 0pt;"}
[[Of  
course, the debate currently happening amongst medical research
charities in  
many respects reflects wider debates about OA: Gold versus Green, IPR,
roles  
and responsibilities and so on. However, medical research charities have
an  
important perspective on the discussion and can make a valuable
contribution to  
it. I hope this research helps to get their voices
heard.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"calibri\" , \"sans-serif\";"}
:::

::: {style="margin: 0cm 0cm 0pt;"}
:::

::: {style="margin: 0cm 0cm 0pt;"}
[[Pinfield, S (2013). Medical Research charities and open access.
*Learned Publishing,* **26(4),** 285-302. doi:
10.1087/20130409 <http://dx.doi.org/10.1087/20130409>]{style="font-family: \"arial\";"}]{style="font-family: \"calibri\" , \"sans-serif\";"}
:::

  
[*Stephen teaches on several postgraduate programmes and pursues
research in a number of issues including scholarly communications
(particularly OA), research data management, and information strategy.
Before becoming an academic, Stephen was for 23 years an information
professional, latterly Chief Information Officer at the University of
Nottingham where he managed a converged library and IT services
Department. At Nottingham, he was founding Director of the Centre for
Research Communications, which runs a number of OA-related services,
such as SHERPA RoMEO, and carried out research and development projects
in various areas of scholarly practice and communication futures.
Stephen has been active for a number of years in OA developments at
institutional, national and international
levels.*]{style="font-family: \"arial\";"}
:::


[
<em>
 [This post is by our guest, Dr]{style=“font-family: "helvetica neue" , "arial" , "helvetica" , sans-serif;”}[[ Stephen Pinfield, a Senior Lecturer in the Information School at the University of Sheffield.
</em>

Medical research charities and Open Access

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[To start, I should say that all at Europe PMC support Open  
Access. This is just a short list of some issues that can be
frustrating...]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

  

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[[[1.[    ]{style="font-size-adjust: none; font-stretch: normal; font: 7pt/normal \"Times New Roman\";"}]{style="mso-list: Ignore;"}]{style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"}The
often incorrect definition of green and gold  
routes to Open
Access]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[I am a relative newcomer to Open  
Access having only been working in this area for a couple of years.
Before that  
I was a research scientist, and the movement had largely passed me by,
with the  
exception of noticing that I didn't have to click through the university
journal  
subscription pages to download some
articles.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[Having said that, I have now lost  
count of the number of meetings I've been to about Open Access where
the  
introduction has included an incorrect definition of the distinction
between  
green and gold open access. 'Green' often gets described as free,
whereas  
'gold' you have to pay for. I've already said that I'm a newbie in this
area,  
so I will refer you to Peter Suber's
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[Open
Access](http://cyber.law.harvard.edu/hoap/Open_Access_(the_book))]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[  
for a definitive
explanation.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[In brief, green is self-archiving  
in a repository and gold is open access delivered by journals. There may
be  
associated costs, but that is not the defining
difference.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[[[2.[    ]{style="font-size-adjust: none; font-stretch: normal; font: 7pt/normal \"Times New Roman\";"}]{style="mso-list: Ignore;"}]{style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"}The
constant argument between Open Access  
advocates about which route, green or gold, is
best.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[It is an important discussion, but sometimes it can diminish the
central  
message about the
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[benefits
of Open
Access](http://blogs.rcuk.ac.uk/2012/08/10/the-benefits-of-open-access/)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[
-- some of which are being highlighted this week by the [[[Accelerating
Science Award Program](http://asap.plos.org/)]{style="color: blue;"}
(ASAP) which recognises individuals who have applied  
scientific research -- published through Open Access -- to innovate in
any field  
and benefit society.]{lang="EN-US"
style="mso-ansi-language: EN-US;"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[Crucially, Europe PMC enables both green and gold routes to Open
Access.  
So, researchers (or their
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[funders](http://europepmc.org/Funders/)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[)  
can choose which route to use -- most funders offer the flexibilty of
both
routes.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[Of course, it's more complicated than that, as the 'choice' is often  
affected by publishing options, for example. But, just for today, the
simple  
take-home message is that you can go 'green' using the Manuscript
Submission  
Service via
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[Europe
PMC
plus](http://plus.europepmc.org/)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[,
or 'gold'  
by publishing Open Access with a publisher who deposits their contents
or  
individual Open Access articles with us (you can find out more on the
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[journal
list](http://europepmc.org/journalList)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[).]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[  
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  

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[[[3.[    ]{style="font-size-adjust: none; font-stretch: normal; font: 7pt/normal \"Times New Roman\";"}]{style="mso-list: Ignore;"}]{style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"}That
Open Access can be so much
effort!]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[In theory it's a matter of a few  
mouse clicks to make an article Open Access, but in reality a researcher
needs  
to understand the impact that funder, institutional and publisher Open
Access  
policies can have on each other.[  ]{style="mso-spacerun: yes;"}And  
they already have enough to do carrying out their
research.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[We know that the current system  
is not perfect, and that the researcher is usually the one at the
receiving end  
of sometimes conflicting advice in this area. We don't have a solution
just  
yet, but hopefully it's worth sharing that the 24
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[Europe
PMC
funders](http://europepmc.org/Funders/)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[
are talking to each  
other, and to publishers and institutions to try and reach agreements
that will  
make things easier on researchers in the future. These conversations can
take  
time, but they are
happening.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[![](https://1.bp.blogspot.com/-BoEPh1lh-GE/Ul5Yh-xZH5I/AAAAAAAAAIY/3W7WhjZpvug/s400/shutterstock_127171886.jpg){decoding="async"
loading="lazy" border="0" height="277"
width="400"}](http://1.bp.blogspot.com/-BoEPh1lh-GE/Ul5Yh-xZH5I/AAAAAAAAAIY/3W7WhjZpvug/s1600/shutterstock_127171886.jpg){style="margin-left: 1em; margin-right: 1em;"}
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::: {style="margin: 0cm 0cm 10pt 18pt; text-align: center;"}
[shutterstock_127171886]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif; font-size: xx-small;"}
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[]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

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[[[4.[    ]{style="font-size-adjust: none; font-stretch: normal; font: 7pt/normal \"Times New Roman\";"}]{style="mso-list: Ignore;"}]{style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[This
next one is not an irritation with Open  
Access, but with the mis-guided conflation of Open Access with poor or
no peer  
review.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[This reared its head again only a few weeks ago in a
(non-peer-reviewed)
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[article](http://www.sciencemag.org/content/342/6154/60.full)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[
published  
by Science where the author had submitted a spoof paper to a sub-set of
Open Access journals. His conclusion was that there is 'little or no
\[peer review\] scrutiny' at many open access journals'. Others have
already made a far better job than I could of  
addressing the flaws in the design and conclusions described in that
article,  
for example,
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[here](http://www.theguardian.com/higher-education-network/blog/2013/oct/04/science-hoax-peer-review-open-access?CMP=twt_gu)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[  
and
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[here](http://im2punt0.wordpress.com/2013/10/04/science-mag-sting-of-oa-journals-is-it-about-open-access-or-about-peer-review/)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[.
My impression from comments on Twitter and blogs is that there is  
generally agreement that the research calls into question the integrity
of the  
peer review system, and is nothing to do with Open Access (beyond the
fact that  
the only journals included in the study were Open Access). In fact, some
Open  
Access publishers are taking the lead in trying to address some of the
problems  
long-associated with the peer review process, such as
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[eLife](http://elife.elifesciences.org/content/2/e00799)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[
and the Nature
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[Frontiers](http://www.frontiersin.org/about/reviewsystem)]{style="color: blue; font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[
series of  
journals.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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Last, and by no means least:  
[]{style="font-family: \"arial\";"}

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[[[5.[    ]{style="font-size-adjust: none; font-stretch: normal; font: 7pt/normal \"Times New Roman\";"}]{style="mso-list: Ignore;"}]{style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"}Articles
about Open  
Access that are not themselves Open
Access.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

 
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[I  
know I'm not the only person to find this odd/frustrating/completely  
counter-intuitive. But, really? Is it some kind of elaborate joke on the
part  
of the
authors?]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[To read about some more frustrations with Open Access, this time from
the perspective of a science librarian dealing with Open Access content,
I recommend reading this post (['How open is
it?](http://britishlibrary.typepad.co.uk/science/2013/10/how-open-is-it.html)')
by Elizabeth Newbold at the British Library -- we sit near to each
other, so it's been interesting comparing notes this
week!]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[There are a lot of exciting things happening during Open Access  
week (21-27 October 2013). I hope everyone has a good week, whatever
they're  
doing and wherever they are in the
world.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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[I will be busy getting ready to launch our science-writing  
competition, Access to Understanding 2014, in partnership with the
British  
Library. Look out here and on Twitter
[@EuropePMC_news](https://twitter.com/EuropePMC_news) in November for
further  
announcements.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
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﻿
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[To start, I should say that all at Europe PMC support Open Access. This is just a short list of some issues that can be frustrating…]{style=“font-family: "helvetica neue" , "arial" , "helvetica" , sans-serif;”}  [1.[    ]{style=“font-size-adjust: none; font-stretch: normal;

Messaggi di Rogue Scholar

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Medical research charities and Open Access

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