Europe PMC Team

::: {dir="ltr" style="text-align: left;"}
[I have just been to the BioBricks Fondation SB6.0 conference, an
international Synthetic Biology conference, this year hosted in the UK
at Imperial College London. Synthetic Biology is one of the most recent
scientific disciplines, and draws on the themes of nature, science and
engineering 'to connect fields in new ways by improving the process of
taking a new biological design from conception to execution' (from SB6.0
programme: introduction from the executive programme
team).]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
It was a good opportunity to raise awareness of Europe PubMed Central
(Europe PMC), a resource that provides free and open access to
biomedical and life sciences literature, as the synthetic biology
discipline also celebrates openness -- the BioBricks Foundation's
mission is to ensure that research is conducted in an open and ethical
manner to benefit all people and the
planet.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
Being an international conference, the questions posed about
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[Europe
PMC]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}](http://europepmc.org/)[
differed slightly to those asked when
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[I
visit an
HEI]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}](http://blog.europepmc.org/2013/06/why-should-i-use-europe-pmc-isnt-it.html)[,
usually in the UK. Some have asked: 'Why Europe PMC? Why does there need
to be 'another' PubMed?' -- imagine an indignant tone when the question
is
asked!]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}  
[  
So this seemed like a good opportunity to explain, and to set the record
straight that this is done in collaboration with PMC. Essentially,
the [long term goal is to create a network of digital archives that can
share all of their respective locally deposited content with others in
the network. There are three primary reasons for doing
this:]{style="background-color: rgba(255, 255, 255, 0); text-align: left;"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

- [The probablity of an archive surviving over the long term is greater
  if there are working copies of the archive in regular use at multiple
  sites around the
  world.]{style="background-color: rgba(255 , 255 , 255 , 0); font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
- [[A producer or funder of research literature often will be more
  inclined to make the primary deposit of its material to a locally or
  regionally affiliated archive, rather than to one operated elsewhere
  in the world -- *you can find out more about the Europe PMC funders
  [here](http://europepmc.org/Funders/).*]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="background-color: rgba(255 , 255 , 255 , 0); font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
- [Each site can integrate the journal articles in the archive with
  related material, such as national or regional practice guidelines,
  that has particular significance to its
  users.]{style="background-color: rgba(255 , 255 , 255 , 0); font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

[(from [<http://www.ncbi.nlm.nih.gov/pmc/about/pmci/>)]{style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-tap-highlight-color: rgba(26, 26, 26, 0.296875); font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

[]{style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969);"}

::: {style="margin: 0cm 0cm 0pt;"}
[[Having a  
number of instances of the PMC database is modelled on the idea adopted
for genomic data.
The ]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[International
Nucleotide Sequence Database
Collaboration]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}](http://www.insdc.org/)[
comprises the DNA DataBank of Japan (DDBJ), the European Molecular
Biology Laboratory (EMBL), and GenBank at NCBI. These three databases
exchange data on a daily basis, but all three interfaces offer different
functionality that benefit the molecular biology
community.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969);"}
:::

[  
]{style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969);"}

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[Europe PMC offers many additional features that have been informed by
researcher wants and requirements, for
example:]{style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

</div>

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- [[In addition to the PMC full text, Europe PMC also enables you to
  search the PubMed abstracts, biological patents records and
  ]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[more]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}](http://europepmc.org/contentrss)[,
  from a *single* search
  box.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}]{style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
- [Information discovery is streamlined by directly linking out to gene,
  protein and chemical compound databases -- and this list is constantly
  growing.]{style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
- [The citation network provides 'cited by' information for each
  article, and you can now identify highly cited articles by using the
  citation sort
  tool.]{style="-webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

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[Coming
soon:]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

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- [The Europe PMC External Links Service, which will enable people to
  publish links from articles in Europe PMC to related information or
  tools.
  ]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}
- [Incorporation of ORCIDs into Europe
  PMC.]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}

<div>

[Find out more about these new developments on this blog, or by
following us on Twitter
]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}[[@EuropePMC_News]{style="font-family: \"helvetica neue\" , \"arial\" , \"helvetica\" , sans-serif;"}](https://twitter.com/EuropePMC_news)

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:::


I have just been to the BioBricks Fondation SB6.0 conference, an international Synthetic Biology conference, this year hosted in the UK at Imperial College London.

Why do we need &#8216;another&#8217; PubMed?

Stephen Matheson

[[![ResearchBlogging.org](http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png){style="border: 0pt none;"}](http://www.researchblogging.org/)]{style="float: left; padding-bottom: 8px; padding-left: 8px; padding-right: 8px; padding-top: 8px; padding: 8px;"}It
is of course a cliche to state that eukaryotic cells (i.e., cells that
are not bacteria) are complex. In the case of an animal, tens of
thousands of proteins engage in fantastically elaborate interactions
that somehow coax a single cell into generating a unique and magnificent
organism. These interactions are often portrayed as exquisitely precise,
using metaphorical images such as
\'[lock-and-key](http://en.wikipedia.org/wiki/Enzyme){_mce_href="http://en.wikipedia.org/wiki/Enzyme"}\'
and employing [diagrams that resemble subway
maps](https://www.nature.com/documents/nrc_posters_subpathways.pdf){_mce_href="http://www.nature.com/nrc/posters/subpathways/index.html"}.  
  
Many of these interacting proteins are enzymes that modify other
proteins, and many of those enzymes are of a particular type
called [kinases](http://en.wikipedia.org/wiki/Kinase){_mce_href="http://en.wikipedia.org/wiki/Kinase"}.
Kinases do just one thing: they attach phosphate groups to other
molecules. This kind of modification is centrally important in cell
biology, and one way to tell is to look at how many kinases there are:
the [human genome contains about 500 kinase
genes](http://kinase.com/human/kinome/){_mce_href="http://kinase.com/human/kinome/"}.  
  
Now, kinases tend to be pretty picky about who they stick phosphate
onto, and this specificity is known to involve the business end of the
kinase, called the [active
site](http://www.ncbi.nlm.nih.gov/books/NBK26911/figure/A505/){_mce_href="http://www.ncbi.nlm.nih.gov/books/NBK26911/figure/A505/"}.
The active site is (generally) the part of the kinase that physically
interacts with the target and transfers the phosphate. You might think
that this interaction, between kinase and target, through the active
site, would be by far the most important factor in determining the
specificity of kinase function. But that\'s probably not the case.  
[Continue
reading\...](http://sfmatheson.blogspot.com/2011/07/evolution-cheats-or-how-to-get-old.html#more)


It is of course a cliche to state that eukaryotic cells (i.e., cells that are not bacteria) are complex. In the case of an animal, tens of thousands of proteins engage in fantastically elaborate interactions that somehow coax a single cell into generating a unique and magnificent organism.

Rogue Scholar Beiträge

Why do we need ‘another’ PubMed?

Evolution cheats, or how to get an old enzyme to do new tricks