Europe PMC Team

[This month, Europe PMC released a new version of
]{style="font-family: Arial; font-size: 11pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;"}[[SciLite]{style="color: #1155cc; font-family: Arial; font-size: 11pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;"}](http://blog.europepmc.org/2016/09/scilite-annotations.html){style="text-decoration: none;"}[,
a powerful tool for highlighting annotations in life sciences
publications. SciLite is powered by the Europe PMC annotation platform
via the open
]{style="font-family: Arial; font-size: 11pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;"}[[annotation
API]{style="color: #1155cc; font-family: Arial; font-size: 11pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;"}](https://europepmc.org/AnnotationsAPI){style="text-decoration: none;"}[,
which provides access to over 1.3 billion annotations. Highlighting
annotations in the text enables users to easily scan the article and
locate key biological entities, such as genes/proteins, accession
numbers, protein interactions, diseases, gene-disease relationship and
more.]{style="font-family: Arial; font-size: 11pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;"}

[[![](https://lh3.googleusercontent.com/EfI4L3T2vEPdEX-k-cbMkaimLxWfyBWjOGV_O-DXoTEDNVZkQYWK_hPBrq6pRFkUv0BOXXnbHGY4X05krDX3068iUznN9WRgDW3NDctT6Sqm0IuejneyuZ6oNUuofRpNSG-aHksw){decoding="async"
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[SciLite annotations has been redesigned to improve the speed of
information retrieval and assist scientists and database curators
]{style="font-family: Arial; font-size: 11pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;"}[to
scan articles, extract facts and evidence from the biomedical
literature, as well as locate the primary data cited in a given
publication.
]{style="background-color: white; color: #1d1c1d; font-family: Arial; font-size: 11.5pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;"}[Imagine
yourself being able to locate and quickly visualise a protein structure
of your interest on a single page! This is how SciLite helps with
speeding scientific
discovery.]{style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;"}

[Annotations can be accessed via the 'Annotations' option on the
right-hand side on the article page. Clicking on 'Annotations' opens a
new panel and selected terms will be highlighted in the text of the
article. Notice that annotations can only be highlighted on articles
with an open access
license. ]{style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;"}

[[![](https://lh6.googleusercontent.com/N3keOWTbirOq2SaoVoQI91zZIjDWTh33xQbrrVKo0wIm9AGqUwmIHqzweJwayXBVFBhpvQt_42O8I7CcNAHVxOp36I_28kf5EJ5DGcrjVmv2-ZgZUHlzR3TjAYDAfBgJDFC1HRBm){decoding="async"
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[  
]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}

[The new SciLite version includes new annotation types, a new annotation
panel interface and new features. Annotation types now include cell,
cell lines, clinical drugs, molecular processes, organ tissues, pathway,
anatomy and phenotype. The new panel offers easy navigation through
annotations and displays a popup window with a quick link to relevant
data
resources.]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}

[  
]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}

[[![](https://lh4.googleusercontent.com/QpDypc_CAwBmDI3e3EpkPwyVgXzI5JUOBhXz_bVCYElc6O8k8fTX_ibYMuDmmR2_mbbWf5ziFf-bOWg--4_GILCFLn5pE55l6z0umbJiGFnP76GWlnBs1_QUOg5W01Gtcs1xwyls){decoding="async"
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[Additionally, the new version offers a chemical structure viewer.
Readers are able to visualise protein and chemical structures in the
annotation panel as well as in the highlighted
text.]{style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;"}

[[![](https://lh5.googleusercontent.com/KuxmD_NkJIVDPUIXrhe7hMA1lnMXDcdBzHXoNL3yeEgqpPhFcbpwlqKdwlD22Rt3snlZpDid9aKH1mIoKvQl8TTrqHc7NsTsEfDjsDZkRU2ylaoHuY4BVEESB0m-ztNC9JDb68JO){decoding="async"
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width="602"}]{style="border: none; display: inline-block; height: 817px; overflow: hidden; width: 602px;"}]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}

[Highlighted annotations display links to relevant database records
enabling users to locate the primary data in the text by linking text
mined and curated bioentities to public life sciences databases.
Additionally, the new improvements include options to endorse, report
errors or share the annotation via a linkback
URL.]{style="font-family: Arial; font-size: 11pt; white-space: pre-wrap;"}

[[![](https://lh5.googleusercontent.com/fWd9txA8kPgc0GbYzYruvMOyYLOv3oq3fId_jIzvD1E2fEyummvCm-c4o16kwt2XyutfWT7maFVKxO4t9a37TTPXDVsIDyPFnh5u5i0dOK-u2lSW3CbAJl0Mje8A_OjBsyVScRAu){decoding="async"
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width="602"}]{style="border: none; display: inline-block; height: 387px; overflow: hidden; width: 602px;"}]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}

[Identifying a plethora of complex biological terms and concepts in
publications was made possible due to a successful partnership with a
variety of text mining groups that use text mining algorithms to
identify different types of biological entities, and
]{style="font-family: Arial; font-size: 11pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;"}[enable
text miners to showcase their work to a wider public via SciLite
annotations.]{style="font-family: Arial; font-size: 11.5pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;"}[ ]{style="font-family: Arial; font-size: 11pt; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;"}

[Europe PMC acknowledges all the annotation providers for cooperating
towards submitting their annotations and
]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}[welcomes
new contributions from text-mining and curation communities to share
annotations via the
]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11.5pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}[[annotations
submission
service]{style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 11.5pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;"}](https://europepmc.org/AnnotationsSubmission){style="text-decoration: none;"}[.
Europe PMC would also like to thank all the participants who took part
in usability sessions, to test and feedback on the improvements to the
Scilite Annotations
tool.]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11.5pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}

[  
]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11.5pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}

[Want to know more about SciLite, annotation APIs or submitting
annotations? Get in touch with
]{style="background-color: transparent; color: black; font-family: Arial; font-size: 11pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}[[annotations@europepmc.org]{style="background-color: white; color: #1155cc; font-family: Arial; font-size: 11.5pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration-skip: none; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;"}]{style="text-decoration: none;"}[. ]{style="background-color: white; color: black; font-family: Arial; font-size: 11.5pt; font-style: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-ligatures: normal; font-variant-position: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"}

  


This month, Europe PMC released a new version of SciLite, a powerful tool for highlighting annotations in life sciences publications. SciLite is powered by the Europe PMC annotation platform via the open annotation API, which provides access to over 1.3 billion annotations.

Messages de Rogue Scholar

Announcing the new version of SciLite – the Europe PMC tool for highlighting annotations