News blog

Updates from Europe PMC, a global database of life sciences literature

Europe PMC team

 | 9 September 2016


SciLite Annotations

Manual curation is vital for maintaining quality information in biological databases. However, with the exponential growth in biological data this approach is both challenging and time consuming. We wanted to create a scalable and sustainable process which could complement manual curation.   

We recently launched a new service – SciLite – that allows text-mined annotations to be displayed on research articles. The aim of this effort is to promote sustainability of curated databases by bridging the gap between literature and data. To this end, SciLite:

  • supports database curation processes, by highlighting biological concepts, making it easier to find key concepts described in articles;
  • provides a mechanism to link those concepts to the related resources, for efficient data integration. 

SciLite’s open design enables community-driven annotations, from text-mining groups, and manual annotations, to be made available to Europe PMC users.

What are SciLite annotations?

SciLite annotations enable biological terms and concepts, such as genes/proteins, diseases, organisms and accession numbers, to be highlighted on full text articles in Europe PMC. Using the check-boxes on the right-hand side of article pages, readers can select the types of concepts that they are most interested in and matching annotations for that article will be highlighted on the article text as below. 

Clicking on the highlighted terms in the text opens a popup with a link to related database record. In the example below, an interactive Protein Data Bank (PDB) structure model is also provided when you click on a highlighted PDB accession number.

When annotations are provided by the text-mining community, the source of the annotation is displayed. In the example below, the Gene Reference into Function (GeneRIF) annotations were provided by the Text Mining group at HES-SO, Geneva, Switzerland.

Another text-mining group – NaCTeM – has provided phosphorylation event annotations, as shown below.

Take a look at this example article with annotations.

Annotations are displayed on articles with a CC-BY, CC-BY-NC or CC-0 license.

How are annotations generated?

The biological terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. Any text-mining group can participate in this scheme. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model, and stored in a triple store via the EMBL-EBI RDF Platform. If you are a text miner, find out how to provide annotations to Europe PMC at our SciLite annotations page.

We’re improving annotations with your help

Because annotations are generated automatically by text mining algorithms, we want to ensure that annotations are useful to users of Europe PMC. On each annotation there is the opportunity to provide feedback by either marking the annotation as incorrect, or endorsing useful annotations.
Screenshot showing feedback feature for an annotation
This information is fed back to the Europe PMC team and will be acted upon, helping to improve the annotations overall.

Post a comment

I agree to the limited use of my personal data as described in the Europe PMC advanced user services privacy policy.

Creative Commons Licence
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Subscribe to the Europe PMC News blog to receive the latest updates

This website requires cookies, and the limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice and cookie policy.

Partnerships & funding

Europe PMC is a service of the Europe PMC Funders' Group, in partnership with EMBL’s European Bioinformatics Institute (EMBL-EBI); and in cooperation with the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NCBI/NLM) . It includes content provided to the PubMed Central (NLM/PMC) archive by participating publishers.