Europe PMC in 2017

Abstract

Europe PMC (https://europepmc.org) is a comprehensive resource of biomedical research publications that offers advanced tools for search, retrieval, and interaction with the scientific literature. This article outlines new developments since 2014. In addition to delivering the core database and services, Europe PMC focuses on three areas of development: individual user services, data integration, and infrastructure to support text and data mining. Europe PMC now provides user accounts to save search queries and claim publications to ORCIDs, as well as open access profiles for authors based on public ORCID records. We continue to foster connections between scientific data and literature in a number of ways. All the data behind the paper - whether in structured archives, generic archives or as supplemental files - are now available via links to the BioStudies database. Text-mined biological concepts, including database accession numbers and data DOIs, are highlighted in the text and linked to the appropriate data resources. The SciLite community annotation platform accepts text-mining results from various contributors and overlays them on research articles as licence allows. In addition, text miners and developers can access all open content via APIs or via the FTP site.

Figure 1.

Searching for authors in Europe PMC. If the name of the author in the search query matches a name on an ORCID record in Europe PMC, the user will see a ‘Suggested Authors’ box on top of their results list. The box will provide additional information about the author, such as affiliation (if available), number of publications and citations, to help the user decide if this was the researcher they were looking for.

Figure 2.

Affiliation information display. Affiliation information can be found on the publication abstract under the list of authors. Users can select an individual affiliation, which then highlights the names of the authors affiliated with that particular institution.

Figure 3.

Author profiles in Europe PMC. An author profile showcases published works of a given author with an ORCID in Europe PMC. (A) The publication graph combines a bar chart, representing the number of publications per year, and a line graph, which shows the number of citations per year. Open access publications are highlighted in blue, with articles for which free full text is available depicted in light blue, and articles licensed for reuse represented with a darker shade. (B) The publication list includes all articles in Europe PMC claimed to the author's ORCID record. For any given publication we display citation counts along with a graph showing citation count per year. The list can be sorted by ‘date’ or ‘times cited’.

Figure 4.

Author profile links on abstract pages in Europe PMC. Users will see a popup menu when clicking on the author's name in the list. The menu will contain a link to the author's profile and ORCID record, along with additional search options.

Figure 5.

User accounts in Europe PMC. Users can sign into Europe PMC to save their searches. To create an alert about new publications matching a query it is possible to set up a customised RSS feed based on a saved search by clicking on the RSS icon next to the search results.

Figure 6.

SciLite annotations in Europe PMC. Text-mined terms can be highlighted in the publication text using the SciLite annotations tool. (A) The annotations menu enables the user to highlight a selection of colour-coded annotations in the text (PMCID:PMC2430719). (B) To see a list of individual terms, users may click on the right arrow next to the annotation type. A selection of terms found most frequently in the text appears, together with up/down navigation buttons, which allow the user to jump to selected terms in the text. (C) An entire sentence is highlighted for gene–disease associations and protein–protein interactions. In case of overlapping annotations it is possible to view the annotation types appearing under the same highlight by selecting the annotation of interest in the popup box (PMID:11431700). (D) Clicking on the highlighted terms in the text opens a popup box with information about the given annotation, including a link to related database record, the source of the annotation, and the feedback link. In some cases, the popup will also contain a visual data preview, for example the menu for the annotated Protein Data Bank accession number will display an interactive thumbnail of the macromolecular structure (PMCID:PMC4014462).