Posts in Category: Literature/Data Integration

02 Nov 2020

Europe PMC Text-annotator is now open source

Introducing Text-annotator

Europe PMC has open-sourced Text-annotator, a JavaScript library to locate and annotate plain text in HTML. The annotation process includes:

  1. Search: Search for a piece of plain text in the HTML; on finding it, store its location identified by an index and then return the index for later annotation.

28 Jan 2020

New release: Europe PMC Web Services 6.3

Today Europe PMC released Web Services version 6.3, updating its SOAP and RESTful APIs. Programmatic users can now find more fields available in the core response of these services

Multiple author affiliations

In the previous version, author affiliations were a single value. The new version 6.3 includes a list of multiple affiliations.

28 Jan 2020

Europe PMC API use cases page

Connecting the programmatic user community

Europe PMC makes its open access content and metadata available for building new applications. With a developer tab specially designed for programmatic users and with detailed documentation, the aim is to make it easy to integrate Europe PMC APIs into new services and thereby improve life science research.

16 Oct 2019

PDBe integrates Europe PMC APIs

PDBe exposes literature metadata by integrating Europe PMC REST APIs

PDBe, a member of the Worldwide Protein Bank, is a European resource that maintains a free and publicly available archive of macromolecular structures. The public can easily find information on protein structure and metadata associated with protein structure. PDBe also exposes enriched metadata from other sources such as publications and citations, which are retrieved through Europe PMC APIs.

20 Aug 2019

Europe PMC project for eLife Innovation Sprint

How to find the perfect preprint

The eLife Innovation Sprint is a yearly collaborative hackathon for developers, designers, researchers, technologists, science communicators, and everyone enthusiastic about open science. The premise of the Sprint is simple – the current science publishing system is slow, inefficient and insanely expensive. What we need are open science ideas that could be turned into prototypes to address the challenges we face in science publishing. All Sprint outputs have to be openly available, use open-source licenses for code and software, and permissive licenses (such as CC-BY) for other content.

This year the Europe PMC team will participate in the Sprint with a proposal to improve the discoverability of relevant scientific preprints. Dayane Araujo (Technical Outreach Officer) and Michael Parkin (Data Scientist) will be working on a tool to sort through ~80,000 life science preprints, and they need your help.

04 Jun 2018

Integrating Literature and Data

Data is at the heart of research. Scientific papers describe how data has been obtained, analysed, and what conclusions have been drawn. But it is the data that comprises the essential evidence, which confirms or disproves the original hypothesis. In the life sciences it is essential to look at scientific literature in the context of other publications, the data it builds on and other data linked to the publication. At Europe PMC we have developed a number of features to support data discovery and reuse.

As one of the ELIXIR Core Resources, Europe PMC benefits from excellent links to essential research data hubs located at EMBL-EBI. This helps us interweave publications and data, enriching the graph of research objects, and help researchers discover linked and related data.

The literature-data links come in different forms and shapes. An article might be citing a DOI for a dataset in a repository, or describe a protein structure cited as an accession number for PDBe database. An publication itself might be cited by a database, such as Flybase or even a Wikipedia article. Europe PMC obtains such literature-data links in three ways: