New literature API: Europe PMC Annotations

Europe PMC annotations API provides programmatic access to annotations text-mined from biomedical abstracts and open-access, full-text articles in Europe PMC.

New literature API: Europe PMC Annotations

14 Nov 2017 - 16:02

We are excited to announce the launch of our Literature Annotations API, which provides programmatic access to targeted information text-mined from millions of biomedical abstracts and open-access, full-text articles in Europe PMC. Users can now retrieve, for example, all mentions of a particular chemical entity found in the Results section of all papers, or all articles that discuss involvement of a specific gene or protein in their disease of interest.

How it works

Europe PMC hosts a community annotation platform that consolidates text-mined annotations from various contributors, including the SIB Swiss Institute of Bioinformatics, DisGeNET, Open Targets Platform, IntAct, NaCTEM and Europe PMC's own text-mining pipeline.

The platform provides several annotation types, such as core named entities (gene/protein names, organisms, diseases, chemicals, Gene Ontology terms, and accession numbers), biological events (phosphorylation) and functions (gene function). It also provides functional relations (gene–disease associations and protein–protein interactions).

What you can retrieve

Annotations API allows you to retrieve:

  • Any annotations contained in the selected list of articles.
  • Annotations of articles that have at least one annotation that tags a specific entity (e.g. NRGN, metformin, or cancer)
  • Annotations of article that have two entities that relate to each other, for example in a gene-disease relationship (e.g. NRGN-schizophrenia)
  • Annotations contributed by a specific provider (e.g. Open Targets)
  • Annotations of a specific type (e.g. organisms)
  • Annotations found in a specific article section (e.g. “Materials and Methods”).

How you can combine parameters

Users can combine a number of parameters (e.g. annotation type, annotation provider, or article section) to specify their query.

The filter parameter allows you to switch between two options: retrieving only specified annotations for each article, or retrieving all the annotations limited to the list of articles that contain the specified annotation.

Output formats

Output formats include XML, ID_LIST, JSON and JSON-LD, which produces a linked data representation of the annotations for annotations exchange across different platforms, making it easier to consume the data.

Your feedback welcome

We hope the new Annotation API will enable a wider community of biomedical scientists to capitalise on the results of text-mining to benefit their own research. We are always looking to improve our services, so your feedback is warmly welcome. If you would like to post your feedback or receive notifications about API releases in the future you can join Europe PMC developers group.

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