NLP processing of PubMed

Natural Language Processing based on a query to Europe PMC Open Access database.

Europe PMC resources

Europe PMC API documentation

Link to resources:

• Full developer friendly web service guide

A nice video tutorial on the Europe PMC REST API

Link to the video

Rest API search = module to search the publication database. fullTextXML = module to retrieve the full text of Open Access articles.

Creating the query per article type

To search for research-article or review for instance:

From the Europe PMC documentation:
User query. Possible options are:

• a keyword or combination of keywords (e.g. HPV virus).
• a phrase with enclosing speech marks (e.g. "human malaria").
• a fielded search (e.g. auth:stoehr). Available search fields are listed in the Appendix 1 of the Reference Guide or can be retrieved using the fields module of the API.
• a specific publication (e.g. ext_id:781840 src:med) Specify ext_id as the article identifier, and src as the source database. List of the data sources can be found on the help pages or in section 3 of the Reference Guide.

pub_type:research-article

Example query: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=trichome%20pub_type:research-article&pageSize=20

Wellcome Trust Utilities

Papers to read

Building a PubMed knowledge graph

Building a knowledge graph from PubMed