Using Europe PMC RESTful 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.

By integrating knowledge from Europe PMC open-access publications, PDBe provides entries with 3D macromolecular structures in context with literature highlighting the impact of a given structure on scientific research. The first step in the integration process is to map the PDB IDs to PubMed IDs (e.g PDB “1cbs” has “PMID7704533” as its primary publication). The second step is to use the Europe PMC REST API GET /search request to retrieve the publications by PMID, which will populate a PDBe page with fields such as publication DOI, title, authorList, journal and abstract.

Illustration showing how the webservices response becomes text on a webpage in PDBe Figure 1: Europe PMC’s search API response becomes a page on PDBe

PDBe also retrieves citation counts through the Europe PMC REST API GET /citations request for each PMID. The response is manipulated in order to display the number and links to reviews and experimental articles citing a given publication.

Illustration showing how the webservices response becomes text on a webpage in PDBe Figure 2: Europe PMC’s citations API response becomes a page on PDBe

The integration of Europe PMC APIs in PDBe web services was very simple. Once we knew what data we were interested in, we just needed to use the correct API endpoint with the corresponding parameters to populate PDBe database with data gleaned from the response. This data is then used for PDBe pages and PDBe REST API providing richer context to protein structure records.