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. 2021 Nov 5;37(21):3950-3952.
doi: 10.1093/bioinformatics/btab424.

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data

Sreenath Nair  1 , Mihály Váradi  1 , Nurul Nadzirin  1 , Lukáš Pravda  1 , Stephen Anyango  1 , Saqib Mir  1 , John Berrisford  1 , David Armstrong  1 , Aleksandras Gutmanas  1 , Sameer Velankar  1
Affiliations

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data

Sreenath Nair et al. Bioinformatics. .

Abstract

Summary: The PDBe aggregated API is an open-access and open-source RESTful API that provides programmatic access to a wealth of macromolecular structural data and their functional and biophysical annotations through 80+ API endpoints. The API is powered by the PDBe graph database (https://pdbe.org/graph-schema), an open-access integrative knowledge graph that can be used as a discovery tool to answer complex biological questions.

Availability and implementation: The PDBe aggregated API provides up-to-date access to the PDBe graph database, which has weekly releases with the latest data from the Protein Data Bank, integrated with updated annotations from UniProt, Pfam, CATH, SCOP and the PDBe-KB partner resources. The complete list of all the available API endpoints and their descriptions are available at https://pdbe.org/graph-api. The source code of the Python 3.6+ API application is publicly available at https://gitlab.ebi.ac.uk/pdbe-kb/services/pdbe-graph-api.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
(A) An overview of how the PDBe aggregated API provides programmatic access to the PDBe knowledge graph, which combines data from PDBe and PDBe-KB. The graph data model of the underlying database provides a more intuitive representation of molecular entities and their relations. (B) A high-level schematic for a data retrieval procedure, starting from the UniProt accession of Thrombin (P00734). Users can combine data from multiple API endpoints, such as the annotations, interaction interfaces and ligand binding site endpoints to compile data on which ligand molecules bind to Thrombin at the same region as its natural inhibitor, Hirudin. A link to a step-by-step procedure is provided in the main text
See this image and copyright information in PMC

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