BioExcel/PDBe Hackathon



The current PDBe REST API (in production since 2015) offers a variety of API endpoints (calls) to retrieve and query PDB and PDBe-KB data. PDBe-KB is a new community-driven resource managed by the PDBe team, which collates added value annotations relating to PDB structures.

PDBe team has recently prototyped a new API based on Neo4J graph database technology. This new database contains all of the SIFTS information, including cross-references to UniRef90 clusters, validation data, and information related to residue conservation, annotations contributed by PDBe-KB partner resources (e.g., functional sites, residue flexibility, predicted or observed binding sites). Further added value annotations will become available as new partners contribute them to the PDBe-KB resource. This new prototype API thus allows queries based on UniProtKB accessions and UniProtKB residues (in addition to ones based on PDB codes), and provides access to the above data contained in the graph database. The hack-a-thon will provide an opportunity to work with the PDBe team members to learn more about the API and request new API calls that could be developed already during the hack-a-thon.

Each API endpoint is a logical grouping of a number of data items that generally would be used together. The individual API endpoints are further grouped into categories. The current production system totals 89 endpoints delivering information keyed mostly on PDB entry codes (constituent molecules, experimental setup, citations, validation, quaternary structure, cross-references to other bioinformatics resources, etc). A powerful programmatic interface to write queries to retrieve/filter PDB entries is also available.

The prototype graph-based API reimplemented 35 of the above production endpoints, and has additional 7 endpoints that allow retrieval of PDB and PDBe-KB annotations for UniProtKB accessions, and for individual residues in a PDB entry or in a UniProtKB sequence.

Suggested agenda:
– Presentation of use cases
– Introduce the production and prototype APIs
– Guided hands-on implementation of the use case(s)
– Identification of additional API calls that can potentially be implemented during the hack-a-thon.


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Date/Time
05 Nov, 2018 - 06 Nov, 2018
09:00 - 17:30

Location
EMBL-EBI

Categories

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