InterMine-Institut Pasteur knowledge exchange

InterMine is an ELIXIR recommended interoperability resource, and Institut Pasteur is a non-profit biomedical research foundation and part of ELIXIR France, with a strong focus on infectious diseases. The Institut Pasteur has played a major role in the sequencing of a number of bacteria involved in such diseases, and the publication of their genomes. A number of these are currently available in databases based on older proprietary technology stacks (http://genolist.pasteur.fr/). We propose to enable a member from the Institut to visit Cambridge, where the InterMine team is based, for 10 working days, to learn how to load data from a legacy database into a new InterMine instance.

Expected Impact: “Digital preservation” is a term for the concrete, proactive steps required to keep data and database systems readable and useable - so preventing the so-called “digital dark age” phenomenon. One preventative measure recommended by Smit et al is to transform data,
refreshing it by moving it to current easily-readable formats (Smit, Van Der Hoeven, and Giaretta 2011). By using InterMine to reserve these data, researchers will be able to take advantage of a database system which explicitly strives to be FAIR and has existing documentation, flexible advanced queries, API client libraries in six languages, tutorials, and a common interface that already is utilised by dozens of existing databases (registry.intermine.org).

Duration: 

1 February 2020 to 31 May 2020

Nodes involved: 

Platform/Community: 

People involved: 

Gos Micklem
Hervé Ménager