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Publication . Report . 2014

REPORT: BioMedBridges standards workshop

Conte, Nathalie; Hancocks, Tom; Suhr, Stephanie;
Open Access  
Published: 02 Dec 2014
Publisher: Zenodo
This workshop, co-organized by BioMedBridges WP3 and 12, was held on 24-25 June and hosted by BioMedBridges partners at VUMC in Amsterdam. Attendees included BioMedBridges personnel, members from the ESFRI BMS research infrastructures and invited external experts from existing standards organisations. The following aspects of data standardisation were explored: Defining entity identifiers and identifiers best practice Development of a Meta models and Mappings Registry for biomedical standards Data integration occurs when a query proceeds through multiple data sets, thereby relating diverse data extracted from different data sources. Standards and data harmonisation is a prerequisite to data integration, a primary aim of the BioMedBridges project. For the various ESFRI projects to exchange and integrate data in a meaningful way there needs to be agreement on how biomedical data is annotated, formatted and organised. Whilst an ultimate aim would be a single database, with a standardised user interface (UI), this is unlikely and a system of federated databases each specialising in a particular data type is more achievable. Provided that standardisation is implemented across the databases, a common UI could be deployed to allow integrated and simultaneous searching of data. The use of entity identifiers and common standards is essential to achieve the above vision, but many challenges exist. The complex and varied nature of the biomedical sciences, and biology in general, means that each researcher can have their own requirements and reasons for structuring their data in a particular format. To capture the possible extent of these variables, standards would require a high degree of granularity. Therefore organisation is required within the community and compromise needs to be sought.

data interoperability, standards, identifiers

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