What’s a “standard”?
In a digital world, standards of many types are essential for underpinning interoperability between data, tools, and the underlying infrastructure that these tools use. Without applying standards, information collected in an experiment may be insufficient to ensure reproducibility, or data may not be able to be efficiently exchanged between different tools and environments, requiring a large amount of manual re-formatting and intervention. Furthermore, the standards can be linked to training material around tools and data.
– Reporting Guidelines (e.g. diagnostic reporting guidelines, minimum info specs, etc)
– Data Models/Formats (e.g. exchange formats, markup languages, etc)
– Terminologies (e.g. controlled vocabularies, ontologies, staging systems, etc)
There are more than 600 community-endorsed standards in the life, environmental and biomedical sciences.
Why should I care?
If you’re interested in enabling yourself, your collaborators, the wider research community (or machines) to discover, access, integrate and analyse, task-appropriate data with associated algorithms and workflows (i.e. making data Findable, Accessible, Interoperable, and Re-usable (or “FAIR”), applying standards is critically important. Standards and the use of them also underpin the interlinking of life science infrastructure.
Funders and or journals may also recommend or require the use of data standards.
How can I find out if there’s a standard I should consider using?
It’s simple – you can search FAIRsharing.org (formerly known as biosharing.org) – a curated global registry of standards, databases that employ the standards and data policies that require or recommend the use of the standards.
FAIRsharing enables you to find standards that are relevant to your work, understand their maturity, and to find tools and databases that implement them.
More information about FAIRsharing and how Australians researchers can access it, use it, or contribute to it can be found in our interview with Dr Peter McQuilton – content lead for the FAIRsharing project based at the University of Oxford’s e-Research Centre (OERC).
EMBL-ABR Node participation in standards development
An important initiative involving several large-scale bioinformatics initiatives around the world is working on a solution, BioSchemas, which aims to extend the existing schema.org system to focus on biological data. The EMBL-ABR Melbourne Bioinformatics Node is part of the BioSchemas effort, and involved in the BioSchemas Tool Group, for the development of a schema for Tools. More information here.
GOBLET (the Global Organisation for Bioinformatics Learning, Education & Training) develops bioinformatics training material, and is undertaking an effort to map bioschemas to this training material. Dr Sonika Tyagi from the EMBL-ABR Monash University Node chairs this standards committee.
Information standard development for metabolic data are being coordinated by the international Metabolomics Society. Dr Saravanan Dayalan of the EMBL-ABR Metabolomics Australia Node is a member of the Data Standards Task Group of the Metabolomics Society that is tasked with establishing these standards.
For more information about the EMBL-ABR Standards Key Area, please contact Saravanan Dayalan, Standards Coordinator.