Tag Archives: Isa

New ISA Model and Serialization Specifications released!

Over the last few months, the ISA Team has been working hard on editing a long-awaited release of the ISA Model and Serialization Specifications 1.0.

The original ISA-Tab specification was published as a Release Candidate document in 2008, documenting the initial work that forms the ISA framework, with a further update in 2009. Since then, we have done work on a new serialization in JSON, ISA-JSON, and abstracted out the data model from both the tabular and JSON formats.

ISA Model and Specs diagram

The ISA Model and Serialization Specifications consist of three specification documents:

  1. ISA Abstract Model – a data model of ISA objects/entities and their relation to one another
  2. ISA-Tab format – the tabular serialization format of the Abstract Model
  3. ISA-JSON format – the JSON serialization format of the Abstract Model.

The specifications are licensed under CC BY-SA 4.0 , and you can cite the specifications with:

Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Gonzalez-Beltran, Alejandra, Johnson David & the ISA Community. (2016, October 28). ISA Model and Serialization Specifications 1.0. Zenodo. http://doi.org/10.5281/zenodo.163640.

To view the latest version online, please visit http://isa-specs.readthedocs.io/en/latest/

Plant Science takes a focus on ISA

Back in April this year, Dr David Johnson from the ISA team gave a presentation on “Data Infrastructures to Foster Data Reuse” at a workshop on Integrating Large Data into Plant Science: From Big Data to Discovery hosted by GARnet (the UK network for Arabidopsis researchers) and Egenis (the Exeter Centre for the Study of the Life Sciences). The workshop was held at Dartington Hall in Devon, South West England, and was well attended by researchers from the plant and biological science community worldwide as well as representatives from industry from organisations such as Syngenta.

David presented on ISA, as well as on biosharing.org, as candidate data infrastructure resources for enabling data reuse in the plant sciences, as well as presenting an example of how one might encode high-throughput plant phenotyping in ISA tab.

We have observed the uptake of the ISA tab format across the broad range of life sciences, but view its adoption, with a view to making data FAIR (Findable, Accessible, Interoperable and Reusable), in the plant sciences as essential for the field. In particular centres such as the UK’s National Plant Phenomics Centre in Aberystwyth, Wales, could benefit hugely from adopting ISA where there are emerging challenges in data management, in particular as automation of data collection is a significant driver in modern plant-based research and agritech.

There are also existing data analysis platforms such as Araport (the Arabidopsis information Portal), TAIR (The Arabidopsis Information Resources) and BioDare (Biological Data Repository) that could benefit from standardizing their experimental data, as well as ongoing efforts to create open data resources in the plant sciences, such as the Collaborative Open Plant Omics (COPO) project, that will be using the new ISA JSON format as native data objects.

You can check out David’s presentation on SlideShare.