ISA Model and Serialization Specifications

Status: ISA Model and Serialization Specifications 1.0 (28 October 2016)

The key words “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”, “SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this document are to be interpreted as described by RFC 2119.

The ISA Model and Serialization Specifications are licensed under CC BY-SA 4.0.

The ISA Model and Serialization Specifications are maintained by Susanna-Assunta Sansone [1], Philippe Rocca-Serra [1], Alejandra Gonzalez-Beltran [1] and David Johnson [1] on behalf of the ISA Community.

[1]	(1, 2, 3, 4) Oxford e-Research Centre, University of Oxford, UK.

If you wish to make comments regarding these specifications, please see the page on how to contribute.

Introduction

ISA is a metadata framework to manage an increasingly diverse set of life science, environmental and biomedical experiments that employ one or a combination of technologies. Built around the Investigation (the project context), Study (a unit of research) and Assay (analytical measurements) concepts, ISA helps you to provide rich descriptions of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) so that the resulting data and discoveries are reproducible and reusable.

Note

For an introduction to ISA, please read the paper, Towards interoperable bioscience data published in Nature Genetics. For more details on the ISA framework and supported tools, please see http://www.isa-tools.org

The ISA Model and Serialization Specifications define an Abstract Model of the metadata framework. The ISA Abstract Model has been implemented in two format specifications, ISA-Tab and ISA-JSON, both of which have supporting tools and services associated with them. The format specifications are also available for additional tooling to take advantage of ISA-formatted content.

These specifications are primarily aimed at software engineers to facilitate the development of automated export from databases, or import into analytical or other tools.

• 1. ISA Abstract Model
  • 1.1. Investigation, Study, Assay
  • 1.2. Ontology Annotation
  • 1.3. Ontology Source
  • 1.4. Unit
  • 1.5. Publication
  • 1.6. Contact
• 2. ISA-Tab format
  • 2.1. Format
  • 2.2. Investigation File
  • 2.3. Study and Assay files
• 3. ISA-JSON format
  • 3.1. Format
  • 3.2. Schemas
  • 3.3. Content rules
• 4. Software tools
• 5. Contributing
  • 5.1. License
  • 5.2. Contributors

Revision History

Version	Date	Description
1.0	2016-10-28	Final release of ISA Model and Serialization specifications [2]
1.0	2009-01-13	Final release of ISA-Tab specification [3]
1.0RC1	2008-11-26	First release candidate of ISA-Tab specification [4]

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

[3]	Rocca-Serra, Philippe, Sansone, Susanna-Assunta, & Brandizi, Marco. (2009, January 13). Specification documentation: ISA-TAB 1.0. Zenodo. http://doi.org/10.5281/zenodo.161355

[4]	Rocca-Serra, Philippe, Sansone, Susanna-Assunta, & Brandizi, Marco. (2008, November 24). Specification documentation: release candidate 1, ISA-TAB 1.0. Zenodo. http://doi.org/10.5281/zenodo.161350