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Package to convert ISA-TAB files into RDF data using different semantic frameworks (OWL ontologies).

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ISA-Tab is a tabular format for the description of experimental steps. It originated for describing multi-omic and multi-assay experiments in the life sciences, but since its inception has also been used in other domains.

The ISA-Tab format constitutes ISA infrastructure syntactic layer (see the figure below), defining the syntactic elements for the description of experiments.

The ISA-Tab specification defines the way in which the ISA syntactic elements can be combined, providing a grammar layer for the infrastructure.

The ISA configurations are a set of templates or patterns that organise ISA elements for specific domains, so that they comply with the ISA grammar.

The ISA-Tab format supports ontology-annotations, which can be embedded into the generic elements.

On top of these layers of the ISA infrastructure, we have built a linkedISA representation, which exploits the ontology annotations and relies on the Resource Description Framework (RDF) and semantic mappings, as a first step for applying the linked data approach for ISA-Tab.

ISA layers

linkedISA has been implemented as a Java package relying on the OWL API that parses ISA-Tab files and generates an Resource Description Framework (RDF) representation, relying on mapping files from the ISA syntax to different semantic frameworks (or Web Ontology Language --- OWL --- ontologies).

The linkedISA project was previously called ISA2OWL, but we have decided to rename it, as we think that linkedISA reflects better the objectives of the project.

For more details, read the linkedISA publication:

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Mapping Files

The linkedISA conversion engine has been decoupled from the ontologies used in the resulting RDF representation. The conversion relies on parsing one or more mapping files, that align the ISA syntax to the specific ontology terms. We provide some mappings to a few ontologies with the implementation, namely: to the Ontology for Biomedical Investigations (OBI), the Provenance ontology (PROV-O) and the SemanticsScience Integrated Ontology (SIO). The mappings were created using the OntoMaton widget for Google Spreadsheets and are available here: In addition, the conversion engine relies on an ontology descring the ISA elements, which is available at and maintained in the GitHub repository


SPARQL Queries for linkedISA

Retrieve investigations with related studies and assays.


Retrieve study factors and levels

Queries over Scientific Data datasets

Nature Publishing Group's Scientific Data is an open-access, peer-reviewed publication for descriptions of scientifically valuable datasets.

Authors and Contributors

linkedISA is a project by the core ISA-tools team.

The mappings from the ISA syntax to multiple ontologies and SPARQL queries were developed by Philippe Rocca-Serra (@proccaserra) and Alejandra Gonzalez-Beltran (@agbeltran).

The linkedISA software component has been developed by Alejandra Gonzalez-Beltran (@agbeltran)

The linkedISA logos were designed by Eamonn Maguire (@eamonmag) from Antarctic Design.

Support or Contact

Having you got questions about linkedISA? Please, contact the ISA Team.


CPAL License, available at linkedISA license.