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.
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:http://purl.org/isaterms and maintained in the GitHub repository https://github.com/ISA-tools/linkedISA-ontologies
SPARQL Queries for linkedISARetrieve investigations with related studies and assays.
Queries over Scientific Data datasetsNature Publishing Group's Scientific Data is an open-access, peer-reviewed publication for descriptions of scientifically valuable datasets.
- Retrieve all the studies in Scientific Data
- Retrieve investigation with related studies and assays.
- Study factors and levels
- Study factor levels count
linkedISA is a project by the core ISA-tools team.
Having you got questions about linkedISA? Please, contact the ISA Team.
CPAL License, available at linkedISA license.