Another Word For It Patrick Durusau on Topic Maps and Semantic Diversity

July 15, 2012

ISA-TAB

Filed under: Bioinformatics,Biomedical,Genome — Patrick Durusau @ 9:06 am

ISA-TAB format page at SourceForge.

Where you will find:

ISA-TAB 1.0 – Candidate release (PDF file)

Example ISA-TAB files.

ISAValidator

Abstract from ISA-TAB 1.0:

This document describes ISA-TAB, a general purpose framework with which to capture and communicate the complex metadata required to interpret experiments employing combinations of technologies, and the associated data files. Sections 1 to 3 introduce the ISA-TAB proposal, describe the rationale behind its development, provide an overview of its structure and relate it to other formats. Section 4 describes the specification in detail; section 5 provides examples of design patterns.

ISA-TAB builds on the existing paradigm that is MAGE-TAB – a tab-delimited format to exchange microarray data. ISA-TAB necessarily maintains backward compatibility with existing MAGE-TAB files to facilitate adoption; conserving the simplicity of MAGE-TAB for simple experimental designs, while incorporating new features to capture the full complexity of experiments employing a combination of technologies. Like MAGE-TAB before it, ISA-TAB is simply a format; the decision on how to regulate its use (i.e. enforcing completion of mandatory fields or use of a controlled terminology) is a matter for those communities, which will implement the format in their systems and for which submission and exchange of minimal information is critical. In this case, an additional layer or of constraints should be agreed and required on top of the ISA-TAB specification.

Knowledge of the MAGE-TAB format is required, on which see: MAGE-TAB.

As terminologies/vocabularies/ontologies evolve, ISA-TAB formatted files are a good example of targets for topic maps.

Researchers can continue their use of ISA-TAB formatted files undisturbed by changes in terminology, vocabulary or even ontology due to the semantic navigation layer provided by topic maps.

Or perhaps more correctly, one researcher or librarian can create a mapping of such changes that benefit all the other members of their lab.

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