Biomedical Engineering Reference
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details (or meta-data), and provides the ability to convert experimental
meta-data into various formats (e.g. for submission to some public
databases) or to retain it in local storage. The suite's components are
variously intended either for experimentalists or those supporting them.
The editor tool (ISAcreator) offers familiar spreadsheet-based data entry
and facilitates ontology-based curation at source via the BioPortal [11]
and the Ontology Lookup Service [12]. Support for conformance to
relevant minimum requirements, and the use of specifi ed terminologies,
is confi gurable across the suite (via the support-person-focused
ISAconfi gurator tool); it can be rigid or fl exible to meet in-house
requirements. The BioInvestigation Index is a searchable repository
through which experimental meta-data and the associated data fi les can be
managed and shared among the users granted access to them (including
publicly). Conversion to and from any of a growing number of acceptable
formats is enabled by a further module (the ISAconverter tool) [13-15].
The ISA software suite is available for download from the project web site,
including the component's technical documentation and users' guide [16].
New collaborative activities continue to move the ISA community along
the path to knowledge discovery through broad-scope data integration.
For example, work is in progress to (1) augment the ISA code base with
Application Programming Interfaces (APIs) to support further collaborative
development; (2) facilitate visualization, manipulation and analysis data
analysis, informed by the experimental context (the rISA, a R-package for
ISA-Tab formatted fi les) using existing open source analysis platforms [17,
18]; (3) explore cloud-based resource management systems through the
ISA suite being deployed on a Bio-Linux platform [19]; and (4) use
semantic web approaches to make existing knowledge available for
linking, querying, and reasoning in collaboration with the World Wide
Web Consortium (W3C) Semantic Web for Health Care and Life Sciences
Interest Group (HCLSIG)'s Scientifi c Discourse task force [20].
7.3.3 The ISA commons
As the collaboration continues to grow and new groups join in, we are on
the path to building the ISA commons [21], a growing, exemplar ecosystem
of data curation and sharing solutions built on the ISA framework. Rooted
in real case studies, this framework is already used by many communities
in domains as diverse as environmental health, stem cell discovery,
toxicogenomics, environmental genomics, plant metabolomics and
metagenomics while maintaining cross-domain compatibility. For
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