“Coming together is a beginning;
keeping together is progress;
working together is success.”
— Henry Ford
Enabling the meaningful sharing and re-use of data across the research community is critical to the NCI’s mission to convene the community to work cooperatively on addressing the causes, diagnosis, and treatment of cancer. Data sharing is facilitated by providing practical, usable formats for consistent data representation. Nanomedicine is inherently interdisciplinary and it is necessary to integrate results with those obtained from other groups and disciplines. Data integration requires standards-based data collection. Over the past two years, the National Cancer Informatics Program’s Nanotechnology Working Group (Nano WG) — a collaborative effort of several federal, academic, and private institutions — has worked to specify a standard format for the exchange of nanoparticle characterization data.
The spreadsheet format for capturing annotations was pioneered by the microarray community. This has proved to be a successful approach: researchers are familiar with spreadsheets, and barriers to using the format are few. The spreadsheet approach has been extended to support a broader range of research data: for example, ISA-TAB allows researchers to capture annotations describing Investigation, Study and Assay for life-science, environmental, and biomedical experiments. More recently, the Nano WG has extended ISA-TAB format by adding the necessary fields to support nanoparticle information, to create ISA-TAB-Nano. To better support the creation of ISA-TAB-Nano files by end users, the group wanted to extend the ISA Tools Software Suite (developed by Oxford University) to support validation of ISA-TAB-Nano files. Collaboration with the ISA community (ISA Commons) enables Nano WG to reuse and extend ISA tools to support ISA-TAB-Nano. These tools make it easier for users to manage and exchange Nanotechnology data.
Over the course of two days, the Code Fest brought together ISA Tools developers (Oxford University), ISA-TAB-Nano developers (PNNL, NCI, SAIC-Frederick) and ISA-TAB-Nano users (Nanomaterial Registry) to specify and create the necessary extensions to the ISA validator, a tool that screens ISA files for formatting problems. Nano WG has been collaborating virtually with the ISA team for several years but meeting in person allowed us to obtain better understanding of the structure and logic behind the specifications, and facilitated discussion of changes that need to be made to better align these specifications. We set up the desktop environment in support of ISA tools development and forked the ISA validator code to the NCIP GitHub for making our changes. During the workshop we worked on understanding the ISA Validator extensions needed to support the nanoparticle-specific needs represented in ISA-TAB-Nano. We also setup a web service for ISA-TAB validation and once the ISAValidator changes supporting ISA-TAB-Nano are complete, the web service will be reconfigured to perform the ISA-TAB-Nano validation as well. Web service allows users to submit ISA-TAB-Nano files for validation, and receive error reports listing required fixes.
ISA-TAB-Nano provides both individual investigators and data repositories a platform to collect and share data in a standards-based manner. Open and collaborative development of standards and specifications is necessary in order to capture requirements from a broad community of users, and to make sure everyone is in agreement about what data need to be captured and how the data are represented. A specification built by the community is more likely to be adopted and maintained by the community. The objective is to increase use of ISA-TAB-Nano in order to facilitate collection of large datasets that can be used for analysis of nanotechnology data, and ultimately development of therapeutic nanoparticles.
Mervi Heiskanen, Ph.D., is Program Manager at the Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute (NCI). You may connect with Mervi via LinkedIn.