MICheckout: Supporting compliance with consensus reporting requirements

Lead Research Organisation: EMBL - European Bioinformatics Institute
Department Name: Microarray Group

Abstract

In recent years, the methods by which biological scientists conduct experiments have become increasingly complex. To ensure that the data from such experiments is described in a manner that supports analysis by other scientists, various groups have drawn up Minimum Information (MI) checklist documents for their area. These documents describe the information that should be collected to appropriately describe a particular piece of equipment or method. MI checklists serve to ensure that data are properly set in context, so as to support their correct interpretation, validation or reuse. However, such MI checklists are usually developed independently, from within particular biologically- or technologically-delineated areas (for example, plant biology, or mass spectrometry). Consequently, the full range of checklists can be difficult to establish without intensive searching, and tracking their evolution is non-trivial; they are also inevitably partially-redundant one against another (i.e. they overlap in their subject areas), and where they overlap arbitrary decisions on wording and structure make integration difficult. This presents significant difficulties for the users of checklists; for example, in the area of systems biology, where data from many different areas are routinely combined. The MIBBI (Minimum Information for Biological and Biomedical Investigations) project is working to integrate these many checklists and will ultimately produce a set of checklists that cover diverse areas while avoiding the problems of overlap. What is needed though is a simple mechanism for biologists to acquire an appropriate checklist for their particular investigation. This proposal seeks support for the development of a tool that will; (i) allow scientists to find the checklists they need; (ii) provide them with two different mechanisms to capture the information their checklist requires (Excel or online forms); (iii) offer space in a searchable public repository in which to store data sets (working in tandem with the online forms). MICheckout, once developed, will be available at the MIBBI website and will satisfy all the three requirements listed in the previous paragraph. Overall, MICheckout will increase use of MI checklists, which will improve the quality of publicly-available data sets (and therefore their reuse), which ultimately means that more value is being generated from the initial investment in the science by funders such as BBSRC.

Technical Summary

MICheckout is designed to assist users (i.e. experimentalists) to comply with the appropriate MIBBI modules (containing checklists for reporting particular kinds of bioscience activities) when compiling a report. The tool will make the use of appropriate modules into a straightforward process, even for complex multidisciplinary investigations. MICheckout will also, in addition to providing access to checklists, offer two mechanisms for capturing the data required by the modules. The first is a custom Excel spreadsheet; this can be used directly to capture the data required by the user's combination of MIBBI modules. The second utilises the GenCat resource; in this case, an XML Schema document reflecting the user's needs will be produced by MICheckout and automatically sent to GenCat, which will then render it as a web form. GenCat will be able to capture data entered this way, optionally storing that data in its searchable XML repository. The use cases for MICheckout are: 1. Experimentalists looking for MI checklists appropriate to their workflow (browse only): > Requires that the appropriate set of MIBBI modules be compiled and presented on screen as HTML. 2. Experimentalists in need of a (meta)data capture mechanism appropriate to their needs: > Downloadable Excel spreadsheet for data capture. > Bespoke, downloadable XML Schema, with the option to have GenCat render that schema as web forms. > Publicly searchable, massively cross-domain XML repository in which to store data sets (XML instances) captured by the use of GenCat forms. 3. Reviewers assessing the degree of compliance of an experiment report on behalf of a journal or funder: > Again requires that the appropriate set of MIBBI modules be compiled and presented on screen as HTML. 4. Software and database developers searching for use cases to direct their own development: > Selected MIBBI modules compiled and either presented on screen as HTML or made available as a downloadable XML Schema.

Publications

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Description Implementing the minimum requirement standards are much more difficult than publishing them
Exploitation Route Many bioinformatics groups around the world are still developing the minimal reporting requirements, then can learn from our experience
Sectors Digital/Communication/Information Technologies (including Software)

 
Description This allowed the bioinformatics community to systematize the reporting requirements for archival submissions
First Year Of Impact 2013
Sector Digital/Communication/Information Technologies (including Software)
Impact Types Societal