Minimum Information Standards

Abstract: The VPH/Physiome project is developing tools and model databases for computational physiology based on three primary model encoding standards: CellML, SBML and FieldML. For the modelling community these standards are the equivalent of the DICOM standard for the clinical imaging community and it is important that the tools adhere to these standards to ensure that models from different groups can be curated, annotated, reused and combined. This chapter discusses the development and use of the VPH/Physiome standards, tools and databases, and also discusses the minimum information standards and ontology-based metadata standards that are complementary to the markup language standards. Data standards are not as well developed as the model encoding standards (with the DICOM standard for medical image encoding being the outstanding exception) but one new data standard being developed as part of the VPH/Physiome suite is BioSignalML and this is described here also. The PMR2 (Physiome Model Repository 2) database for CellML and FieldML files is also described, together with the Application Programming Interfaces (APIs) that facilitate access to the models from the visualization (cmgui and GIMIAS) or computational (OpenCMISS, OpenCell/OpenCOR and other) software.

Abstract: Minimum Information Standards James Hutchinson Links [A] http://mibbi.sourceforge.net/portal.shtml [B] http://www.mged.org/Workgroups/MIAME/miame.html [C] http://www.ncbi.nlm.nih.gov/geo/ [D] http://www.gene-quantification.info/ [E] http://www.rdml.org/ [F] http://miataproject.org/ [G] http://flowcyt.sourceforge.net/ [H] http://www.psidev.info/miabe [I] https://pubchem.ncbi.nlm.nih.gov/ [J] https://www.ebi.ac.uk/chembl/ [K] http://www.ebi.ac.uk/chebi/ To properly evaluate the conclusions of a scientific communication, readers must have access to certain essential information about experimental context, design, conduct, and analysis. As in other fields of biological research, the complexity and volume of transplantation experiments continue to increase, so clear reporting becomes ever more important. Consequently, there is growing enthusiasm among scientists and publishers for minimum information standards prescribingwhich “data about the data”must accompany certain types of experiment. Such standards impose greater transparency, but also make it easier for researchers to find, access, and integrate published information. Reporting standards thatwere originally developed by independent groups of specialists are now being gathered by the Minimum Information for Biological and Biomedical Investigations project, which aims to eliminate redundancybetween sets of standards and to introduce a controlled vocabulary (A). This article collates web-based resources related to minimum information standards with relevance to the readership of Transplantation. TheMinimum Information about a Microarray Experiment (MIAME) guidelines were the archetype of such reporting standards and are nowwidely demanded by journals when publishing gene expression profiling studies by microarray. The MIAME checklist is concerned with 6 critical elements including: provision of the raw data for each hybridization; provision of the final processed and normalized dataset, essential sample annotation including experimental parameters, complete description of the experimental design, sufficient annotation of the array, and provision of essential laboratory and data processing protocols [B]. Authors can allow access to their datasets in various ways, including submission to a public library, such as the Gene Expression Omnibus repository at NCBI [C]. Critically, the development and adoption of MIAME has not only improved the comprehensibility and