Taylor CF, Field D, Sansone SA, et al.. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK. ,
Nature Biotechnology (Impact Factor: 41.51). 09/2008; 26(8):889-96. DOI: 10.1038/nbt.1411
Source: PubMed


The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated development of such checklists. European Union Framework VI project META- PHOR (Food-ST-2006-03622)

Download full-text


Available from: Javier Santoyo-Lopez
  • Source
    • "Three well-known approaches are the approximated non-mechanistic kinetic equations (Heijnen, 2005), ensemble metabolic modeling (Tran et al., 2008) and hybrid modeling approaches (Bulik et al., 2009). Moreover, standardization and curation efforts for comparing kinetic measurements, simulation experiments, and annotation standards to facilitate the exchange and integration of quantitative data and models were also published over the last years (Bergmann et al., 2014;Smallbone et al., 2013a;Taylor et al., 2008;van Eunen et al., 2010). Kinetic models have been used for a large variety of applications including the estimation of optimal drug concentrations (Torella et al., 2010), (re-) design of metabolic systems (Visser et al., 2004) and in synthetic biology (Marchisio and Stelling, 2009). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Kinetic models of cellular metabolism are important tools for the rational design of metabolic engineering strategies and to explain properties of complex biological systems. The recent developments in high-throughput experimental data are leading to new computational approaches for building kinetic models of metabolism. Herein, we briefly survey the available databases, standards and software tools that can be applied for kinetic models of metabolism. In addition, we give an overview about recently developed ordinary differential equations (ODE)-based kinetic models of metabolism and some of the main applications of such models are illustrated in guiding metabolic engineering design. Finally, we review the kinetic modeling approaches of large-scale networks that are emerging, discussing their main advantages, challenges and limitations.
    Full-text · Article · Dec 2015 · Journal of Biotechnology
  • Source
    • "A checklist service subsequently queries the Minim annotations as an aid to make sufficiently complete ROs [24]. The idea of using a checklist to perform quality assessment is inspired by related checklist-based approaches in bioinformatics, such as the Minimum Information for Biological and Biomedical Information (MIBBI)-style models [25]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as “which particular data was input to a particular workflow to test a particular hypothesis?”, and “which particular conclusions were drawn from a particular workflow?”. Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. The Research Object is available at The Wf4Ever Research Object Model is available at
    Full-text · Article · Sep 2014 · Journal of Biomedical Semantics
  • Source
    • "Reporting guidelines now exist for randomised controlled trials (CONSORT) (Schulz et al. 2010), observational studies (STROBE) (Von Elm et al. 2007), non-randomised evaluation studies (TREND) (Des Jarlais et al. 2004), economic studies (Mason & Drummond, 1995), psychological studies (American Psychological Association, 2010), self-report data (Stone & Shiffman, 2002), and animal studies (Kilkenny et al. 2010). Online databases, such as the EQUATOR website (Simera et al. 2010) and the MIBBI project (Taylor et al. 2008), have been established to provide regularly updated lists of reporting guidelines and minimum information checklists. These guidelines are useful resources for reviewers seeking to understand the type of information that might be reported in primary studies in their field. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Systematic reviews and meta-analyses are used to combine results across studies to determine an overall effect. Meta-analysis is especially useful for combining evidence to inform social policy, but meta-analyses of applied social science research may encounter practical issues arising from the nature of the research domain. The current paper identifies potential resolutions to four issues that may be encountered in systematic reviews and meta-analyses in social research. The four issues are: scoping and targeting research questions appropriate for meta-analysis; selecting eligibility criteria where primary studies vary in research design and choice of outcome measures; dealing with inconsistent reporting in primary studies; and identifying sources of heterogeneity with multiple confounded moderators. The paper presents an overview of each issue with a review of potential resolutions, identified from similar issues encountered in meta-analysis in medical and biological sciences. The discussion aims to share and improve methodology in systematic reviews and meta-analysis by promoting cross-disciplinary communication, that is, to encourage 'viewing through different lenses'.
    Full-text · Article · Sep 2014 · SpringerPlus
Show more