PNNL

Abstract

Background One purpose of the biomedical literature is to report results in sufficient detail so that the methods of data collection and analysis can be independently replicated and verified. In order to ensure that this level of detail is provided in published works, a minimum information specification is needed for each experimental data type and for this specification to be a requirement for publication in peer-reviewed journals. This is especially beneficial for researchers working with complex data types and experiments. A data content specification has already been widely accepted by, and directly benefited, the microarray community, and efforts are well underway to develop a comparable specification for proteomics data types. However, no similar specification exists for visual interpretation-based tissue protein and transcript abundance/localization experiments (hereafter referred to as ‘gene expression localization experiments’), such as in situ hybridization and experiments involving immunohistochemistry. Results Here we present for consideration a specification, called the “Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)”. It is modelled after the MIAME (Minimum Information About a Microarray Experiment) specification for microarray experiments. Data specifications like MIAME and MISFISHIE specify the information content without specifying a format for encoding that information. The MISFISHIE specification describes six types of information that should be provided for each gene expression localization experiment: Experimental Design, Biomaterials and Treatments, Reporters, Staining, Imaging Data, and Image Characterizations. A general checklist is provided for quick and easy reference and to promote adherence to the specification. We consider that most articles describing gene expression localization studies do not fully provide the minimum information needed for independent verification of results. In a small survey of 32 journal articles from the past five years, we found that approximately 90% of them did not meet all the requirements, although many met most of them. We propose that requiring authors to provide the minimum experimental detail about gene expression localization studies would facilitate reproducibility and interpretability of results by fellow investigators. Furthermore, inclusion of specific experimental details such as reagents and methods in publications would ultimately allow others to readily search the literature for these data items, especially given the ongoing trend towards open access full text journals. Conclusion This specification was initially developed by members of the NIH/NIDDK Stem Cell Genome Anatomy Projects consortium (http://www.scgap.org ) to facilitate data sharing within the consortium. Use of the specification has benefited the consortium and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal. Should the community accept the final proposal, we would encourage reviewers, journal editors and funding agencies to promote compliance with MISFISHIE for all studies that report gene expression localization data so that all published data and resulting conclusions may be correctly interpreted, and that independent investigators would have the necessary information that would enable them to repeat the experiment. More information and examples may be obtained at http://mged.sourceforge.net/misfishie/.