MIACME is the Minimum Information About Cell Migration Experiments reporting guideline, which is being developed by the Cell Migration Standardisation Organisation (CMSO). CMSO's goal is to facilitate the development of community standards for the field of cell migration and is supported by the MULTIMOT project of European Commission's H2020 programme. The needs for these guidelines and other related standards were identified by [[Masuzzo2014]].
This document introduces MIACME v0.3, which is a checklist, or list of elements, for the minimal description of cell migration experiments. The document and checklist has been developed within the Cell Migration commmunity, and feedback is welcome.
MIACME v0.3 is the third version of MIACME checklist. For information about the previous versions, please visit the main MIACME page.
In particular, the two previous specifications are available at:
During its development, MIACME has undergone a refinement process, through which it has been improved, extended and tested against the representation of specific cell migration experiments. The CMSO has engaged with relevant stakeholders in the cell migration community in order to reach agreement on the minimal descriptors required to understand, interpret, evaluate, replicate and disseminate cell migration experiments.
The goal behind the guidelines is to make the data produced in cell migration experiments FAIR (Findable, Accessible, Interoperable, and Reusable) [[Wilkinson2016]] and to promote data access, data discovery, data preservation, maximise data re-use and repurpose through efficient annotation for long term archiving, and ultimately, enable reproducibility of cell migration experiments.
This document is published by the Cell Migration Standardisation Organisation Minimal Reporting Requirements Working Group as MIACME v0.3, which is a Working Draft of the MIACME specification.
MIACME is developed with and for the cell migration community to describe cell migration experiments.
We welcome and appreciate contributions. To make comments regarding this document and/or the associated reporting guideline, participation is possible in a variety of ways:
The MIACME reporting guideline and its associated documentation is made available under the terms of the CC BY-SA 4.0 license.
Reporting guidelines, or minimum information checklists, have been proposed as a way to understand the context, methods, data and conclusions of experiments in different domains [[Taylor2008]].
These reporting guidelines for the life, environmental and biomedical sciences are maintained in the FAIRSharing portal. Their purpose and evolution have been considered in the development of MIACME. While many of the original reporting guidelines were simply a list of desired content information, many times available only in narrative form (e.g. in a PDF document), MIACME, whose information is also available in FAIRsharing, is taking a step further and formalising the requirements for reporting cell migration experiments.
MIACME comprises a checklist, or list of elements, for the minimal description of cell migration experiments. This release, version 0.3, is the result of discussions in the community and a refinement of MIACME v0.2. after further input and further example representations from existing datasets and experimental setups.
MIACME v0.3 is composed of three main sections for the description of cell migration experiments:
These high-level sections and entities for MIACME v0.3 are shown here:
The elements above are also presented in a more detailed form as a table. The table details the entities and properties, together with their definitions, their cardinality and requirement level, as well as recommended sources for their annotation, examples and notes. Defining this common set of metadata to guide researchers in reporting scientific context is important for data repositories, journals and funders in the cell migration domain.
MIACME v0.3 spreadsheet can be accessed in ods format,
two cvs files (cell migration csv
and generic csv) and
The spreadsheet can also be viewed here and accessed as a Google document:
We have split the spreadsheet in two worksheets:
The spreadsheet contains the following information:
The following figure provides an overview of MIACME entities, their relationships and cardinalities:
The top part of the figure includes the generic elements to describe entities such as investigations and studies, contact people, organisations, grants. The bottom part show the three specific sections for cell migration experiments: experimental setup, imaging condition and data.
In addition to identifying the minimum set of descriptors for cell migration experiments, the working group worked on identifying MIACME descriptors for specific datasets associated with publications. This exercise also looked into identifying ontology terms that could be used for annotating the descriptors and its values. Then, a list of the ontologies use was collected in a tabular form. The results of this exercise can be accessed in this rich text file.
The development of MIACME follows an iterative process. MIACME v0.3 was derived as a revision of MIACME v0.2, based on input from:
In order to facilitate the description of MIACME-compliant cell migration datasets, CMSO is relying on the ISA model. ISA stands for Investigation (the project context), Study (a unit of research), and Assay (the analytical measurements). The ISA model supports rich descriptions of the experimental metadata, making the associate data reproducible and reusable.
The metadata framework associated with the ISA model encompasses a series of open source software tools that faciliate the manipulation of datasets described with the ISA model.
For MIACME, we provide a set of configuration files (or templates), allowing researchers to describe their datasets using the ISAcreator tool:
These configuration files are XML files providing a template of the ISA model including the specific recommendations given by the MIACME reporting guideline. Using these templates in the ISAcreator tool (see the next section) is a way for researchers to provide the metadata for their experiment.
Given the MIACME ISA-Tab configurations described above, researchers could use the ISAcreator tool to produce MIACME-compliant metadata about their experiments. ISAcreator is a Java-based desktop application that supports spreadsheet-like functionality. By loading the
A version of ISAcreator including the MIACME configuration files is made available at the ISAcreator-MIACME repository. There you will also find information on how to run and use ISAcreator.
The Cell Migration Standardization Organization acknowledges funding from the European Union's Horizon 2020 Programme under Grant Agreement 634107 (PHC32-2014).