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 v0.2, which is a checklist, or list of elements, for the minimal description of cell migration experiments with focus on in vitro experiments. The document and checklist are open for comments.
MIACME v0.2 is the second version of MIACME checklist. For information about the previous version, please visit the MIACME v0.1 specification.
During its development, MIACME is expected to undergo a refinement process, through which it will be improved and extended and tested against the representation of specific cell migration experiments. The CMSO will engage all the 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. MIACME's goal 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 v0.2, 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 BioSharing portal. Their purpose and evolution have been considered in the development of MIACME, which is also registered in BioSharing. 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 record is also available in BioSharing, 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 0.2, is the result of discussions in the community and a simplification of MIACME v0.1. after identifying the main descriptors for reporting cell migration experiments.
MIACME v0.2 identified three main sections for the description of cell migration experiments:
These high-level sections and entities for MIACME v0.2 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 v0.2 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.
Another outcome of MIACME v0.2 has been an initial representation of the entities relying on JSON schemas, which can be accessed in the schemas folder.
In order to make clear the differences between MIACME v0.1 and v0.2, the following figure was produced:
The development of MIACME follows an iterative process. MIACME v2.0 was derived as a revision of MIACME v1.0, based on input from:
MIACME v0.1 was derived by considering discussions among participants in the working group and multiple sources, such as:
The Cell Migration Standardization Organization acknowledges funding from the European Union's Horizon 2020 Programme under Grant Agreement 634107 (PHC32-2014).