MIACME is the Minimum Information About Cell Migration Experiments reporting guideline, which has been 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 v1.1, which is a checklist, or list of elements, for the minimal description of cell migration experiments. The document and checklist have been developed within the Cell Migration commmunity, and feedback is welcome.

MIACME v1.1 is a stable version of MIACME checklist, arising after 4 previous versions. For information about the previous versions, please visit the main MIACME page.

The previous specifications are available at:

• MIACME v1.0 specification
• MIACME v0.3 specification
• MIACME v0.2 specification
• MIACME v0.1 specification

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.

The guidelines are presented in several formats: from a spreadsheet enumerating the different elements, their definitions, cardinalities and requirement level (if the descriptor SHOULD/MAY/MUST be included) to a machine-actionable representation following the JSON schema format. More details about these formats is provided below.

Background

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, allowing for validation of compliance against this reporting guideline.

MIACME Reporting Guideline

MIACME comprises a checklist, or list of elements, for the minimal description of cell migration experiments. This release, version 1.1, is the result of a refinement of MIACME v0.1. after further input and further example representations from existing datasets and experimental setups. In particular, the change from v1.0 to v1.1 is the addition of more detail information related to the datasets produced in the experiment, now considering raw images dataset, processed images dataset and extracted features dataset. The previous version, considered the addition of pixel information based on the Open Microscopy Environment (OME) schema.

MIACME v1.1, as before, is composed of three main sections for the description of cell migration experiments:

1. Experimental setup: identifying the main elements of the experiment such as the type of assay, the perturbation or interference applied, the microenvironment (substrat for in vitro experiments or tissue for in vivo experiments), the cell type and, optionally, the medium.
2. Imaging condition: describing the imaging modality, the temporal resolution, a description of the different imaging channels and, optionally, the objective lesn.
3. Data: providing information about the raw or processed images, the total number of raw images and extracted features, when available.

These high-level sections and entities for MIACME v1.1 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 v1.1 added the following elements to MIACME 1.0:

• an entity for dataset, including fields for description, license and others - this allows MIACME to reuse existing vocabularies for dataset description such as DCAT, schema.org/Dataset or DATS.
• now the data is considered as datasets raw data, processed data and extracted features

MIACME v1.1 spreadsheet can be accessed in ods format, two cvs files (cell migration csv and generic csv) and xlsx format. The spreadsheet can also be viewed here and accessed as a Google document:

We split the spreadsheet in two worksheets:

1. A worksheet with generic elements for describing the experiment and related entities, such as investigation, study, contacts, publications.
2. A worksheet with the three main sections defined for describing cell migration experiments

The spreadsheet contains the following information:

• Entity: An object that can exist independently and can be identified uniquely.
• Entity Annotation: An ontology concept that annotates the corresponding entity.
• Property: An attribute describing the corresponding entity.
• Property Annotation: An ontology concept that annotates the corresponding property.
• Condition on Property: The corresponding property should satisfy the specified condition (e.g. should be provided only if another property has a specific value).
• Definition: A statement of the exact meaning of the entity and/or property.
• Value Type: The type of a property value.
• Recommended resource: The recommended resources (e.g. ontology or database) that should be used to assign the values for the corresponding Entity/Property pair.
• Cardinality: The expected number of occurrences for a particular property.
• Requirement level: Following RFC 2119, a word indicating the level of necessity for a particular property.
• Evidence: A reference to the document, article, schema, discussion that yields a particular entity or property necessary to be included and its requirement level.
• Example(s): Typical cases for the values of a particular property.
• Notes: Additional comments that may help the interpretation and representation of the corresponding entity and/or property.

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 has been a representation of the entities relying on JSON schemas, which is a vocabulary that allows to validate and annotate JavaScript Object Notation (JSON) documents. The schemas are prepared to support the data to be in JSON for Linking Data (JSON-LD) format. The schemas can be accessed in the schemas folder. In version 1.0, we have also added JSON-LD context files. JSON-LD is JSON for linked data, supporting interconnecting web information. Context files represent a mapping between terms in JSON to vocabularies that provide data semantics. The JSON-LD context files can be accessed in the contexts folder.

The MIACME schema can be visualised here:

The development of MIACME followed an iterative process. MIACME v1.1 was derived as a revision of MIACME v1.0, based on input from researchers reporting their datasets using MIACME.

MIACME ISA-Tab configurations

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 ISA model can be serialised in multiple formats, including tabular format (ISA-Tab), the JavaScript Object Notation (JSON) and Resource Description Framework (RDF).

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:

A configuration for a single assay, where the user needs to specify the measurement and technology. A configuration considering multiple assays, where the user can select the assay type (e.g. 3D cell tracking assay, capillary chamber migration assay)

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.

Creation of MIACME-compliant metadata

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.

Future plans