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Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis

Alessandro Rigano, View ORCID ProfileCaterina Strambio-De-Castillia
doi: https://doi.org/10.1101/155036
Alessandro Rigano
1Program in Molecular Medicine University of Massachusetts Medical School Worcester, MA 01605
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Caterina Strambio-De-Castillia
1Program in Molecular Medicine University of Massachusetts Medical School Worcester, MA 01605
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Abstract

The proposed Minimum Information About Particle Tracking Experiments (MIAPTE) reporting guidelines described here aim to deliver a set of rules representing the minimal information required to report and support interpretation and assessment of data arising from intracellular multiple particle tracking (MPT) experiments. Examples of such experiments are those tracking viral particles as they move from the site of entry to the site of replication within an infected cell, or those following vesicular dynamics during secretion, endocytosis, or exocytosis. By promoting development of community standards, we hope that MIAPTE will contribute to making MPT data FAIR (Findable Accessible Interoperable and Reusable). Ultimately, the goal of MIAPTE is to promote and maximize data access, discovery, preservation, re-use, and repurposing through efficient annotation, and ultimately to enable reproducibility of particle tracking experiments. This document introduces MIAPTE v0.2, which updates the version that was posted to Fairsharing.org in October 2016. MIAPTE v0.2 is presented with the specific intent of soliciting comments from the particle tracking community with the purpose of extending and improving the model. The MIAPTE guidelines are intended for different categories of users: 1) Scientists with the desire to make new results available in a way that can be interpreted unequivocally by both humans and machines. For this class of users, MIAPTE provides data descriptors to define data entry terms and the analysis workflow in a unified manner. 2) Scientists wishing to evaluate, replicate and re-analyze results published by others. For this class of users MIAPTE provides descriptors that define the analysis procedures in a manner that facilitates its reproduction. 3) Developers who want to take advantage of the schema of MIAPTE to produce MIAPTE compatible tools. MIAPTE consists of a list of controlled vocabulary (CV) terms that describe elements and properties for the minimal description of particle tracking experiments, with a focus on viral and vesicular traffic within cells. As part of this submission we provide entity relationship (ER) diagrams that show the relationship between terms. Finally, we also provide documents containing the MIAPTE-compliant XML schema describing the data model used by Open Microscopy Environment inteGrated Analysis (OMEGA), our novel particle tracking data analysis and management tool, which is reported in a separate manuscript. MIAPTE is structured in two sub-sections: 1) Section 1 contains elements, attributes and data structures describing the results of particle tracking, namely: particles, links, trajectories and trajectory segments. 2) Section 2 contains elements that provide details about the algorithmic procedure utilized to produce and analyze trajectories as well as the results of trajectory analysis. In addition MIAPTE includes those OME-XML elements that are required to capture the acquisition parameters and the structure of images to be subjected to particle tracking.

Footnotes

  • Abbreviations
    MPT
    multiple particle tracking.
    MIBBI
    minimum information about biological and biomedical investigations.
    OME
    open microscopy environment
    SPT
    single particle tracking

  • This document establishes a checklist for the minimum information required to report multiple particle tracking (MPT) experiments, in a manner compliant with the Minimum Information for Biological and Biomedical Investigations (MIBBI) guidelines (http://www.nature.com/nbt/journal/v26/n8/full/nbt.1411.html). Guidelines presented here are intended to be sufficient to support the effective (re-)interpretation and (re-)assessment of the data as well as the potential reproduction of the experimental and analytical workflow that generated it.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted July 13, 2017.
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Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis
Alessandro Rigano, Caterina Strambio-De-Castillia
bioRxiv 155036; doi: https://doi.org/10.1101/155036
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Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis
Alessandro Rigano, Caterina Strambio-De-Castillia
bioRxiv 155036; doi: https://doi.org/10.1101/155036

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