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CMSO Minimal reporting requirements

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Minimal reporting requirements for cell migration - update from Working Group 1 of the Cell Migration Standardisation Organisation

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CMSO Minimal reporting requirements

  1. 1. Minimal reporting requirements for cell migration (WG1) Alejandra Gonzalez-Beltran Oxford e-Research Centre, University of Oxford @alegonbel CSMO Workshop, 19th June 2017, Essen, Germany
  2. 2. Working Group Objectives ● Formulation of a reporting guideline for Cell Migration experiments (MIACME) supporting the requirements to make data produced in such experiments FAIR (Findable Accessible Interoperable and Reusable) ● Reach agreement from the community on the minimal descriptors (and extended descriptors) required to understand, interpret, evaluate, replicate and disseminate cell migration experiments ● Use MIACME to promote data access, data discovery, data preservation and to maximise data re-use and repurpose through efficient annotation for long term archiving ● Ultimately, enable reproducibility of cell migration experiments
  3. 3. MIACME development ● Gradient of information (data discovery/access/preservation to understand, interpret, evaluate, re-use, repurpose, replicate, reproduce) ● Iterative process: (design → test → refine → evaluate) cycle ● “Minimal” set of descriptors ○ Strike the right balance between number of descriptors and the objectives for collecting them ○ “Minimal” is dependent on experiment type ■ Consider core set of descriptors and extensions, if necessary ○ “Optimal” set of descriptors ● Community-led process ○ Community consensus is key to agree on a standard way of reporting cell migration experiments
  4. 4. https://github.com/CellMigStandOrg/MIACME
  5. 5. Community-driven development http://cellmigstandorg.github.io/MIACME/v0.2/spec/
  6. 6. MIACME development - timeline ● Pre-inaugural workshop compilation of material ● 1st CMSO workshop ○ Raking of descriptors ○ MIACME survey ● MIACME v0.1 - (released January 2017) ● 2nd CMSO workshop ○ Revised MIACME v0.1, simplification: selected minimal descriptors ○ Evaluation through the representation of experiments ● MIACME v0.2 (ready for release)
  7. 7. https://biosharing.org/collection/MIBBI
  8. 8. MIACME available in Biosharing portal of standards (and related Standards, Databases and Policies) https://biosharing.org/bsg-s000642
  9. 9. MIACME Survey to identify and rank possible MIACME descriptors http://tiny.cc/miacme-survey
  10. 10. MIACME Descriptors Ranking http://tiny.cc/miacme-ranking
  11. 11. MIACME v0.1 http://tiny.cc/miacme-0-1-fig
  12. 12. MIACME v0.1 list of descriptors Focused on in vitro experiments http://tiny.cc/miacme-live
  13. 13. MIACME v0.1 Specification http://cellmigstandorg.github.io/MIACME/v0.1/spec/
  14. 14. MIACME v0.2 - Experimental setup Assay type Interference Microenv substrate Microenv tissue Cell type Medium Experimental setup single-cell migration, collective cell migration, developmental assay, immune response, chemotaxic, microfluidic, wound-healing, spheroid RNAi, gene construct, chemicals, serum, substrate stiffness ------------------------- specific protein glass, plastic, ECM, gel ------------------------- Collagen, fibronectin mouse, dermis, Zebrafish embryo cell line, primary cell, endogenous cell EGF, HGF one or the other
  15. 15. MIACME v0.2 - Imaging condition Imaging condition Imaging modality confocal microscopy, spinning disk, wide-field, multi-photon, light-sheet, super-resolution, phase-contrast Temporal resolution end-point, time-lapse Duration and frequency Objective Channel readout 1..n 36 hours, 10 minutes 20x, oil conditional on time-lapse Specific protein/subcellular compartment, traction force beads, ratio (FRET), cell body/bodies ----------------------------- - antibody, FP-tagged, dye
  16. 16. MIACME v0.2 - Data Data (1..n) Raw images YES or NO Total number of images conditional on YES 250 Processed images Extracted features trajectories (x, y, t), derived quantities like cell speed, persistence of motion, shape features (cell area, cell solidity, cell perimeter…) filtered images, deconvoluted images, masked images, images with tracks overlay, traction flow, PIV flow fields
  17. 17. MIACME v0.2
  18. 18. Roadmap MIACME v0.2 has focused on identifying the main descriptors. In the next steps, we will: ● produce more examples of MIACME-compliant descriptions of different types of cell migration experiments for evaluation ● include further requirements related to semantic artifacts and other external resources ● consider relationship/alignment with other resources, e.g. MIACA - Minimum Information About a Cellular Assay ● release new versions of the MIACME checklist after incorporating the feedback received
  19. 19. Workshop Work Plan Proposal ● Revision of MIACME v0.2 ○ Provide comments on current descriptors and suggestions for additions / modifications ○ Has the simplification reached the right balance? ● Collect publications/experiments/datasets to be described with MIACME ○ Work in on own publication/dataset ○ Peer assessment ● Analysis of groups’ experimental setups ● Create task forces to deal with specific experiment types ● Work on automatic extraction of some MIACME metadata ○ e.g. objective and temporal resolution ● Interactions with other working groups to consider MIACME in relation to ○ Semantic artifacts and other external resources ○ Formats and APIs
  20. 20. Acknowledgements Paola Masuzzo Marleen van Troys Philippe Rocca-Serra All Working Group 1 members
  21. 21. Thank you! Questions?

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