MIOP

Minimum Information about an Omic Protocol” (MIOP)

Created: 20.10.2023. Last edited: 21.10.2023
Project Title Minimum Information about an Omic Protocol (MIOP)

Principle Investigators

Katie J. Pitz, Monterey Bay Aquarium Research Institute, USA kpitz@mbari.org

Team members

Katie J. Pitz, Monterey Bay Aquarium Research Institute, USA kpitz@mbari.org
Neil Davies, UC Gump South Pacific Research Station, Moorea, French Polynesia ndavies@berkeley.edu
Jodie van de Kamp, Commonwealth Scientific and Industrial Research Organisation, Australia, Jodie.Vandekamp@csiro.au
Raissa Meyer, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Germany, raissa.meyer@awi.de
Christina Pavloudi, PSL Research University: EPHE-UPVD-CNRS, France & Laboratoire d’Excellence “CORAIL” (CRIOBE), French Polynesia, cpavloud@hcmr.gr
Nick W. Jeffery, Bedford Institute of Oceanography, Canada, Nick.jeffery@dfo-mpo.gc.ca
Chris Meyer, Smithsonian Institution, National Museum of Natural History, USA, meyerc@si.edu
Pier Luigi Buttigieg, Alfred Wegener Institute,

Elevator Pitch Protocols used to generate omics datasets are often buried in publications and out of date with current sampling efforts. The Minimum Information for an Omics Protocol specifications (MIOP) will contribute to FAIR searchable protocols enabling their discovery and (re)use. MIOP includes consideration not only of relevant scientific metadata but also the CARE principles and metadata pertaining to ethical, legal, and social issues that are as vital for the interpretation and (re)use of omic data and the biosamples from which they are derived.

Project Summary Methodological information is essential to understanding the biomolecular data it generates (its limitations, strengths, and the ability to integrate and compare it with other datasets). However, in the biomolecular community, this information is often buried in publications that lack sufficient detail and are neither machine-readable nor actionable. This is an issue across environments. Within the marine environment, the Better Biomolecular Ocean Practices (BeBOP), an endorsed UN Ocean Decade Project and part of the IOC-UNESCO Ocean Best Practices System (OBPS), has started an effort to exhume and empower these critical information artifacts. Within BeBOP, we are developing machine-readable templates and new metadata specifications that are designed to work together to enable open-access sharing of protocol information. This new standard, called Minimum Information about an Omics Protocol or MIOP, records the relevant scientific metadata but also metadata pertaining to ethical, legal, and social issues that are as vital for the interpretation and (re)use of omic data and the biosamples from which they are derived. MIOP is designed with the goal of being incorporated into the GSC, using similar software infrastructure (yaml files). This work is done in alignment with strategic Ocean Biomolecular Observing Network (OBON) partners in ocean observing and contributing to OBON’s aims for capacity sharing and inter-programme coordination (OBON - OceanPractices; both UN Ocean Decade programmes).

What will this project aim to contribute to the GSC? MIOP is a standardized way to capture and exchange protocol metadata across the wider genomics communities towards increasing the use and visibility of omics protocols.

Have you spoken about the project already within GSC? The MIOP concept was presented at the GSC’s 22nd Meeting (GSC22), and further outlined at GSC23.

Which existing projects, if any, does this one replace/complement/subsume/expand? The project was initiated at the Evolving and Sustaining Ocean Best Practices IV OBPS Workshop 18; 21-25 & 30 Sep 2020 (https://doi.org/10.25607/OBP-1036) through the Omics and eDNA Working Group (Co-leads: Neil Davies, Raïssa Meyer, Katie Pitz, and Robyn Samuel). The MIOP concept was presented at the GSC’s 22nd Meeting (GSC22) held in March 2022: UNESCO-IOC: Ocean Best Practices System & Ocean Data and Information System / MIOP - Minimum information about an omics protocol - Kathleen Pitz (MBARI)

A first version of MIOP was released via github, (Kathleen Pitz, Raïssa Meyer, & Pier Luigi Buttigieg. (2023). BeBOP-OBON/miop: MIOP release v0.1.0 (v0.1). Zenodo. https://doi.org/10.5281/zenodo.7637660).

How does this project fit into GSC’s mission statement? Standardised protocols are a vital part of making data interoperable, which is one of the key points in the GSC mission statement.

Will you start a GSC working group?

How do you wish to further engage the GSC?

Do you already have a website or do you wish to create a home page for the project in the GSC website?

What other resources might you like from what the GSC can offer?

What kind of timeline are you working to for building consensus, releasing a first version etc?

How is this work currently funded?

What are your current plans for publishing/promoting the project?

References or relevant websites For our current website and working space, see https://bebop-obon.github.io/miop.html ; https://github.com/BeBOP-OBON/miop. MIOP terms are defined in a yaml file here: https://github.com/BeBOP-OBON/miop/blob/main/model/schema/terms.yaml.

MIOP standard: https://github.com/BeBOP-OBON/miop BeBOP github page: https://github.com/BeBOP-OBON Protocol templates: https://github.com/BeBOP-OBON/0_protocol_collection_template OBPS task team website: https://www.oceanbestpractices.org/about/task-teams/obps-task-team-21-03-omics-edna-protocol-management/

An example of an institution using the protocol templates within a github webpage: https://bebop-obon.github.io/mbari_protocol_collection/

OmicBON https://geobon.org/bons/thematic-bon/omic-bon/ Ocean Biomolecular Observing Network (OBON): https://www.obon-ocean.org/ Ocean Practices for the Decade (OceanPractices): https://www.oceanbestpractices.org/ocean-practices-for-the-decade/

Simpson, P., Pearlman, F. and Pearlman, J. (eds) (2021) Evolving and Sustaining Ocean Best Practices Workshop IV, 18; 21-25 & 30 Sep 2020 [Online]: Proceedings, Volumes 1 & 2. Paris, France, UNESCO, 66pp. & 115pp. (IOC Workshop Report No. 294, Vols. 1 & 2). DOI: https://doi.org/10.25607/OBP-1036