Applying Open Science principles to make a better use of IOTC data

Barde, Julien; Grasset, Bastien; CHASSOT, Emmanuel; Bonhommeau, Sylvain; Blondel, Emmanuel

doi:10.5281/zenodo.17745020

Applying Open Science principles to make a better use of IOTC data

Barde, Julien; Grasset, Bastien; CHASSOT, Emmanuel; Bonhommeau, Sylvain; Blondel, Emmanuel

Publisher: Zenodo
DOI: 10.5281/zenodo.17745020
Repository: zenodo.org
Language: en

Abstract

In this paper, we further discuss known issues, achievements and challenges to improve IOTC resources management and we attempt to identify opportunities brought by Open Science principles to face them. For a regional organization like IOTC, we recommend to promote and implement these good practices internally at the Secretariat level as well as externally to expose and disseminate resources though multiple channels for the sake of users (CPCs or wider audience). Such practices appear to be instrumental as well when reusing external contributions or when sub-contracting or delegating tasks to CPCs. We also showcase how such good practices can be implemented "at no cost" in a simple and efficient way by relying on external infrastructures. As a demonstrator we showcase how IOTC size class datasets management can be improved to better feed external initiatives like the Global Tuna Atlas datasets update and related Shiny apps. We explain how this approach can be used beyond fisheries data management and visualization to foster the publication and reproducibility of additional research work like stock assessment models runs outputs.

Full text

Applying Open Science principles to make a better use of IOTC data Julien Barde, Bastien Grasset, Emmanuel Chassot, Sylvain Bonhommeau, Emmanuel Blondel Open Science pillars (UNESCO) 2 + Context of reproducibility crisis Open Science pillars (UNESCO) 3 + Context of reproducibility crisis Open Science: how ? Context of reproducibility crisis => work can be replicated with: •data : • data repositories to assign DOIs • implement standards : data structure and formats • data papers • code • forge / git • assign identifiers : e.g. DOI, Software Heritage •environment : • versions of programming language and related packages (R, Python): e.g. renv • also the OS and system packages • Standards to foster interoperability 4 Current IOTC Website will disappear ! 5 You see a problem, I see an opportunity ! Open Science: good practices for IOTC ? IOTC scientific work will become more reproducible by sharing : •data along with metadata (data dictionaries, code lists..) •code : e.g. BET stock assessment •execution environment : easy to access, restore, deploy.. • other scientific resources : •forms, •reports, •working papers, •slides, • …and other educationnal resources Long term access ensured and easy by assigning DOIs with e.g. Zenodo 6 Open Science: benefits ? Reproducible work: • saves time •trust : reviewers of an article can check / replicate • can be reused in other domains • increase citations • can be deployed on a server: e.g. • Shiny app • Stock assessment model and reproduce specific runs • HPC (High Performance computing) • ... 7 Cost ? ●psychological (may be counterintuitive) ● lower efficiency ? Slowing down at first.. Open Science: interoperability ? Standards to foster interoperability for fisheries data • data structures : • fisheries: CWP • biodiversity: GBIF • data formats : • csv or parquet rather than xlsx • spatial : e.g. GeoPackage rather than Shapefile. • Open-source software (OSS) : QGIS, GeoServer • runtime environment : Docker .. 8 Different version DOIs to manage the life stages of a dataset changing over time Open Science: life cycle of digital objects 8 Current IOTC Website will disappear ! 16 …but all resources with a DOI will remain online with the same URL for the next 20 years at least, they can feed the new site but not only. Conclusion - Outlooks Open Science good practices are recommended worldwide: ● reproducibility crisis ● in summary : ○ what should be shared: working papers, data, code, runtime environment.. ○ how ? data repositories (e.g. Zenodo / GBIF..), infrastructures (GitHub, ..) ● for who ? ○ IOTC ○ CPCs ○ Consultants / Sub-contractors : very easy when you pay We recommend that IOTC adopt these good practices by default and ASAP, making the Website migration an opportunity. 17 Acknowledgements This work has received support from the current HORIZON BlueCloud 2026 (grant No. 101094227) and past European OpenAIRE-Connect H2020 research project (grant No. 731011). 18 ● OFCF Photo library => IOTC community ? Without transferring ownership ● IODA : Indian Ocean Digital Atlas to be deployed in Sri Lanka ● GTA vs FishStatJ comparison to be reconducted every year ? ● GBIF / Darwin Core, DOI assigned by data repositories GBIF, Zenodo: ○ size class data ○ IOTTP data ○ biological database ● … 19 Other examples ?