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Fairy Tales and Data Reuse hash://md5/81421f5597446b9a3eacc8f9991f4bff

Poelen, Jorrit Hoite

Publisher
Zenodo
DOI
10.5281/zenodo.17646740
Repository
zenodo.org
Language
en

Abstract

Presented at the 17-19 Nov 2025 kick-off meeting in Freising, Germany of the EU Horizon’s ProPollSoil project “Understanding and managing soil health impacts to protect soil-dependent pollinators” https://doi.org/10.3030/101219108. Adapted from: Poelen, J.H. (2025) Fairy Tales and Digital Research Data. hash://md5/74cabb19c6dcf3e2eea27a38acf4fb76 Zenodo. https://doi.org/10.5281/zenodo.17625448 Cite As Poelen, J.H. (2025) Fairy Tales and Data Reuse. Zenodo. https://doi.org/10.5281/zenodo.17646740 License CC BY 4.0. For license text, see https://creativecommons.org/licenses/by/4.0/. Guiding Question How do you ensure your data is reused? Digital Data are hard to reuse […] In 2016, the ‘FAIR Guiding Principles for scientific data management and stewardship’1 were published in Scientific Data. The authors intended to provide guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets. The principles emphasise machine-actionability (i.e., the capacity of computational systems to find, access, interoperate, and reuse data with none or minimal human intervention) because humans increasingly rely on computational support to deal with data as a result of the increase in volume, complexity, and creation speed of data. […] 2 Biodiversity Data are hard to reuse […] “The various books and journals of ornithology and entomology are like a row of beehives containing an immense amount of valuable honey, which has been stored up in separate cells by the bees that made it. The advantage, and at the same time the difficulty, of ecological work is that it attempts to provide conceptions which can link up into some complete scheme the colossal store of facts about natural history which has accumulated up to date in this rather haphazard manner. […] Until more organised information about the subject is available, it is only possible to give a few instances of some of the more clear­cut niches which happen to have been worked out. […]” 3 Biodiversity Data are hard to reuse […] “The various books and journals of ornithology and entomology are like a row of beehives containing an immense amount of valuable honey, which has been stored up in separate cells by the bees that made it. The advantage, and at the same time the difficulty, of ecological work is that it attempts to provide conceptions which can link up into some complete scheme the colossal store of facts about natural history which has accumulated up to date in this rather haphazard manner. […] Until more organised information about the subject is available, it is only possible to give a few instances of some of the more clear­cut niches which happen to have been worked out. […]” 4 Biodiversity Data are hard to reuse […] “The various books and journals of ornithology and entomology are like a row of beehives containing an immense amount of valuable honey, which has been stored up in separate cells by the bees that made it. The advantage, and at the same time the difficulty, of ecological work is that it attempts to provide conceptions which can link up into some complete scheme the colossal store of facts about natural history which has accumulated up to date in this rather haphazard manner. […] Until more organised information about the subject is available, it is only possible to give a few instances of some of the more clear­cut niches which happen to have been worked out. […]” 5 Who or what keeps our Digital Biodiversity Data reusable? the FAIR Data Fairy. Awareness of the complexity of reusing digital data. Common sense data reuse and review practices. Who or what keeps our Digital Biodiversity Data reusable? the FAIR Data Fairy. Who is this FAIR Data Fairy? Awareness of the complexity of reusing digital data. Common sense data reuse and review practices. Is GBIF our FAIR Data Fairy? GBIF Secretariat provides a publication framework for biodiversity data, but is neither the owner nor custodian of such data, and therefore is not responsible for the actual content served by Data Publishers. GBIF Secretariat cannot guarantee the quality or completeness of data, nor does it guarantee uninterrupted data access services. Users employ these data and services at their own risk. 6. Is GBIF our FAIR Data Fairy? GBIF Secretariat provides a publication framework for biodiversity data, but is neither the owner nor custodian of such data, and therefore is not responsible for the actual content served by Data Publishers. GBIF Secretariat cannot guarantee the quality or completeness of data, nor does it guarantee uninterrupted data access services. Users employ these data and services at their own risk. 7. No! GBIF provides a framework in which standardized biodiversity datasets can be registered, reviewed, and queried. However, you are responsible for ensuring that the data continues to be fit for reuse. Is Zenodo our FAIR Data Fairy? […] Data files are versioned. Records are not versioned. […] Records can be retracted from public view; however, the data files and record are preserved. […] Items will be retained for the lifetime of the repository. This is currently the lifetime of the host laboratory CERN, which currently has an experimental programme defined for the next 20 years at least. […] All data files are stored in CERN Data Centres, primarily Geneva, with replicas in Budapest. […] In case of closure of the repository, best efforts will be made to integrate all content into suitable alternative institutional and/or subject based repositories. […] 8. Is Zenodo our FAIR Data Fairy? […] Data files are versioned. Records are not versioned. […] Records can be retracted from public view; however, the data files and record are preserved. […] Items will be retained for the lifetime of the repository. This is currently the lifetime of the host laboratory CERN, which currently has an experimental programme defined for the next 20 years at least. […] All data files are stored in CERN Data Centres, primarily Geneva, with replicas in Budapest. […] In case of closure of the repository, best efforts will be made to integrate all content into suitable alternative institutional and/or subject based repositories. […] 9. No! Zenodo provides a framework in which digital works can be deposited, found, and retrieved. However, you are responsible for ensuring that the data continues to be fit for reuse. FAIR Data Fairy is a Cousin of the Poop Fairy. FAIR Data Fairy is a Cousin of the Poop Fairy. Recent Reminders of FAIR Data Fairy Absence Scholarly data… cannot be found because it is left unpublished on a personal laptop or desk drawer cannot be accessed due to “data available on request” of retired/deceased author is lost due to malicious activity (e.g., hacking, ransonware) or human error (oops!) is published using custom schemas instead of schemas used by others is published in proprietary or machine unfriendly file formats (e.g., xlsx, docx, pdf) is riddled with data inconsistencies and typos cannot be easily reused/linked/integrated with other datasets/projects are effectively excluded during peer review process due to time constraints Who or what keeps our Digital Biodiversity Data reusable? the FAIR Data Fairy Awareness of the complexity of reusing digital data. Common sense data reuse and review practices. Guiding Questions How do you reuse/review your own (past, present, future) digital research data? How do you reuse/review third party (past, present, future) digital research data? Who or what keeps our Digital Biodiversity Data reusable? the FAIR Data Fairy Awareness of the complexity of reusing digital data. Common sense data reuse and review practices. Peer Review for Digital Biodiversity Data What is so neat about peer review? How to review digital data? The Neat Thing about Peer Review Even before Mainly after the invention of the book press, books and scrolls scholarly journals and academic societies10 have been pretty successful in transferring scientific knowledge across generations and around the world. Books Scholarly journals are kept around the world in (little) public libraries, academic institutions, private collections and national archives. Books Printed scholarly journals are wireless, their content cannot be easily altered remotely, changes can be detected (ripped out pages), and they need no power to operate. (note to self: archive digital only journals) Typically, scholarly journals employ a peer review process to select scholarly works of interest and increase their quality through review cycles and discourse. The Neat Thing about Physical Books Even before Mainly after the invention of the book press, books and scrolls scholarly journals and academic societies11 have been pretty successful in transferring scientific knowledge across generations and around the world. Books Scholarly journals are kept around the world in (little) public libraries, academic institutions, private collections and national archives. Books Printed scholarly journals are wireless, their content cannot be easily altered remotely, changes can be detected (ripped out pages), and they need no power to operate. (note to self: archive digital only journals) Typically, scholarly journals employ a peer review process to select scholarly works of interest and increase their quality through review cycles and discourse. Idea … what if we treat digital data more like a peer-reviewed publication instead of some haphazardly organized data appendix? Steps to Reviewing Digital Data To enable the discovery of existing species interaction datasets, Global Biotic Interactions (GloBI) continuously tracks existing datasets and integrates the discovered interaction records. These integrated interaction records form the basis of the GloBI’s interpreted interaction data. 12 Step 1. automatically discover species interaction datasets Step 2. automatically access up-to-date datasets and versioned them Step 3. automatically parse data and link/integrate with other datasets (e.g., taxonomic resources) Step 4. automatically produce derived data products and data services Step 5. automatically publish derived datasets and associated GloBI data reviews Step 6. semi-manual solicit feedback and encourage discussion through open access and Step 7. repeat continuously until (not yet planned) retirement Steps to Reviewing Digital Data: Example A spinose ear tick (Otobius megnini) a mammalian parasites (Lindström, A. 2017). from: Fowler, S. 2020. Extracting Parasite Interaction Data from a Scientific Paper using Google Sheets. Accessed on 2025-11-19 on https://www.globalbioticinteractions.org/2020/08/25/extracting-parasite-interaction-data/ Steps to Reviewing Digital Data: Example An example of the Google Sheets spreadsheet used for transcribing data. GloBI accessed the transcribed data set through open source scripts accessible on GitHub. Once every other day the data was indexed into GloBI data products. (Fowler, S. 2020) Steps to Reviewing Digital Data: Example Elton, Nomer, & Preston. (2025). Versioned Archive and Review of Biotic Interactions and Taxon Names Found within globalbioticinteractions/light2019 hash://md5/c9dad8bc30bcac362bcb8116444af31d. Zenodo. doi:10.5281/zenodo.16416949 Steps to Reviewing Digital Data: Example GloBI interactive search results as accessed on 2025-11-19 via https://www.globalbioticinteractions.org Steps to Reviewing Digital Data: Example GloBI interactive search results as accessed on 2025-11-19 via https://www.globalbioticinteractions.org Steps to Reviewing Digital Data: Example Step 1. use Elton 13 to discover dataset metadata at https://github.com/globalbioticinteractions/light2019 Step 2. use Elton to access and version csv file available through Google Sheet 1Fo…DxY Step 3. use Elton and Nomer to align taxonomic names with NCBI taxonomy, Catalogue of Life etc. Step 4. use Elton, Nomer, pandoc to produce derived datasets and a data review. Step 5. use Preston to publish derived datasets and associated GloBI data review to Zenodo. Step 6. semi-manual solicit feedback and encourage discussion through email, meetings and open data platforms Step 7. repeat continuously until (not yet planned) retirement Who or what keeps our Digital Biodiversity Data around? the FAIR Data Fairy Awareness of the complexity of reusing digital data. Common sense data reuse and review practices. Guiding Question What is one of your experiences that comes to mind in which digital data was unfindable, riddled with errors or otherwise hard to reuse? Share your horror story! And Remember Thank you! Made possible (in part) by Horizon Europe’s 101219108 For questions/comments/ideas, please do reach out to: Jorrit H. Poelen https://jhpoelen.nl [email protected] https://orcid.org/0000-0003-3138-4118 Guiding Question How do you ensure your data is reused? Wilkinson, et al. 2016, Sci Data doi:10.1038/sdata.2016.18↩︎ Accessed on 2025-11-19 at https://www.go-fair.org/fair-principles/.↩︎ Charles Elton, 1927. Animal Ecology. pp 65-66. doi:10.5962/bhl.title.7435↩︎ Charles Elton, 1927. Animal Ecology. pp 65-66. doi:10.5962/bhl.title.7435↩︎ Charles Elton, 1927. Animal Ecology. pp 65-66. doi:10.5962/bhl.title.7435↩︎ https://www.gbif.org/terms/data-user as accessed on 2025-10-13↩︎ https://www.gbif.org/terms/data-user as accessed on 2025-10-13↩︎ https://about.zenodo.org/policies/ as accessed on 2025-11-05↩︎ https://about.zenodo.org/policies/ as accessed on 2025-11-05↩︎ First journal “Philosophical Transactions” was launched in 1665 according to https://royalsocietypublishing.org/journal/rstl accessed on 2025-11-19.↩︎ First journal “Philosophical Transactions” was launched in 1665 according to https://royalsocietypublishing.org/journal/rstl accessed on 2025-11-19.↩︎ https://globalbioticinteractions.org/process accessed on 2025-11-19↩︎ For review robots description see: https://globalbioticinteractions.org/process↩︎

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Fairy Tales and Data Reuse Jorrit H. Poelen 2025-11-19 Presented at the 17-19 Nov 2025 kick-off meeting in Freising, Germany of the EU Horizon’s ProPollSoil project “Understanding and managing soil health impacts to protect soil-dependent pollinators” https://doi.org/10.3030/101219108. Adapted from: Poelen, J.H. (2025) Fairy Tales and Digital Research Data. hash://md5/74cabb19c6dcf3e2eea27a38acf4fb76 Zenodo. https://doi.org/10.5281/zenodo.17625448 Cite As Poelen, J.H. (2025) Fairy Tales and Data Reuse. Zenodo. https://doi.org/10.5281/zenodo.17646740 License CC BY 4.0. For license text, see https://creativecommons.org/licenses/by/4.0/. Guiding Question How do you ensure your data is reused? Digital Data are hard to reuse [. . . ] In 2016, the ‘FAIR Guiding Principles for scientific data management and stewardship’ 1 were published in Scientific Data. The authors intended to provide guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets. The principles emphasise machine-actionability (i.e., the capacity of computational systems to find, access, interoperate, and reuse data with none or minimal human intervention) because humans increasingly rely on computational support to deal with data as a result of the increase in volume, complexity, and creation speed of data. [. . . ] 2 1Wilkinson, et al. 2016, Sci Data doi:10.1038/sdata.2016.18 2Accessed on 2025-11-19 at https://www.go-fair.org/fair-principles/. Biodiversity Data are hard to reuse [. . . ] “The various books and journals of ornithology and entomology are like a row of beehives containing an immense amount of valuable honey, which has been stored up in separate cells by the bees that made it. The advantage, and at the same time the difficulty, of ecological work is that it attempts to provide conceptions which can link up into some complete scheme the colossal store of facts about natural history which has accumulated up to date in this rather haphazard manner. [. . . ] Until more organised information about the subject is available, it is only possible to give a few instances of some of the more clearcut niches which happen to have been worked out. [. . . ]” 3 3Charles Elton, 1927. Animal Ecology. pp 65-66. doi:10.5962/bhl.title.7435 Biodiversity Data are hard to reuse [. . . ] “The various books and journals of ornithology and entomology are like a row of beehives containing an immense amount of valuable honey, which has been stored up in separate cells by the bees that made it. The advantage, and at the same time the difficulty, of ecological work is that it attempts to provide conceptions which can link up into some complete scheme the colossal store of facts about natural history which has accumulated up to date in this rather haphazard manner. [. . . ] Until more organised information about the subject is available, it is only possible to give a few instances of some of the more clearcut niches which happen to have been worked out. [. . . ]” 4 4Charles Elton, 1927. Animal Ecology. pp 65-66. doi:10.5962/bhl.title.7435 Biodiversity Data are hard to reuse [. . . ] “The various books and journals of ornithology and entomology are like a row of beehives containing an immense amount of valuable honey, which has been stored up in separate cells by the bees that made it. The advantage, and at the same time the difficulty, of ecological work is that it attempts to provide conceptions which can link up into some complete scheme the colossal store of facts about natural history which has accumulated up to date in this rather haphazard manner. [. . . ] Until more organised information about the subject is available, it is only possible to give a few instances of some of the more clearcut niches which happen to have been worked out. [. . . ]” 5 5Charles Elton, 1927. Animal Ecology. pp 65-66. doi:10.5962/bhl.title.7435 FAIR Data Fairy is a Cousin of the Poop Fairy. FAIR Data Fairy is a Cousin of the Poop Fairy. Recent Reminders of FAIR Data Fairy Absence Scholarly data. . . ▶ cannot be found because it is left unpublished on a personal laptop or desk drawer ▶cannot be accessed due to “data available on request” of retired/deceased author ▶ is lost due to malicious activity (e.g., hacking, ransonware) or human error (oops!) ▶is published using custom schemas instead of schemas used by others ▶ is published in proprietary or machine unfriendly file formats (e.g., xlsx, docx, pdf) ▶is riddled with data inconsistencies and typos ▶cannot be easily reused/linked/integrated with other datasets/projects ▶are effectively excluded during peer review process due to time constraints Who or what keeps our Digital Biodiversity Data reusable? a) the FAIR Data Fairy b) Awareness of the complexity of reusing digital data. c) Common sense data reuse and review practices. Guiding Questions How do you reuse/review your own (past, present, future) digital research data? How do you reuse/review third party (past, present, future) digital research data? Who or what keeps our Digital Biodiversity Data reusable? a) the FAIR Data Fairy b) Awareness of the complexity of reusing digital data. c) Common sense data reuse and review practices. Peer Review for Digital Biodiversity Data ▶What is so neat about peer review? ▶How to review digital data? The Neat Thing about Peer Review Even before Mainly after the invention of the book press, books and scrolls scholarly journals and academic societies10 have been pretty successful in transferring scientific knowledge across generations and around the world. Books Scholarly journals are kept around the world in (little) public libraries, academic institutions, private collections and national archives. Books Printed scholarly journals are wireless, their content cannot be easily altered remotely, changes can be detected (ripped out pages), and they need no power to operate. (note to self: archive digital only journals) Typically, scholarly journals employ a peer review process to select scholarly works of interest and increase their quality through review cycles and discourse. 10First journal “Philosophical Transactions” was launched in 1665 according to https://royalsocietypublishing.org/journal/rstl accessed on 2025-11-19. The Neat Thing about Physical Books Even before Mainly after the invention of the book press, books and scrolls scholarly journals and academic societies11 have been pretty successful in transferring scientific knowledge across generations and around the world. Books Scholarly journals are kept around the world in (little) public libraries, academic institutions, private collections and national archives. Books Printed scholarly journals are wireless, their content cannot be easily altered remotely, changes can be detected (ripped out pages), and they need no power to operate. (note to self: archive digital only journals) Typically, scholarly journals employ a peer review process to select scholarly works of interest and increase their quality through review cycles and discourse. Idea . . . what if we treat digital data more like a peer-reviewed publication instead of some haphazardly organized data appendix? 11First journal “Philosophical Transactions” was launched in 1665 according to https://royalsocietypublishing.org/journal/rstl accessed on 2025-11-19. Steps to Reviewing Digital Data To enable the discovery of existing species interaction datasets, Global Biotic Interactions (GloBI) continuously tracks existing datasets and integrates the discovered interaction records. These integrated interaction records form the basis of the GloBI’s interpreted interaction data. 12 Step 1. automatically discover species interaction datasets Step 2. automatically access up-to-date datasets and versioned them Step 3. automatically parse data and link/integrate with other datasets (e.g., taxonomic resources) Step 4. automatically produce derived data products and data services Step 5. automatically publish derived datasets and associated GloBI data reviews Step 6. semi-manual solicit feedback and encourage discussion through open access and Step 7. repeat continuously until (not yet planned) retirement 12https://globalbioticinteractions.org/process accessed on 2025-11-19 Who or what keeps our Digital Biodiversity Data around? a) the FAIR Data Fairy b) Awareness of the complexity of reusing digital data. c) Common sense data reuse and review practices. Guiding Question What is one of your experiences that comes to mind in which digital data was unfindable, riddled with errors or otherwise hard to reuse? Share your horror story! And Remember Thank you! Made possible (in part) by Horizon Europe’s 101219108 For questions/comments/ideas, please do reach out to: Jorrit H. Poelen https://jhpoelen.nl [email protected] https://orcid.org/0000-0003-3138-4118 Guiding Question How do you ensure your data is reused?