Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research
Nanosafety assessment, which seeks to evaluate the risks from exposure to nanoscale materials, spans materials synthesis and characterisation, exposure science, toxicology, and computational approaches, resulting in complex experimental workflows and diverse data types. Managing the data flows, with...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Beilstein-Institut
2025-01-01
|
| Series: | Beilstein Journal of Nanotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.3762/bjnano.16.7 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832544802929901568 |
|---|---|
| author | Benjamin Punz Maja Brajnik Joh Dokler Jaleesia D. Amos Litty Johnson Katie Reilly Anastasios G. Papadiamantis Amaia Green Etxabe Lee Walker Diego S. T. Martinez Steffi Friedrichs Klaus M. Weltring Nazende Günday-Türeli Claus Svendsen Christine Ogilvie Hendren Mark R. Wiesner Martin Himly Iseult Lynch Thomas E. Exner |
| author_facet | Benjamin Punz Maja Brajnik Joh Dokler Jaleesia D. Amos Litty Johnson Katie Reilly Anastasios G. Papadiamantis Amaia Green Etxabe Lee Walker Diego S. T. Martinez Steffi Friedrichs Klaus M. Weltring Nazende Günday-Türeli Claus Svendsen Christine Ogilvie Hendren Mark R. Wiesner Martin Himly Iseult Lynch Thomas E. Exner |
| author_sort | Benjamin Punz |
| collection | DOAJ |
| description | Nanosafety assessment, which seeks to evaluate the risks from exposure to nanoscale materials, spans materials synthesis and characterisation, exposure science, toxicology, and computational approaches, resulting in complex experimental workflows and diverse data types. Managing the data flows, with a focus on provenance (who generated the data and for what purpose) and quality (how was the data generated, using which protocol with which controls), as part of good research output management, is necessary to maximise the reuse potential and value of the data. Instance maps have been developed and evolved to visualise experimental nanosafety workflows and to bridge the gap between the theoretical principles of FAIR (Findable, Accessible, Interoperable and Re-usable) data and the everyday practice of experimental researchers. Instance maps are most effective when applied at the study design stage to associate the workflow with the nanomaterials, environmental conditions, method descriptions, protocols, biological and computational models to be used, and the data flows arising from study execution. Application of the InstanceMaps tool (described herein) to research workflows of increasing complexity is presented to demonstrate its utility, starting from (i) documentation of a nanomaterial’s synthesis, functionalisation, and characterisation, over (ii) assessment of a nanomaterial’s transformations in complex media, (iii) description of the culturing of ecotoxicity model organisms Daphnia magna and their use in standardised tests for nanomaterials ecotoxicity assessment, and (iv) visualisation of complex workflows in human immunotoxicity assessment using cell lines and primary cellular models, to (v) the use of the instance map approach for the coordination of materials and data flows in complex multipartner collaborative projects and for the demonstration of case studies. Finally, areas for future development of the instance map approach and the tool are highlighted. |
| format | Article |
| id | doaj-art-1329231d0e9d456a82aa23ab2c369b43 |
| institution | Kabale University |
| issn | 2190-4286 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Beilstein-Institut |
| record_format | Article |
| series | Beilstein Journal of Nanotechnology |
| spelling | doaj-art-1329231d0e9d456a82aa23ab2c369b432025-02-03T09:10:12ZengBeilstein-InstitutBeilstein Journal of Nanotechnology2190-42862025-01-01161577710.3762/bjnano.16.72190-4286-16-7Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety researchBenjamin Punz0Maja Brajnik1Joh Dokler2Jaleesia D. Amos3Litty Johnson4Katie Reilly5Anastasios G. Papadiamantis6Amaia Green Etxabe7Lee Walker8Diego S. T. Martinez9Steffi Friedrichs10Klaus M. Weltring11Nazende Günday-Türeli12Claus Svendsen13Christine Ogilvie Hendren14Mark R. Wiesner15Martin Himly16Iseult Lynch17Thomas E. Exner18Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria Seven Past Nine d.o.o., Hribljane 10, 1380 Cerknica, Slovenia Seven Past Nine d.o.o., Hribljane 10, 1380 Cerknica, Slovenia Center for the Environmental Implications of Nano Technology (CEINT), Civil & Environmental Engineering, Duke University, Durham, North Carolina, 2770y8, USA Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom UK Centre for Ecology and Hydrology, Pollution, Wallingford, Oxfordshire, United Kingdom UK Centre for Ecology and Hydrology, Pollution, Wallingford, Oxfordshire, United Kingdom Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil AcumenIST SRL, Etterbeek, BelgiumGesellschaft für Bioanalytik Münster, Mendelstraße 17, 48149 Münster, Germany MyBiotech GmbH, Industriestrasse 1B, 66802 Überherrn, GermanyUK Centre for Ecology and Hydrology, Pollution, Wallingford, Oxfordshire, United Kingdom Department of Geological and Environmental Sciences, Appalachian State University, Boone, USA Center for the Environmental Implications of Nano Technology (CEINT), Civil & Environmental Engineering, Duke University, Durham, North Carolina, 2770y8, USA Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom Seven Past Nine GmbH, Rebacker 68, 79650 Schopfheim, GermanyNanosafety assessment, which seeks to evaluate the risks from exposure to nanoscale materials, spans materials synthesis and characterisation, exposure science, toxicology, and computational approaches, resulting in complex experimental workflows and diverse data types. Managing the data flows, with a focus on provenance (who generated the data and for what purpose) and quality (how was the data generated, using which protocol with which controls), as part of good research output management, is necessary to maximise the reuse potential and value of the data. Instance maps have been developed and evolved to visualise experimental nanosafety workflows and to bridge the gap between the theoretical principles of FAIR (Findable, Accessible, Interoperable and Re-usable) data and the everyday practice of experimental researchers. Instance maps are most effective when applied at the study design stage to associate the workflow with the nanomaterials, environmental conditions, method descriptions, protocols, biological and computational models to be used, and the data flows arising from study execution. Application of the InstanceMaps tool (described herein) to research workflows of increasing complexity is presented to demonstrate its utility, starting from (i) documentation of a nanomaterial’s synthesis, functionalisation, and characterisation, over (ii) assessment of a nanomaterial’s transformations in complex media, (iii) description of the culturing of ecotoxicity model organisms Daphnia magna and their use in standardised tests for nanomaterials ecotoxicity assessment, and (iv) visualisation of complex workflows in human immunotoxicity assessment using cell lines and primary cellular models, to (v) the use of the instance map approach for the coordination of materials and data flows in complex multipartner collaborative projects and for the demonstration of case studies. Finally, areas for future development of the instance map approach and the tool are highlighted.https://doi.org/10.3762/bjnano.16.7data collection and quality controldata provenanceexperimental workflow visualisationfairnanomaterial life cycle stagesstudy design |
| spellingShingle | Benjamin Punz Maja Brajnik Joh Dokler Jaleesia D. Amos Litty Johnson Katie Reilly Anastasios G. Papadiamantis Amaia Green Etxabe Lee Walker Diego S. T. Martinez Steffi Friedrichs Klaus M. Weltring Nazende Günday-Türeli Claus Svendsen Christine Ogilvie Hendren Mark R. Wiesner Martin Himly Iseult Lynch Thomas E. Exner Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research Beilstein Journal of Nanotechnology data collection and quality control data provenance experimental workflow visualisation fair nanomaterial life cycle stages study design |
| title | Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research |
| title_full | Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research |
| title_fullStr | Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research |
| title_full_unstemmed | Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research |
| title_short | Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research |
| title_sort | instance maps as an organising concept for complex experimental workflows as demonstrated for nano material safety research |
| topic | data collection and quality control data provenance experimental workflow visualisation fair nanomaterial life cycle stages study design |
| url | https://doi.org/10.3762/bjnano.16.7 |
| work_keys_str_mv | AT benjaminpunz instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT majabrajnik instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT johdokler instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT jaleesiadamos instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT littyjohnson instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT katiereilly instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT anastasiosgpapadiamantis instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT amaiagreenetxabe instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT leewalker instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT diegostmartinez instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT steffifriedrichs instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT klausmweltring instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT nazendegundaytureli instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT claussvendsen instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT christineogilviehendren instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT markrwiesner instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT martinhimly instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT iseultlynch instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch AT thomaseexner instancemapsasanorganisingconceptforcomplexexperimentalworkflowsasdemonstratedfornanomaterialsafetyresearch |