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Caosdb Alexander Schlemmer (MPIDS, G ottingen) CaosDB 1 / 25 - PowerPoint PPT Presentation

Jan 13, 2024 •334 likes •575 views

Evaluation of the semantic research data management system CaosDB in glaciology Alexander Schlemmer 1,* , Henrik tom W orden 1,* , Johannes Freitag 2 , Timm Fitschen 1,* , Johanna Kerch 2 , York Schlomann 2 , Daniel Hornung 1,* , Ilka Weikusat 2

  1. Evaluation of the semantic research data management system CaosDB in glaciology Alexander Schlemmer 1,* , Henrik tom W¨ orden 1,* , Johannes Freitag 2 , Timm Fitschen 1,* , Johanna Kerch 2 , York Schlomann 2 , Daniel Hornung 1,* , Ilka Weikusat 2 , Ulrich Parlitz 1 , Frank Wilhelms 2 and Stefan Luther 1 MPI for Dynamics and Self-Organization, G¨ ottingen (1) AWI for Polar and Marine Research, Bremerhaven (2) IndiScale GmbH i.G. (*) 2019-06-05 Caosdb Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 1 / 25

  2. CaosDB Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 2 / 25

  3. Important Requirements for Research Data Management Simple but expressive search functionality Ability to store every data format, at any file size Possibility to store, link and retrieve raw data, processed data, analysis results and documentation Support all kinds of data analysis software, from simple scripts to high-level software Minimally invasive workflow Scientific environments change often: Need for flexible data model Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 3 / 25

  4. Research Data Management during Data Analysis Data Aquisition Data Publication Data Repositories Electronic Lab Notebooks ePIC / PID A 290 A 121 Exp 002 Metadata z.B. RSpace, IDBS E-WorkBook, Biovia Data Analysis Scientist picture: 201705 Scientist bench F.svg from commons.wikimedia.org/wiki/Category:Life_science_images_from_DBCLS , CC-BY 4.0 Bookshelf: https://openclipart.org/detail/289378/bookshelf-with-blue-books Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 4 / 25

  5. CaosDB Overview Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 7 / 25

  6. State and Future of the Project CaosDB is a scientific project at the Research Group Biomedical Physics (MPI G¨ ottingen) It is developed since ≈ 8 years and running stable since ≈ 2016 CaosDB has been released as OpenSource software in 2018 Service Company: IndiScale GmbH i.G. CaosDB is currently tested in other workgroups in and outside of G¨ ottingen → Very positive feedback Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 8 / 25

  7. CaosDB in Glaciology at the AWI in Bremerhaven Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 9 / 25

  8. Aims of the Collaborative Project System for efficient management of ice core boxes → Future extension to sample management Testing of the flexible data model of CaosDB in the context of polar research Evaluation of CaosDB in a different scientific environment Feedback from new users Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 10 / 25

  9. Ice Cores Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 11 / 25

  10. UML diagram of the data model Box Properties obligatory Number (TEXT) Content (TEXT) BoxT ype (BoxT ype) Location (TEXT) Responsible (Person) Palette (Palette) oldVersion (REFERENCE) CarrierNumber (INTEGER) Loan (Loan) Loan Palette Properties recommended BoxT ype Properties Box (Box) Borrower (Person) obligatory Properties loanRequested (DATETIME) Number (TEXT) obligatory loanAccepted (DATETIME) maximumNumberOfBoxes (INTEGER) Width (DOUBLE) lent (DATETIME) accessible (BOOLEAN) Length (DOUBLE) returnRequested (DATETIME) StorageArea (TEXT) Height (DOUBLE) returned (DATETIME) Aisle (TEXT) Kind (TEXT) expectedReturn (DATETIME) Site (TEXT) comment (TEXT) Level (TEXT) destination (TEXT) StorageDate (DATETIME) returnAccepted (DATETIME) exhaustContents (BOOLEAN) Person Properties recommended fi rstName (TEXT) lastName (TEXT) email (TEXT) Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 12 / 25

  11. Querying the Data Model FIND Record Box with Number = "0258" SELECT Number, Content from Box with Content like "ice" FIND Record Box with palette with number = "12" FIND Fabric which references Section which references Bag which references PPStrip which references Core with name = "EGRIP" Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 13 / 25

  12. WebUI Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 14 / 25

  13. Implementation of the Loan Workflow Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 15 / 25

  14. Implementation of the Loan Workflow Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 16 / 25

  15. Implementation of the Loan Workflow Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 17 / 25

  16. Full Ice Core Box Loan Workflow Box Record in Updates Borrow Loan Accepted Lent Loan Requested Updates Return Loan Record in Manual Return Reference Return Accepted Return Requested Automatic Return Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 18 / 25

  17. Automatic Return Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 19 / 25

  18. Searching Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 20 / 25

  19. Listings Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 21 / 25

  20. From Box Management to Sample Management Core Core Core Core Core Core Core PPStrip PPStrip PPStrip PPStrip PPStrip PPStrip Bag Bag Bag Bag Bag Section Section Section Section Bag Bag Bag Bag Bag Section Section Section Section Isotope Isotope Isotope Isotope Isotope Isotope CFA CFA CFA CFA CFA CFA LASM LASM LASM Fabric Fabric Fabric Analysis 1 Analysis 1 Analysis 2 Analysis 2 Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 22 / 25

  21. Data Analysis in CaosDB Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 23 / 25

  22. Data Analysis in CaosDB Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 24 / 25

  23. More Information Caosdb OpenSource Project: https://gitlab.gwdg.de/bmp-caosdb Paper on ArXiv: https://arxiv.org/abs/1801.07653 , under review in Data 1 Thank You! 1 Addendum: The paper is now published, https://doi.org/10.3390/data4020083 Alexander Schlemmer (MPIDS, G¨ ottingen) CaosDB 25 / 25

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