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Jan 13, 2024 334 likes •576 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

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Evaluation of the semantic research data management system CaosDB in glaciology

Alexander Schlemmer1,*, Henrik tom W¨

rden1,*, Johannes Freitag2,

Timm Fitschen1,*, Johanna Kerch2, York Schlomann2, Daniel Hornung1,*, Ilka Weikusat2, Ulrich Parlitz1, Frank Wilhelms2 and Stefan Luther1 MPI for Dynamics and Self-Organization, G¨

ttingen (1)

AWI for Polar and Marine Research, Bremerhaven (2) IndiScale GmbH i.G. (*) 2019-06-05

Caosdb

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CaosDB

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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

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Research Data Management during Data Analysis

A 290 A 121 Exp 002

Electronic Lab Notebooks

z.B. RSpace, IDBS E-WorkBook, Biovia

Data Aquisition ePIC / PID

Data Repositories

Metadata

Data Publication 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¨

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CaosDB Overview

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State and Future of the Project

CaosDB is a scientific project at the Research Group Biomedical Physics (MPI G¨

ttingen)

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¨

ttingen

→ Very positive feedback

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CaosDB in Glaciology at the AWI in Bremerhaven

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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

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Ice Cores

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UML diagram of the data model

Box Properties Number (TEXT) Content (TEXT) BoxT ype (BoxT ype) Location (TEXT) Responsible (Person) Palette (Palette)

ldVersion (REFERENCE)

CarrierNumber (INTEGER) Loan (Loan)

bligatory

BoxT ype Properties Width (DOUBLE) Length (DOUBLE) Height (DOUBLE) Kind (TEXT)

bligatory

Person Properties firstName (TEXT) lastName (TEXT) email (TEXT) recommended Loan Properties Box (Box) Borrower (Person) loanRequested (DATETIME) loanAccepted (DATETIME) lent (DATETIME) returnRequested (DATETIME) returned (DATETIME) expectedReturn (DATETIME) comment (TEXT) destination (TEXT) returnAccepted (DATETIME) exhaustContents (BOOLEAN) recommended Palette Properties Number (TEXT) maximumNumberOfBoxes (INTEGER) accessible (BOOLEAN) StorageArea (TEXT) Aisle (TEXT) Site (TEXT) Level (TEXT) StorageDate (DATETIME)

bligatory

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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"

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WebUI

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Implementation of the Loan Workflow

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Implementation of the Loan Workflow

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Implementation of the Loan Workflow

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Full Ice Core Box Loan Workflow

Loan Record in

Loan Requested Loan Accepted Borrow Lent Return Requested Return Return Accepted Manual Return Automatic Return

Box Record in

Updates Updates Reference

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Automatic Return

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Searching

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Listings

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From Box Management to Sample Management

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Core CFA Core PPStrip Isotope Bag CFA Core Bag PPStrip Isotope Bag CFA Section Core Bag PPStrip Section Isotope Bag Fabric LASM CFA Section Core Bag PPStrip Section Isotope Bag Analysis 1 Analysis 2 Fabric LASM CFA Section Core Bag PPStrip Section Isotope Bag Analysis 1 Analysis 2 Fabric LASM CFA Section Core Bag PPStrip Section Isotope

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Data Analysis in CaosDB

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Data Analysis in CaosDB

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More Information

Caosdb

OpenSource Project: https://gitlab.gwdg.de/bmp-caosdb Paper on ArXiv: https://arxiv.org/abs/1801.07653, under review in Data1

Thank You!

1Addendum: The paper is now published, https://doi.org/10.3390/data4020083

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