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Open Science Workshop

Stephanie van de Sandt, Lena Karvovskaya
2022 Zenodo  
AMS organized a workshop on Open Science aimed at all researchers who feel they need an update on this important topic. The workshop was hosted by UBVU, and delved into topics such as OA publishing / sharing data / code / tools / results / open peer review etc. Open Science is the transition to a new, more open and participatory way of conducting, publishing and evaluating scholarly research. Central to this concept is the goal of increasing cooperation and transparency in all research stages.
more » ... his is achieved, among other ways, by sharing research data, publications, software, tools and results as early and open as possible. Open science is a topic that is becoming ever more important, and if you want to take the first dive, or if you are a more experienced open science researcher.
doi:10.5281/zenodo.6565678 fatcat:xq3hmrr5sjdxpinons2clxs2ke

A Tale of Software Citation Pitfalls

Stephanie van de Sandt, Alex Ioannidis
2020 Zenodo  
Open Science contributes in many ways to a Knowledge Ecology. Opening research data and software to scientific and scholarly communities increases not only the transparency of results, but also facilitates the reuse of research artifacts. Citations are recognized as one of the key incentives to make data and software available, as credit is being transmitted to data producers and software developers. Research data and software citations make research results transparent and verifiable but they
more » ... re hard to track, because there is no commonly-shared citation standard across communities. To combat this issue, FORCE11 proposed a set of data and software citation principles as guidance for authors which highlight that credit should be given via formal data and software citations using unique and persistent identifiers (PIDs). Despite their efforts, adoption of citation principles has been advancing slowly, and current citation practices remain idiosyncratic and thus hard to track. This poster demonstrates common pitfalls of software citation practices in the scholarly writing process, which complicate the tracking of software citations: (a) not citing software at all, (b) mentions of the software name only as part of the full text, (c) citing a URL related to software rather than a software PID, and (d) citations to software-related research publications or software papers, which are not trackable by data citation discovery services. These pitfalls result in failure to transmit credit. This poster will introduce one aspect of the interactive game "FAIRytale of Software Citations", which presents the journey of software citations through multiple workflows and the pitfalls of software citations in a narrative with original illustrations. The story features the journey of a scholar carrying tokens of gratitude through the Shiver Forest of Scholarly Writing, facing multiple dangers in his path.
doi:10.5281/zenodo.4263761 fatcat:gegwnv7hlfglfnogxvhvwkpmam

FORAGE: the hunt for existing data citations

Stephanie van de Sandt
2022 Zenodo  
In her talk Stephanie van de Sandt addresses "the hunt for existing data citations". A recording of the talk can be found here:  ... 
doi:10.5281/zenodo.6380081 fatcat:exur3ebbgrbebpienpfsbfl2di

Guides to Choosing Persistent Identifiers - Version 2 [article]

Frances Madden, René van Horik, Stephanie van de Sandt, Artemis Lavasa, Helena Cousijn
2020 Zenodo  
The FREYA Project has compiled short guides to help with choosing persistent identifiers for various types of entities. These are the final version. The first versions were released in May 2020 for community feedback and comment throughout June 2020. Revised versions will be developed in July 2020 and are published here. While not intended to be fully comprehensive, these guides are designed to provide a starting point for anyone thinking about using persistent identifiers in their systems.
more » ... es were created for the following entities: Publications Datasets People Organizations Software A table summarising all of the guides is also available.
doi:10.5281/zenodo.3956569 fatcat:3hhpbdpxsrennlwevtffmx2ngu

Tracking citations to research software via PIDs

Lars Holm Nielsen, Stephanie van de Sandt
2019 Zenodo  
Tracking citations to research software via persistent identifiers is difficult due to dilution of citations over many PIDs assigned to a software package. On top of this, software citations are often consistently being edited out by every actor part of the scholarly communication process such as reference managers, publishers, professors and discovery systems. Thus, the survival rate of a software citation is extremely low in the current scholarly ecosystem. The Sloan-funded Asclepias project
more » ... s a collaboration between a publisher, discovery system and repository with the goal is to promote scientific software into an identifiable, citable, and preservable object. We have built a citation broker, that is currently tracking some 6.000 citations to Zenodo DOIs from NASA ADS, CrossRef and EuropePMC.
doi:10.5281/zenodo.3433148 fatcat:zrifqvkxqneolocplyeewxtw6m

The Definition of Reuse

Stephanie van de Sandt, Sünje Dallmeier-Tiessen, Artemis Lavasa, Vivien Petras
2019 Data Science Journal  
van de Sandt et al: The Definition of Reuse Art. 22, page 6 of 19 van de Sandt et al: The Definition of Reuse Art. 22, page 4 of 19  ...  Summarizing, there is no commonly agreed understanding of reuse or a de-facto standard definition.  ... 
doi:10.5334/dsj-2019-022 fatcat:ouh5j2i6wrca3nte54xdfxpgrq

The 2015 Academic Publishing in Europe Conference

Stephanie van de Sandt
2015 Information, Wissenschaft und Praxis  
Informationswissenschaft Dorotheenstraße 26 10117 Berlin stephanie.  ...  B. zu Wim van der Stelts (Springer) Keynote "Sharingv s.  ... 
doi:10.1515/iwp-2015-0028 fatcat:hbuujjq73bfgfeklykvi3bps44

Practice meets Principle: Tracking Software and Data Citations to Zenodo DOIs [article]

Stephanie van de Sandt, Lars Holm Nielsen, Alexandros Ioannidis, August Muench, Edwin Henneken, Alberto Accomazzi, Chiara Bigarella, Jose Benito Gonzalez Lopez, Sünje Dallmeier-Tiessen
2019 arXiv   pre-print
The Python script used for the venn diagram and for fetching metadata from Zenodo and Github can be found on Zenodo (van de Sandt, Nielsen & Ioannidis (2019) ).  ...  The processed dataset we used for our analysis and the dataset containing usage metrics are published on Zenodo as well (van de Sandt, Ioannidis & Nielsen (2019) ).  ... 
arXiv:1911.00295v1 fatcat:wgdysxp35nczhea54mx2mi43te

D4.2 Using the PID Graph: Provenance in Disciplinary Systems

Artemis Lavasa, Sünje Dallmeier-Tiessen, Stephanie Van De Sandt, Tina Dohna, Ketil Koop-Jakobsen, Uwe Schindler, Christine Ferguson, Johanna McEntyre, Frances Madden, Simon Lambert, Vasily Bunakov, Chris Baars
2019 Zenodo  
The main focus of this deliverable is the different approaches to provenance as understood, expressed, and implemented by the FREYA disciplinary partners in their various pilot applications. The presentations here outline general approaches to provenance in the particular research context of each organisation, current and future implementations, and describe provenance activities that are supported by persistent identifiers. The FREYA project has received funding from the European Union's
more » ... n 2020 research and innovation programme under grant agreement No 777523.
doi:10.5281/zenodo.3249833 fatcat:bbfy2jcujnf23eyy4pyrevm32e

Deliverable 4.6 Emerging and New PID Graph Resource Types in Disciplinary Contexts

Christine Ferguson, Arthur Thouvenin, Robin Dasler, Chris Baars, Artemis Lavasa, Stephanie van de Sandt, Frances Madden, Vasily Bunakov, Natasha Simons, Tina Dohna
2021 Zenodo  
PIDs for software are de-facto minted by a few STFC teams, with the main publishing venues for them being DataCite and Zenodo.  ... 
doi:10.5281/zenodo.4415405 fatcat:dqk62exz7rbp7ixe2sromp3mzq

CERN analysis preservation and reuse framework: FAIR research data services for LHC experiments

Anna Trzcinska, Artemis Lavasa, Diego Rodriguez Rodriguez, Jan Okraska, Pamfilos Fokianos, Rokas Maciulaitis, Sebastian Stefan Feger, Stephanie Van De Sandt, Tibor Simko
2019 Zenodo  
In this paper we present the CERN Analysis Preservation service as a FAIR (Findable, Accessible, Interoperable and Reusable) research data preservation repository platform for LHC experiments. The CERN Analysis Preservation repository allows LHC collaborations to deposit and share the structured information about analyses as well as to capture the individual data assets associated to the analysis. We describe the typical data ingestion pipelines how an individual physicist can preserve and
more » ... their final n-tuples, ROOT macros, Jupyter notebooks or even full analysis workflow code and any intermediate datasets of interest for preservation within the restricted context of experimental collaboration. We discuss the importance of annotating the deposited content with high-level structured information about physics concepts in order to promote information discovery and knowledge sharing inside the collaboration. Finally, we describe techniques taken to facilitate the reusability of preserved data assets by capturing and re-executing reproducible recipes and computational workflows using the REANA Reusable Analysis platform.
doi:10.5281/zenodo.3599434 fatcat:3zrfuzdaenazjarvnpiiwrjkje

Deliverable 4.7 Using the PID Graph: Community Workflows and Discoverability Services

Artemis Lavasa, Stephanie van de Sandt, Pamfilos Fokianos, Christine Ferguson, Henning Hermjakob, Chris Baars, Ricarda Braukmann, Tina Dohna, Uwe Schindler, Frances Madden, Vasily Bunakov, Martin Fenner
2021 Zenodo  
Communications in Computer and Information Science 1057 edited by E Garoufallou, F Fallucchi, E William De Luca, 441-448.  ... 
doi:10.5281/zenodo.4415414 fatcat:3u2k6zugofbyldoixdvszouwmu

Beyond repositories: enabling actionable FAIR open data reuse services in particle physics

Ioannis Tsanaktsidis, Sünje Dallmeier-Tiessen, Tibor Šimko, Stephanie van de Sandt, Pamfilos Fokianos, Dinos Kousidis, Rokas Mačiulaitis, Diego Rodrı́guez, Anna Trzcińska, Artemis Lavasa, Sebastian Feger, Jan Okraska
2019 Zenodo  
We describe experiences from building and operating the CERN Open Data repository platform that manages and disseminates more than one petabyte of open data from particle physics. We discuss the education and research use cases of the platform and we argue that in order to make the FAIR open data fully actionable and reusable by a variety of users, the research data repositories should evolve from focusing on resource-hosting present towards integrated service-provisioning future. We describe
more » ... amples of an on-demand containerised analysis workflow execution environment that permits users to instantiate and explore the preserved open data in a virtually "in situ" manner. We discuss the reuse challenges and the technology solutions designed to overcome them. The developed tools take inspiration from reproducible science practices in the particle physics and life science domains and are applicable to any scientific discipline and any research data repository platform.
doi:10.5281/zenodo.3554271 fatcat:lfj2wklayndefioz6u3sxllalm

Deliverable 4.1 Integration of Mature PID Types

Artemis Lavasa, Sünje Dallmeier-Tiessen, Stephanie Van De Sandt, Ioannis Tsanaktsidis, Anna Trzcinska, Pamfilos Fokianos, Tina Dohna, Ketil Koop-Jakobsen, Uwe Schindler, Barbara Lemon, Rachael Kotarski, Christine Ferguson (+5 others)
2018 Zenodo  
This deliverable reports on the deployment of PID Graph functionality in FREYA's pilot applications. Initial steps for building the PID Graph include advancing the implementation of person-article-data linking, further establishing software citation and publication workflows, and integrating mature PID types into the different disciplinary systems. This first report for Work Package 4 presents considerations and implementations stemming from the first year of work carried out by the pilot
more » ... ations and sets the scene for the future integration of new and emerging PID types.
doi:10.5281/zenodo.2414839 fatcat:wlcjwt75xnaxhfnkhscalcia6q

The Landscape of Research Data Repositories in 2015: A re3data Analysis

Maxi Kindling, Heinz Pampel, Stephanie van de Sandt, Jessika Rücknagel, Paul Vierkant, Gabriele Kloska, Michael Witt, Peter Schirmbacher, Roland Bertelmann, Frank Scholze
2017 D-Lib Magazine  
[19] van de Sandt, S et al . (2017) The Landscape of Research Data Repositories in 2015.  ...  van de Sandt, Humboldt-Universität zu Berlin, Berlin School of Library and Information Science (BSLIS), Germany ORCID:0000-0002-9576-1974 [at] Jessika  ... 
doi:10.1045/march2017-kindling fatcat:e546nmawfbgkpk7hbd4vwfri5q
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