Daniel Arend
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View article: Increasing FAIRness in agrosystem sciences and plant phenomics
Increasing FAIRness in agrosystem sciences and plant phenomics Open
As part of the de.NBI BioHackathon 2023, we here report about our progress on increasingFAIR-compliance in agrosystem sciences and plant phenomics. Through the collaborative effortsof the agrosystem and plant sciences communities, research…
View article: Order from entropy: big data from FAIR data cohorts in the digital age of plant breeding
Order from entropy: big data from FAIR data cohorts in the digital age of plant breeding Open
Lack of interoperable datasets in plant breeding research creates an innovation bottleneck, requiring additional effort to integrate diverse datasets—if access is possible at all. Handling of plant breeding data and metadata must, therefor…
View article: Simplifying and Standardizing the Creation of Data Use Agreements for Life Sciences and Beyond - BH Germany2024
Simplifying and Standardizing the Creation of Data Use Agreements for Life Sciences and Beyond - BH Germany2024 Open
The primary goal of this project is to develop a web application for creating data usage agreements (DUA) in a way that allows automated evaluation of access permissions. Specifically, we want to adhere to the Open Digital Rights Language …
View article: Data management in balance – a decade of balancing pragmatism, sustainability and innovation at plant research center IPK Gatersleben
Data management in balance – a decade of balancing pragmatism, sustainability and innovation at plant research center IPK Gatersleben Open
The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben is a leading international plant science institute specializing in biodiversity and crop plant performance research. Over the last decade, all phases of the …
View article: BioHackEU24 report: Creating user benefit from ARC-ISA RO-Crate machine-actionability & Increasing FAIRness of digital agrosystem resources by extending Bioschemas
BioHackEU24 report: Creating user benefit from ARC-ISA RO-Crate machine-actionability & Increasing FAIRness of digital agrosystem resources by extending Bioschemas Open
As part of the BioHackathon Europe 2024, we here report on the progress that both project 19 and project 24 have made during the event. For the purpose of this report we will present the abstract of both projects and then dive deeper on wh…
View article: Biodiversity food security and pathogens mini symposium
Biodiversity food security and pathogens mini symposium Open
View article: A roadmap for a middleware as a federation service for integrative data retrieval of agricultural data
A roadmap for a middleware as a federation service for integrative data retrieval of agricultural data Open
Agriculture is confronted with several challenges such as climate change, the loss of biodiversity and stagnating productivity. The massive increasing amount of data and new digital technologies promise to overcome them, but they necessita…
View article: Bioschemas Resource Index for Chem and Plants
Bioschemas Resource Index for Chem and Plants Open
As part of the BioHackathon Europe 2023, we here report on the progress of the hacking team preparing a resource index and knowledge graph based on the JSON-LD Bioschemas markup from several resources in the life- and natural sciences, pre…
View article: Long Term Plant Phenomic Data Sharing in Generic Data Repositories (Zenodo, Dataverse, e!Dale) Using MIAPPE
Long Term Plant Phenomic Data Sharing in Generic Data Repositories (Zenodo, Dataverse, e!Dale) Using MIAPPE Open
International audience
View article: BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA
BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA Open
A prevailing paradigm in Research Data Management (RDM) is to publish research datasets in designated archives upon conclusion of a research process. However, it is beneficial to abandon the notion of final or static data artifacts and ins…
View article: Schema.org as a Lightweight Harmonization Approach for NFDI
Schema.org as a Lightweight Harmonization Approach for NFDI Open
Schema.org is a controlled vocabulary that makes it easier for web pages to describe their actual content in a semantic, structured and machine-processable way. It is recognized by major search engines and data aggregators, making it easie…
View article: ELIXIR-CONVERGE D5.5 Report on the remaining four DMP processes
ELIXIR-CONVERGE D5.5 Report on the remaining four DMP processes Open
The main objective of this deliverable is to provide resources that can assist life sciences researchers and data stewards in creating reference Data Management Plans (DMPs) for their research projects. The resources provided in this deliv…
View article: Improving Metadata Collection and Aggregation in Plant Phenotyping Experiments with MIAPPE Wizard and DataPLANT
Improving Metadata Collection and Aggregation in Plant Phenotyping Experiments with MIAPPE Wizard and DataPLANT Open
As part of the BioHackathon Germany 2022, we hereby report on the success of the two projects “MIAPPE Wizard: Enabling easy creation of MIAPPE-compliant ISA metadata for Plant Phenotyping Experiments” and “DataPLANT - Facilitating Research…
View article: Workshop on PIDs within NFDI
Workshop on PIDs within NFDI Open
In order to gain an overview of the current state of the discussion on PIDs and for the identification of use cases for the initiation phase of a PID service within the NFDI basic services, the working group Persistent Identifier of the Se…
View article: FAIRagro: Ein Konsortium in der Nationalen Forschungsdateninfrastruktur (NFDI) für Forschungsdaten in der Agrosystemforschung
FAIRagro: Ein Konsortium in der Nationalen Forschungsdateninfrastruktur (NFDI) für Forschungsdaten in der Agrosystemforschung Open
View article: BioHackEU22 Project 22: Plant data exchange and standard interoperability
BioHackEU22 Project 22: Plant data exchange and standard interoperability Open
Status of discussions around the topic of data standard formats for plant sciences and their interoperability at the BioHackathon Europe 2022 in Paris.
View article: On the way to plant data commons – a genotyping use case
On the way to plant data commons – a genotyping use case Open
Over the last years it has been observed that the progress in data collection in life science has created increasing demand and opportunities for advanced bioinformatics. This includes data management as well as the individual data analysi…
View article: From data to knowledge – big data needs stewardship, a plant phenomics perspective
From data to knowledge – big data needs stewardship, a plant phenomics perspective Open
SUMMARY The research data life cycle from project planning to data publishing is an integral part of current research. Until the last decade, researchers were responsible for all associated phases in addition to the actual research and wer…
View article: Enhancing data publishing workflows with MIAPPE-compliant metadata using isa4j
Enhancing data publishing workflows with MIAPPE-compliant metadata using isa4j Open
View article: Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley
Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley Open
Gene pairs resulting from whole genome duplication (WGD), so-called ohnologous genes, are retained if at least one member of the pair undergoes neo- or sub-functionalization. Phylogenetic analyses of the ohnologous genes ALBOSTRIANS ( HvAS…
View article: Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases Open
This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable …
View article: isa4j: a scalable Java library for creating ISA-Tab metadata
isa4j: a scalable Java library for creating ISA-Tab metadata Open
Experimental data is only useful to other researchers if it is findable, accessible, interoperable, and reusable (FAIR). The ISA-Tab framework enables scientists to publish metadata about their experiments in a plain text, machine-readable…
View article: The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition
The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition Open
Background The FAIR data principle as a commitment to support long-term research data management is widely accepted in the scientific community. Although the ELIXIR Core Data Resources and other established infrastructures provide comprehe…
View article: BRIDGE – A Visual Analytics Web Tool for Barley Genebank Genomics
BRIDGE – A Visual Analytics Web Tool for Barley Genebank Genomics Open
Genebanks harbor a large treasure trove of untapped plant genetic diversity. A growing world population and a changing climate require an increase in the production and development of stress resistant plant cultivars while decreasing the a…
View article: Enabling reusability of plant phenomic datasets with MIAPPE 1.1
Enabling reusability of plant phenomic datasets with MIAPPE 1.1 Open
Summary Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due …
View article: Programmatic Access to FAIRified Digital Plant Genetic Resources
Programmatic Access to FAIRified Digital Plant Genetic Resources Open
Genetic variance within the genotype of population and its mapping to phenotype variance in a systematic and high throughput manner is of interest for biodiversity and breeding research. Beside the established and efficient high throughput…
View article: Mutation of the<i>ALBOSTRIANS</i>Ohnologous Gene<i>HvCMF3</i>Impairs Chloroplast Development and Thylakoid Architecture in Barley due to Reduced Plastid Translation
Mutation of the<i>ALBOSTRIANS</i>Ohnologous Gene<i>HvCMF3</i>Impairs Chloroplast Development and Thylakoid Architecture in Barley due to Reduced Plastid Translation Open
Gene pairs resulting from whole genome duplication (WGD), so-called ohnologous genes, are retained only if at least one gene of the pair undergoes neo- or subfunctionalization. Sequence-based phylogenetic analyses of the ohnologous genes A…
View article: Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection
Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection Open
View article: Digital resources for plant genomics and phenomics at ELIXIR-Germany partner IPK Gatersleben
Digital resources for plant genomics and phenomics at ELIXIR-Germany partner IPK Gatersleben Open
View article: Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection
Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection Open