Research Data Management Support
IBB PAS provides support in research data management for staff and doctoral students.
We offer assistance with the following issues:
– selection of datasets to be shared openly from a research project,
– selection of an appropriate database / repository for the data,
– determining the legal status of the data,
– decisions on data licensing,
– preparation of a research data management plan for a grant application, as well as its modification during the project and reporting on the implementation of the plan.
Please feel free to contact me:
dr Marta Hoffman rdm@ibb.waw.pl phone 3501 (room 401, building C)
Resources
1. Helpsheet meant to support the preparation of a Data Management Plan (DMP) for a research project (document in English):
The document is structured in accordance with the scheme used by the National Science Center (NCN). Since NCN requires the DMP only in English, only an English-language version has been prepared. The document uses examples typical for research projects submitted at IBB PAS – if you have a special situation in your project (non-typical data, patient data, complicated legal situation of the data, etc.), you are welcome to contact me directly.
2. List of suggested data repositories and databases:
Available also as pdf for download: Suggested-databases-2025-v4. The list presented below is partly based on the resource ELIXIR Deposition Databases for Biomolecular Data.
Specialized repositories for selected types of life sciences data – please use these as your first choice:
| ArrayExpress | High-throughput functional genomics data (RNA-seq, ChIP-seq, and other types of gene expression and epigenomics datasets).(Also a good alternative: GEO at NCBI). |
| ENA | Nucleotide sequencing information: raw sequencing data, sequence assembly information and functional annotation.(Alternatively: GenBank, SRA – Sequence Read Archive, TSA – Transcriptome Shotgun Assembly, all at NCBI). |
| EVA | Genetic variation data from all species. |
| IntAct | Molecular interaction data. |
| LIPID MAPS | Information on Lipids and their structures, properties and functions in biological processes. |
| MetaboLights | Metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. |
| BioModels | Computational models of biological processes. |
| ModelArchive | Theoretical models of macromolecular structures. |
| PDBe | Experimentally obtained structures of biological macromolecules. |
| PRIDE | Mass spectrometry-based proteomics data. |
| UniProt | Protein sequence and function data. |
| BioImage Archive | All biological image data, including light microscopy, 2D-electron microscopy. |
| EMPIAR | Raw cryo-EM data and other 3D-electron microscopy images. |
| EMDB | Processed cryo-EM data and other 3D- electron microscopy images. |
| ecbd | European Chemical Biology Database, run by EU-OPENSCREEN, collects experimental results from biological screening programs. Deposit option possible for EU-OPENSCREEN partner sites. |
Domain repositories (accepting all types of research data from a broad but defined field of research) – recommended option for data that does not fit into any specialized repository:
| BioStudies | All data from Life Sciences research that do not fit in specialized archives. Part of the ecosystem of data resources hosted and managed by EMBL-EBI, it is integrated with many of the specialized resources listed above as well as with the literature repository Europe PMC (PubMedCentral). |
| Pangaea | All data from Earth and Environmental Sciences research. PANGAEA is hosted by the Helmholtz Center for Polar and Marine Research and the University of Bremen. |
Generalist repositories for research data (any type of data, any file formats) – for situations where the data is not suitable for domain-specific repositories:
| Zenodo | All research-related data. EC-funded repository run at CERN in Geneva for researchers from all countries. |
| RepOD | All research-related data. This is a general repository managed and hosted by ICM University of Warsaw, for all researchers in Poland. |
3. Presentation – most important aspects of research data management and a Data Management Plan (IBB, June 20, 2024):
Bio
Marta Hoffman is a biologist, she earned her PhD at IBB PAS in the field of yeast genetics. She did a postdoctoral fellowship in the Theoretical Biophysics group at the Humboldt-University in Berlin, and is currently a member of the IBB Laboratory of Lipid Biochemistry .
She gained experience in research data management and issues related to open sharing of data while working (from 2012 to 2017) as a member of the Open Science Platform ICM UW (https://pon.edu.pl/), where she was running the National Open Access Desk of the OpenAIRE (Open Access Infrastructures for Research in Europe, https://openaire.eu/) project, as well as coordinating the Repository for Open Data RepOD (https://repod.icm.edu.pl/) and leading workshops on Research Data Management. She then used and expanded her knowledge of Open Research Data serving in 2019-2020 as a member of the advisory group FAIR Working Group of the EOSC (European Open Science Cloud, https://eosc.eu/), which prepared recommendations for the implementation of FAIR Data principles within the emerging EOSC service, and in 2020-2022 as a member of the advisory group of the project OCRE (Open Clouds for Research Environments, https://www.ocre-project.eu/).