An introduction to the APIs/web services of StrainInfo, MediaDive and BacDive.
Different workflows are key to handling microbiological research data. NFDI4Microbiota offers different workflows and services regarding microbiological research data. This lecture handles three topics, 1. Turning a workflow into an NFDI4Microbiota-compliant workflow, 2. Services provided by NFDI4Microbiota regarding workflow development and 3. Best practice workflows provided by NFDI4Microbiota for microbiological/metagenomics data
NFDI4Microbiota is one life science consortium under the German National Research Data Infrastructure (NFDI) Association. A focus of the consortium is the democratization of access to data and workflows for the microbiology field. Training and education, as well as building a knowledge base, for topics related to this field, are some of the means for achieving these goals. This talk was originally given at the 2nd NFDI4Microbiota annual conference (in 2023). It gives an overview of the overall goals regarding training and education within NFDI4Microbiota, as well as details on the first steps we have taken to reach these goals. Furthermore, we introduce the NFDI4Microbiota Knowledge Base as part of our education efforts.
Recording of the presentation 'NFDI4Microbiota - Services to make data FAIR and Open' as part of the 5th Thuringian RDM Days from June 20-21, 2023, hosted by the Thuringian Competence Network Research Data Management (TKFDM).
A Data Steward is, generally said, a person who is responsible for ensuring the quality of data assets, including metadata. However, the tasks of data stewards are very different and fulfil different requirements. This is also the case in the field of research. Good research data management is essential in research. Data stewards play a crucial role here, as they support researchers in this task and take on the role of intermediaries between the different fields of work. Justine Vandendorpe is working as a data steward at ZB MED for the NFDI cosortia NFDI4microbiota. In this video she explains what her tasks as a data steward look like.
What needs to happen to establish conscientious research data management in the disciplines of the life sciences? How can researchers be convinced and reservations be overcome? These were the questions addressed in a highly interesting panel discussion on February 16, 2023, jointly organised by the NFDI consortia NFDI4Biodiversity, DataPLANT, NFDI4Health and NFDI4Microbiota. Panelists were Dr. Barbara Ebert (NFDI4Biodiversity), Prof. Dr. Konrad Förstner (NFDI4Microbiota), Prof. Dr. Björn Usadel (DataPLANT) and Prof. Dr. Iris Pigeot (NFDI4Health). The discussion was moderated by Dr. Kerstin Elbing (Verband Biologie, Biowissenschaften und Biomedizin in Deutschland e. V. – VBIO). The discussion was introduced by keynote speeches from Dr. Martin Friedrichs-Manthey (NFDI4Biodiversity), Prof. Dr Björn Usadel and Prof. Dr Iris Pigeot. The event was part of the Love Data Week 2023, an international week of action to discuss and reflect on research data together. Under the motto 'Data: Agent of Change' the Love Data Week 2023 was celebrated worldwide from 13-17 February with numerous events on a wide range of research data management (RDM) topics.
Ist wissenschaftliches Arbeiten ohne dezidiertes Forschungsdatenmanagement heute überhaupt noch möglich? Und welche Rolle spielen Infrastrukturen dabei? Darüber spricht Elke Roesner im neuen ZB MED Nachgefragt mit Barbara Götz, Mikrobiologin und Projektmanagerin bei NFDI4Microbiota, und Prof. Dr. Konrad Förstner, Bioinformatiker und Projektleiter bei NFDI4Microbiota. Als Barbara Ende 2017 mit ihrer Promotion beginnt, begegnet ihr am Rande der Begriff der guten wissenschaftlichen Praxis (GWP). Mit dem Begriff des Forschungsdatenmanagements (FDM) - obwohl ein wichtiger Bestandteil, wenn es um die Einhaltung der GWP geht - sieht es etwas anders aus: Im Rahmen der Promotion ist sie viel Labor beschäftigt, muss Versuche planen, Literatur recherchieren, Projektmanagementaufgaben übernehmen - von der FDM-Bewegung, die zu dem Zeitpunkt noch eine eher klein ist, bekommt sie da nicht bewusst etwas mit. Das sieht heute anders aus. Schließlich sind Daten ein wertvoller Schatz für die Forschung und gutes Forschungsdatenmanagement unerlässlich sowohl für die eigene Forschung als auch, wenn es darum geht, anderen Forschenden die Daten zur Verfügung zu stellen und damit die Nachnutzung zu ermöglichen - ein großer Mehrwert für die Forschung. Nicht zuletzt machen auch die explodierenden Datenmengen der letzten Jahre gutes Forschungsdatenmanagement unverzichtbar. Die Nationale Forschungsdateninfrastruktur (NFDI) hat sich daher zum Ziel gesetzt, für das gesamte wissenschaftliche System eine Lösung für die Handhabung von Forschungsdaten zu etablieren. Verschiedene Konsortien aus unterschiedlichen Communitys arbeiten daran Infrastrukturen und Standards für Forschungsdaten zu etablieren. NFDI4Microbiota ist eines dieser Konsortien. Eine ihrer Missionen ist es, Awareness für Forschungsdatenmanagement zu schaffen und die Community zu erreichen. Als zentrale Anlaufstelle für alle Mikrobiolog:innen bietet NFDI4Microbiota Informationen, Trainings und Tools, die es den Forschenden ermöglichen korrekt mit ihren Daten umzugehen. Dies bietet sehr viele Vorteile und Erleichterung für die eigene Forschungsarbeit, wird aber auch beispielsweise von der DFG seit 2022 bei der Benatragung von Forschungsgeldern verbindlich eingefordert. In diesem Videopodcast erklären Barbara Götz und Konrad Förstner wo NFDI4Microbiota heute steht, welche Herausforderungen zu bewältigen sind, wie die Zukunftspläne aussehen und warum es notwendig ist, Wissenschaftler:innen noch früher in ihrer Laufbahn zu erreichen und so das Bewusstsein für Forschungsdatenmanagement in den wissenschaftlichen Communitys zu verankern.
Introducing the National Research Data Infrastructure for the Research of Microbiota (NFDI4Microbiota) - Konrad U. Förstner - BOSC - Poster - ISMB 2022
The lecture introduces all-qualification-level researchers from the life sciences to best practices in Research Data Management (RDM). It starts with fundamental concepts in RDM, such as the FAIR Data Principles and continues by following the research data life cycle, starting with planning a research project, and ending with searching for and reusing research data. The lecture closes with a section on legal issues, including privacy issues and licenses. Where relevant, the lecture is punctuated with discipline-specific examples, as well as presentation of ZB MED services and of the very first results of the NFDI4Health and NFDI4Microbiota consortia. The lecture was held by Birte Lindstädt (Head of Research Data Management) and Katharina Markus (Head of Digital Preservation) as well as the Data Stewards Aliaksandra Shutsko (NFDI4Health) and Justine Vandendorpe (NFDI4Microbiota) from ZB MED.
Tutorial of advance search of the database browser.
Tutorial of the use of the interactive map in the database browser.
Tutorial of quick search of the database browser.
Data Download tutorial.
This is a short introduction video to the consortium NFDI4Microbiota. NFDI4Microbiota is a consortium of the second round of national research data infrastructure (NFDI) consortia. NFDI4Microbiota wants to democratize the access to microbiota data and high-end computational analyses.
On November 9, scientists from various research institutions presented their research topics regarding the National Research Data Infrastructure (NFDI) as part of a science slam. The online event was hosted by Fraunhofer FOKUS together with NFDI e.V. as part of Berlin Science Week 2021. The National Research Data Infrastructure (NFDI) aims to systematically develop, sustainably secure and make the data sets of science and research accessible, as well as networking them (inter-)nationally. It is currently being set up in a process driven by science as a networked structure of individually acting consortia.
Tutorial of advance search of the database browser.
Tutorial of the use of the interactive map in the database browser.
Data Download tutorial.
Data Download tutorial.
Tutorial of quick search of the database browser.
Tutorial of advance search of the database browser.
Tutorial of the use of the interactive map in the database browser.
Tutorial of quick search of the database browser.
This tutorial should also work for macOS.
Data Download tutorial
In this video I describe how to add or edit sequence files to ORAdb and a quick example on how to edit theGene-Protein-Reaction (GPR) rules files.
In This video we introduce the concept and general workflow of OrtSuite
A brief explanation on the different tasks performed in OrtSuite.
Installation guidelines for OrtSuite.
The NFDI4Microbiota Work Programme - Empowering the microbiology community. A lecture by Prof. Dr. Konrad Förstner | ZB MED - Informationszentrum Lebenswissenschaften wird gefördert durch das Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen.