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Expanding the SPHN RDF Schema

This training module will provide researchers with an introduction on how to expand the SPHN RDF Schema using an ontology editor.

Scientific topics: Ontology and terminology, Medical informatics, FAIR data, Data management, Computer science

Operations: Editing, Ontology visualisation, Visualisation, Data handling

Keywords: Clinical data, Data semantics, FAIR, Ontology editing, Protegé, RDF, OWL

Resource type: Video, Training materials, E-learning

Expanding the SPHN RDF Schema http://tess.elixir-uk.org/materials/expanding-the-sphn-rdf-schema This training module will provide researchers with an introduction on how to expand the SPHN RDF Schema using an ontology editor. Kristin Gnodke Sabine Österle Ontology and terminology Medical informatics FAIR data Data management Computer science Clinical data, Data semantics, FAIR, Ontology editing, Protegé, RDF, OWL Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Training Primer (RDF and SPARQL)

This training provides a first introduction to RDF and SPARQL.

Scientific topics: Computer science, Data management, FAIR data, Medical informatics, Ontology and terminology

Operations: Query and retrieval, Database search, Data handling, Data retrieval

Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology

Resource type: Video, Training materials, E-learning

Training Primer (RDF and SPARQL) http://tess.elixir-uk.org/materials/training-primer-rdf-and-sparql This training provides a first introduction to RDF and SPARQL. Sabine Österle Computer science Data management FAIR data Medical informatics Ontology and terminology Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Semantic Standards

This training module provides an introduction on the key semantic standards used within SPHN.

Scientific topics: Ontology and terminology, Medical informatics, FAIR data, Data management, Computer science

Operations: Standardisation and normalisation, Data handling

Keywords: Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD

Resource type: Video, Training materials, E-learning

Semantic Standards http://tess.elixir-uk.org/materials/semantic-standards This training module provides an introduction on the key semantic standards used within SPHN. Sabine Österle Ontology and terminology Medical informatics FAIR data Data management Computer science Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
RDF Schema and Data Visualization

This training module will provide researchers with an introduction on how to explore and visualize the SPHN ontology and mock data.

Scientific topics: Data visualisation, Medical informatics, FAIR data, Data management, Computer science

Operations: Ontology visualisation, Visualisation, Data retrieval, Data handling, Query and retrieval

Keywords: Clinical data, SPARQL, Data visualization, RDF, Knowledge graph, GraphDB, Mock data

Resource type: Video, Training materials, Mock data, E-learning

RDF Schema and Data Visualization http://tess.elixir-uk.org/materials/rdf-schema-and-data-visualization This training module will provide researchers with an introduction on how to explore and visualize the SPHN ontology and mock data. Vasundra Touré Sabine Österle Data visualisation Medical informatics FAIR data Data management Computer science Clinical data, SPARQL, Data visualization, RDF, Knowledge graph, GraphDB, Mock data Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Validate Graph Data with SHACL

This training module will provide researchers with an introduction on SHACL for RDF graphs validation.

Scientific topics: Computer science, Data management, FAIR data, Medical informatics

Operations: Data handling, Validation

Keywords: Clinical data, SHACL, Data validation, RDF, Knowledge graph, GraphDB, RDF, RDF graph validation

Resource type: Video, Training materials, E-learning

Validate Graph Data with SHACL http://tess.elixir-uk.org/materials/validate-graph-data-with-shacl This training module will provide researchers with an introduction on SHACL for RDF graphs validation. Sabine Österle Vasundra Touré Computer science Data management FAIR data Medical informatics Clinical data, SHACL, Data validation, RDF, Knowledge graph, GraphDB, RDF, RDF graph validation Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
How to use Python and R with RDF Data

This training module will provide researchers with an introduction on how use R and Python in combination with SPARQL to query RDF data.

Scientific topics: Medical informatics, FAIR data, Data management, Computer science

Operations: Data retrieval, Data handling, Query and retrieval

Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, Python, R, GraphDB

Resource type: Video, Training materials, Mock data, E-learning

How to use Python and R with RDF Data http://tess.elixir-uk.org/materials/how-to-use-python-and-r-with-rdf-data This training module will provide researchers with an introduction on how use R and Python in combination with SPARQL to query RDF data. Sabine Österle Vasundra Touré Medical informatics FAIR data Data management Computer science Clinical data, SPARQL, Query data, RDF, Knowledge graph, Python, R, GraphDB Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
BioData.pt | ELIXIR PT Training Data Stewards for Life Sciences - Intro Course

BioData.pt | ELIXIR Portugal, in collaboration with several other organizations has designed a program to train the first generation of Data Stewards for the life sciences, to support the implementation of data management, open science and FAIR data principles in Portuguese R&I organizations.

Scientific topics: Data management, Open science, FAIR data

Keywords: Data management plan, data-science, data-analysis, Data Integration, training, open science, data FAIRness, FAIR data, FAIR, FAIR principles, life sciences, data life cycle

Resource type: Training materials

BioData.pt | ELIXIR PT Training Data Stewards for Life Sciences - Intro Course http://tess.elixir-uk.org/materials/biodata-pt-elixir-pt-training-data-stewards-for-life-sciences-intro-course BioData.pt | ELIXIR Portugal, in collaboration with several other organizations has designed a program to train the first generation of Data Stewards for the life sciences, to support the implementation of data management, open science and FAIR data principles in Portuguese R&I organizations. Data management Open science FAIR data Data management plan, data-science, data-analysis, Data Integration, training, open science, data FAIRness, FAIR data, FAIR, FAIR principles, life sciences, data life cycle Researchers
Course design: Considerations for trainers – a Professional Guide

This Professional Guide in the Resources for Training Trainers series introduces a structured approach to course design, highlighting the importance of articulating learning outcomes commensurate with the cognitive complexity of the target learning, prior to devising learning experiences and...

Keywords: Curriculum development, course design, learning outcomes, Bloom's Taxonomy, assessment, course evaluation, training trainers, training material

Course design: Considerations for trainers – a Professional Guide http://tess.elixir-uk.org/materials/course-design-considerations-for-trainers-a-professional-guide This Professional Guide in the Resources for Training Trainers series introduces a structured approach to course design, highlighting the importance of articulating learning outcomes commensurate with the cognitive complexity of the target learning, prior to devising learning experiences and course content. The specific focus here is on face-to-face activities, but the guidance is also relevant for those designing online courses. Curriculum development, course design, learning outcomes, Bloom's Taxonomy, assessment, course evaluation, training trainers, training material Training instructors Trainers Training Designers Anyone who wants to become a good trainer or teacher teachers
Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide

This Practical Guide outlines basic bioinformatics approaches for exploring the SARS-CoV-2 genome and its corresponding proteins, focusing on the protein exposed on the viral particle surface: the spike protein. The ways in which bioinformatics can be harnessed to study a new virus, its genome,...

Keywords: Bioinformatics for schools, basic bioinformatics, SARS-CoV-2 pandemic, genome analysis, protein sequence analysis, protein structure analysis, virus variants, spike protein, training material

Resource type: Training materials

Using bioinformatics to hunt SARS-CoV-2, its variants & its origins – a practical guide http://tess.elixir-uk.org/materials/using-bioinformatics-to-hunt-sars-cov-2-its-variants-its-origins-a-practical-guide This Practical Guide outlines basic bioinformatics approaches for exploring the SARS-CoV-2 genome and its corresponding proteins, focusing on the protein exposed on the viral particle surface: the spike protein. The ways in which bioinformatics can be harnessed to study a new virus, its genome, its proteins, its origins and its evolution are explored. Bioinformatics for schools, basic bioinformatics, SARS-CoV-2 pandemic, genome analysis, protein sequence analysis, protein structure analysis, virus variants, spike protein, training material Trainers Training instructors Training Designers PhD students post-docs Life Science Researchers
FAIR data - Module 2 (data life cycle)

La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données

Scientific topics: Bioinformatics, Biology, Data management

Operations: Data handling

Keywords: Data preserving, Data storage

Resource type: Slides

FAIR data - Module 2 (data life cycle) http://tess.elixir-uk.org/materials/fair-data-module-2 La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données Bioinformatics Biology Data management Data preserving, Data storage Biologists bioinformaticians Biomedical researchers
FAIR data - Module 1 (research data)

Research data and their centrality in the research process. This material is mostly in French.

Keywords: metadata, Data Life Cycle, Reproducibility, Data management plan

Resource type: Slides

FAIR data - Module 1 (research data) http://tess.elixir-uk.org/materials/fair-data-module-1 Research data and their centrality in the research process. This material is mostly in French. Gautier Sarah Hélène Chiapello Jean-François Dufayard Julien Seiler Lionel Maurel Paulette Lieby Thomas Denecker metadata, Data Life Cycle, Reproducibility, Data management plan Biologists bioinformaticians Biomedical researchers
Introduction à la programmation Python pour la biologie

Cours de Python pour des biologistes par Patrick Fuchs et Pierre Poulain.

Keywords: Python, Programming, Python for Biologists

Introduction à la programmation Python pour la biologie http://tess.elixir-uk.org/materials/introduction-a-la-programmation-python-pour-la-biologie Cours de Python pour des biologistes par Patrick Fuchs et Pierre Poulain. Python, Programming, Python for Biologists
Introduction to Protein Structure Analysis

This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure....

Operations: Visualisation

Keywords: Protein structure visualisation

Resource type: e-learning

Introduction to Protein Structure Analysis http://tess.elixir-uk.org/materials/introduction-to-protein-structure-analysis This training session will provide the basics of protein structure determination and how this information is stored in databases. We will explore and search in online databases containing protein structure information. With the aid of the Yasara View program we will visualize the structure. Different hands-on exercises will allow you to compare the structure of homologues, to predict a structural model of proteins (without any structure information) and to find homologous structures. We will use online tools to quantify various interactions in the structures. ## Objectives * Get to know the data generated from protein structure determination experiments (high-resolution NMR spectroscopy, X-ray crystallography, electron microscopy, ...) and where to get it. * Display protein structure data and compare structures, through the use of Yasara. * Create high-quality graphical representations of the structures. * Calculate the effect of mutations on the stability of your protein. Janick Mathys Protein structure visualisation Life Science Researchers
Data security and encryption

1. Data security 2. Encryption 3. Passwords

Scientific topics: Data management, Data security

Keywords: data encryption

Resource type: Presentation

Data security and encryption http://tess.elixir-uk.org/materials/data-security-and-encryption 1. Data security 2. Encryption 3. Passwords Data management Data security data encryption life scientists
Reusing existing data

- how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub) - licenses - datasets as first-class research products - research software as first-class research products - data citations

Scientific topics: Data management

Keywords: data licenses, software licenses, data journal

Resource type: Presentation

Reusing existing data http://tess.elixir-uk.org/materials/reusing-existing-data - how to find existing data (OmicsDI, pubmed, BioStudies, Google Data search, Data Management Hub) - licenses - datasets as first-class research products - research software as first-class research products - data citations Data management data licenses, software licenses, data journal life scientists
Organising your data: structure and versioning

how to store and organize data safe, easy and efficient - practical recommendation for folder structures and file naming schemes

Scientific topics: Data management

Keywords: data stewardship, data collection

Resource type: Presentation

Organising your data: structure and versioning http://tess.elixir-uk.org/materials/organising-your-data-structure-and-versioning how to store and organize data safe, easy and efficient - practical recommendation for folder structures and file naming schemes Nele Pauwels Data management data stewardship, data collection
FAIRify your data: data documentation and metadata

“Documentation is a love letter that you write to your future self.” Damian Conway (2005) Make your data as useful as possible for “your future self” and others Never forget what you did or how or why you did it Always find beck your precious data (easily) Make data understandable,...

Scientific topics: Data management

Keywords: data documentation, metadata

Resource type: Presentation

FAIRify your data: data documentation and metadata http://tess.elixir-uk.org/materials/fairify-your-data-data-documentation-and-metadata “Documentation is a love letter that you write to your future self.” Damian Conway (2005) Make your data as useful as possible for “your future self” and others Never forget what you did or how or why you did it Always find beck your precious data (easily) Make data understandable, reproducible and reusable by “your future self” and others Avoid misinterpretation Data management data documentation, metadata life scientists
Data Management Plans

dmponline.be - creating data management plans why, what to cover, examples and self-assessment grids

Keywords: Data management planning

Resource type: Presentation

Data Management Plans http://tess.elixir-uk.org/materials/data-management-plans dmponline.be - creating data management plans why, what to cover, examples and self-assessment grids Data management planning life scientists
Privacy and GDPR in the research life cycle

0. The basics 1. Planning your research from a GDPR point of view 2. From planning to collecting your data 3. Structuring and analyzing your data 4. Sharing, publishing, archiving and destroying your data

Scientific topics: Data management

Keywords: GDPR

Resource type: Presentation

Privacy and GDPR in the research life cycle http://tess.elixir-uk.org/materials/privacy-and-gdpr-in-the-research-life-cycle 0. The basics 1. Planning your research from a GDPR point of view 2. From planning to collecting your data 3. Structuring and analyzing your data 4. Sharing, publishing, archiving and destroying your data Data management GDPR life scientists
Research Data Management: Trends and requirements

Paula Oset - Research funders and journal policies

Scientific topics: Data management

Keywords: journal policies, research funding

Resource type: Presentation

Research Data Management: Trends and requirements http://tess.elixir-uk.org/materials/research-data-management-trends-and-requirements Paula Oset - Research funders and journal policies Data management journal policies, research funding life scientists
Introduction to Research Data Management and the data life cycle

RESEARCH DATA MANAGEMENT IN LIFE SCIENCES Introduction to RDM & data lifecycle Thomas Van de Velde (Data steward team Ghent University)

Keywords: research data, data management

Resource type: Presentation

Introduction to Research Data Management and the data life cycle http://tess.elixir-uk.org/materials/introduction-to-research-data-management-and-the-data-life-cycle RESEARCH DATA MANAGEMENT IN LIFE SCIENCES Introduction to RDM & data lifecycle Thomas Van de Velde (Data steward team Ghent University) research data, data management life scientists
Research Data Management in Life Sciences

The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.

Scientific topics: Data management

Resource type: Presentation, Vignette, Video

Research Data Management in Life Sciences http://tess.elixir-uk.org/materials/research-data-management-in-life-sciences The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences. Data management Life Science Researchers
SPARQLing Biology: a beginners course

Course given at BioSB 2019 for biologists about SPARQL.

Scientific topics: Biology

Operations: Query and retrieval

Keywords: Sparql queries, Sparql syntax

Resource type: Tutorial

SPARQLing Biology: a beginners course http://tess.elixir-uk.org/materials/sparqling-biology-a-beginners-course Course given at BioSB 2019 for biologists about SPARQL. Biology Sparql queries, Sparql syntax Biologists Chemists
DE-Sim examples, tutorials, and documentation

*DE-Sim* is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as [NumPy](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html),...

Scientific topics: Computational biology, Mathematics, Computer science, Simulation experiment

Operations: Visualisation, Modelling and simulation

Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science

Resource type: examples, Tutorial, Jupyter notebook, API reference

DE-Sim examples, tutorials, and documentation http://tess.elixir-uk.org/materials/de-sim-examples-tutorials-and-documentation *DE-Sim* is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as [NumPy](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html), [pandas](https://pandas.pydata.org/), and [SQLAlchemy](https://www.sqlalchemy.org/) to build and simulate complex computational models. Similar to [Simula](http://www.simula67.info/), *DE-Sim* models are implemented by defining logical process objects which read the values of a set of shared variables and schedule events to modify their values at discrete instants in time. This website provides examples, tutorials, and documentation for *DE-Sim*. Computational biology Mathematics Computer science Simulation experiment data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science computational scientists Computational biologists bioinformaticians software engineers programmers
BioSimulations tutorial and help

BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and...

Scientific topics: Simulation experiment, Systems biology, Computational biology

Operations: Modelling and simulation, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE

Resource type: Documentation

BioSimulations tutorial and help http://tess.elixir-uk.org/materials/biosimulations-help BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface. Simulation experiment Systems biology Computational biology SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE Life Science Researchers Computational biologists modelers
Initiation to R programming and descriptive statistics

On-line course support for the initiation to R programming and descriptive statistics given to PhD students at Institut Pasteur (Paris, France).

Keywords: R-programming, Descriptive statistics, Statistics, Bioinformatics

Initiation to R programming and descriptive statistics http://tess.elixir-uk.org/materials/initiation-to-r-programming-and-descriptive-statistics On-line course support for the initiation to R programming and descriptive statistics given to PhD students at Institut Pasteur (Paris, France). Blaise Li Étienne Kornobis Sébastien Mella Vincent Guillemot R-programming, Descriptive statistics, Statistics, Bioinformatics PhD students Post-Doctoral Fellows Biologists
Datanator tutorial

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA...

Scientific topics: Omics, Bioinformatics, Systems biology, Cell biology, Molecular biology

Operations: Filtering, Query and retrieval

Keywords: genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis

Resource type: Tutorial

Datanator tutorial http://tess.elixir-uk.org/materials/datanator-tutorial Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. This tutorial provides a brief introduction to the Datanator database and web application. The tutorial illustrates how to search the Datanator database and obtain and refine clouds of data about specific metabolites, RNA, proteins, and reactions of interest. Omics Bioinformatics Systems biology Cell biology Molecular biology genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis mololecular cell biologists systems biologists bioinformaticians Computational biologists modelers
Annotating data using ontologies

This video highlights examples of tools and ontologies which can be used for annotating health data, and how ontologies help to support data ecosystems.

Scientific topics: Ontology and terminology, Data integration and warehousing, Data management

Keywords: Ontologies, Annotation, Data integration

Resource type: Video

Annotating data using ontologies http://tess.elixir-uk.org/materials/annotating-data-using-ontologies This video highlights examples of tools and ontologies which can be used for annotating health data, and how ontologies help to support data ecosystems. Ontology and terminology Data integration and warehousing Data management Ontologies, Annotation, Data integration
Solutions for overcoming cohort data integration challenges using ontology: an introduction

Ontologies are collections of well-defined, hierarchical, controlled vocabulary, linked by logical relationships. This video introduces the concept and benefits of implementing ontologies for solving data integration issues when data is generated by different research groups.

Scientific topics: Data management, Data integration and warehousing, Ontology and terminology

Keywords: Ontologies, Data integration, Annotation

Resource type: Video

Solutions for overcoming cohort data integration challenges using ontology: an introduction http://tess.elixir-uk.org/materials/solutions-for-overcoming-cohort-data-integration-challenges-using-ontology-an-introduction Ontologies are collections of well-defined, hierarchical, controlled vocabulary, linked by logical relationships. This video introduces the concept and benefits of implementing ontologies for solving data integration issues when data is generated by different research groups. Data management Data integration and warehousing Ontology and terminology Ontologies, Data integration, Annotation
Data harmonization and enrichment using EMBL-EBI ontology tools

This video explains how the Zooma annotation tool, the OxO mapping service and the Ontology Lookup Service (OLS) can be used to harmonise and enrich biological and biomedical data. The EMBL-EBI Ontology Tools can be used by both biological curators and software developers. Biological curators...

Scientific topics: Ontology and terminology, Data submission, annotation, and curation, Data management

Keywords: CINECA, data harmonization, Annotation, Ontologies

Resource type: Video

Data harmonization and enrichment using EMBL-EBI ontology tools http://tess.elixir-uk.org/materials/data-harmonization-and-enrichment-using-embl-ebi-ontology-tools This video explains how the Zooma annotation tool, the OxO mapping service and the Ontology Lookup Service (OLS) can be used to harmonise and enrich biological and biomedical data. The EMBL-EBI Ontology Tools can be used by both biological curators and software developers. Biological curators access the tools through their respective websites. REST APIs are available for software developers who want to build systems based on these services. Ontology and terminology Data submission, annotation, and curation Data management CINECA, data harmonization, Annotation, Ontologies biocurators software developers, bioinformaticians