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Querying Data with SPARQL

This training module will provide researcher with an introduction to SPARQL queries for health-related data.

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

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

Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, SNOMED CT, LOINC

Resource type: Video, Training materials with mock data, E-learning

Querying Data with SPARQL http://tess.elixir-uk.org/materials/querying-data-with-sparql This training module will provide researcher with an introduction to SPARQL queries for health-related data. Philip Krauss Sabine Österle Computer science Data management FAIR data Medical informatics Clinical data, SPARQL, Query data, RDF, Knowledge graph, SNOMED CT, LOINC Research Scientists Data Managers Biomedical Researchers Bioinformaticians Data Scientists
Helis Academy course FAIR data stewardship 2021, Day 1, (Reviewing) Data Management Plans

This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021

Scientific topics: FAIR data, Data management

Operations: Data handling

Keywords: Data management planning

Resource type: Slidedeck

Helis Academy course FAIR data stewardship 2021, Day 1, (Reviewing) Data Management Plans http://tess.elixir-uk.org/materials/helis-academy-course-fair-data-stewardship-2021-day-1-reviewing-data-management-plans This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course Day 6, March 31, 2021 FAIR data Data management Data management planning PhD candidate
FAIR data - Module 4 (share and publish data)

Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données

Scientific topics: Data management, Biology, Bioinformatics

Keywords: data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse

Resource type: Slides

FAIR data - Module 4 (share and publish data) http://tess.elixir-uk.org/materials/fair-data-module-4-share-and-publish-data Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données Hélène Chiapello Thomas Denecker Jean-François Dufayard Gautier Sarah Julien Seiler Data management Biology Bioinformatics data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse Biologists bioinformaticians Biomedical researchers
FAIR data - Module 3 (Metadata)

Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données

Scientific topics: Data management, Biology, Bioinformatics

Operations: Data handling

Keywords: metadata, data annotation, life science standards, data sharing

Resource type: Slides

FAIR data - Module 3 (Metadata) http://tess.elixir-uk.org/materials/fair-data-module-3-metadata Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données Jean-François Dufayard Gautier Sarah Paulette Lieby Data management Biology Bioinformatics metadata, data annotation, life science standards, data sharing Biologists bioinformaticians Biomedical researchers
CINECA discovery service catalog

Description and demonstration of the CINECA service catalog

Keywords: Cohort data, Standards, federated data analysis, Beacon queries

Resource type: Series of videos

CINECA discovery service catalog http://tess.elixir-uk.org/materials/cineca-discovery-service-catalog Description and demonstration of the CINECA service catalog Cohort data, Standards, federated data analysis, Beacon queries
A common framework for designing portable federated pipelines

This video describes a common framework for designing portable federated pipelines

Scientific topics: Data architecture, analysis and design

Keywords: data access, federated data analysis

Resource type: Video

A common framework for designing portable federated pipelines http://tess.elixir-uk.org/materials/a-common-framework-for-designing-portable-federated-pipelines This video describes a common framework for designing portable federated pipelines Alvaro Gonzalez Data architecture, analysis and design data access, federated data analysis
FAIR software tools

CINECA webinar discussing the importance of the FAIR principles for software tools used in research

Scientific topics: Software engineering

Keywords: FAIR, software tools, Software

Resource type: Video

FAIR software tools http://tess.elixir-uk.org/materials/fair-software-tools CINECA webinar discussing the importance of the FAIR principles for software tools used in research Software engineering FAIR, software tools, Software
Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality?

CINECA webinar about the basics of FAIR health data.

Scientific topics: Data management

Keywords: FAIR data, Health data, Open science

Resource type: Video

Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality? http://tess.elixir-uk.org/materials/introduction-to-fair-principles-open-science-through-fair-health-data-networks-dream-or-reality CINECA webinar about the basics of FAIR health data. Data management FAIR data, Health data, Open science
Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects

CINECA webinar discussing when to bring compute to the data

Scientific topics: Data architecture, analysis and design

Keywords: Cloud computing, Data analysis, Standards, Translational research

Resource type: Video

Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects http://tess.elixir-uk.org/materials/data-gravity-in-the-life-sciences-lessons-learned-from-the-hca-and-other-federated-data-projects CINECA webinar discussing when to bring compute to the data Data architecture, analysis and design Cloud computing, Data analysis, Standards, Translational research
Annotating data using next generation biobanking ontology (NGBO)

This video explains why we need data standardization and how to annotate data using next generation biobanking ontology (NGBO).

Scientific topics: Ontology and terminology, Data integration and warehousing

Keywords: Standards, Ontologies, Data Integration, data harmonization, Standardised vocabulary

Resource type: Video

Annotating data using next generation biobanking ontology (NGBO) http://tess.elixir-uk.org/materials/annotating-data-using-next-generation-biobanking-ontology-ngbo This video explains why we need data standardization and how to annotate data using next generation biobanking ontology (NGBO). Ontology and terminology Data integration and warehousing Standards, Ontologies, Data Integration, data harmonization, Standardised vocabulary
Applying data standards to the harmonization of COVID-19 datasets from different sources

This video describes how public health genomics has played a key role in international responses to the COVID-19 pandemic, and how data standards are being used to harmonize data across jurisdictions for Canadian COVID-19 surveillance and outbreak investigations.

Scientific topics: Data integration and warehousing

Keywords: Data integration, Standards, Standardised vocabulary, data harmonization, Ontologies

Resource type: Video

Applying data standards to the harmonization of COVID-19 datasets from different sources http://tess.elixir-uk.org/materials/applying-data-standards-to-the-harmonization-of-covid-19-datasets-from-different-sources This video describes how public health genomics has played a key role in international responses to the COVID-19 pandemic, and how data standards are being used to harmonize data across jurisdictions for Canadian COVID-19 surveillance and outbreak investigations. Data integration and warehousing Data integration, Standards, Standardised vocabulary, data harmonization, Ontologies Anyone interested in data standardization and/or the ontology approach (i.e. public, end users).
Useful ontologies for harmonizing cohort data

This video describes a community of practice for interoperable ontology building called the OBO Foundry, and highlights a number of well curated and maintained ontologies that are useful for annotating cohort data.

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

Keywords: Ontologies, Cohort data, data annotation

Resource type: Video

Useful ontologies for harmonizing cohort data http://tess.elixir-uk.org/materials/useful-ontologies-for-harmonizing-cohort-data This video describes a community of practice for interoperable ontology building called the OBO Foundry, and highlights a number of well curated and maintained ontologies that are useful for annotating cohort data. Ontology and terminology Data management Data integration and warehousing Ontologies, Cohort data, data annotation Anyone interested in data standardization and/or the ontology approach (i.e. public, end users).
Status Update Code of Conduct: Teaming up & Talking about it

CINECA webinar about the code of conduct for the sector of health research according to Art. 40 GDPR

Keywords: GDPR, Healthcare research, data harmonization

Resource type: Video

Status Update Code of Conduct: Teaming up & Talking about it http://tess.elixir-uk.org/materials/status-update-code-of-conduct-teaming-up-talking-about-it CINECA webinar about the code of conduct for the sector of health research according to Art. 40 GDPR GDPR, Healthcare research, data harmonization
A Tidy Transcriptomics introduction to RNA-Seq analyses

This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.

Scientific topics: RNA-Seq

Keywords: Differential Expression, Gene Expression, RNA-seq, Transcriptomics

Resource type: Tutorial

A Tidy Transcriptomics introduction to RNA-Seq analyses http://tess.elixir-uk.org/materials/a-tidy-transcriptomics-introduction-to-rna-seq-analyses This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages. RNA-Seq Differential Expression, Gene Expression, RNA-seq, Transcriptomics Biologists
MGnify quick tour

This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets.

Scientific topics: Metagenomics

Keywords: Metagenomics, Sequence analysis, MGnify, Microbiology

Resource type: Tutorial

MGnify quick tour http://tess.elixir-uk.org/materials/mgnify-quick-tour This quick tour provides a brief introduction to MGnify - a free resource for analysis, visualisation and discovery of microbiome (metagenomic, metatranscriptomic, amplicon and assembly) datasets. Ola Tarkowska Lorna Richardson Metagenomics Metagenomics, Sequence analysis, MGnify, Microbiology Life Scientists
Metagenomics Bioinformatics

Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis.

Scientific topics: Metagenomics

Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology

Resource type: Tutorial

Metagenomics Bioinformatics http://tess.elixir-uk.org/materials/metagenomics-bioinformatics Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis. Alex Mitchell Varsha Kale Rob Finn Guillermo Rangel Pineros Rebecca Campos Metagenomics Metagenomics, MGnify, Sequence Analysis, Microbiology Life Scientists
EBI Metagenomics: analysing and exploring metagenomics data

EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets...

Scientific topics: Metagenomics

Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology

Resource type: Webinar

EBI Metagenomics: analysing and exploring metagenomics data http://tess.elixir-uk.org/materials/ebi-metagenomics-analysing-and-exploring-metagenomics-data EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive. Alex Mitchell Metagenomics Metagenomics, MGnify, Sequence Analysis, Microbiology Life Scientists
Analysing and visualising microbiome-derived datasets using the MGnify Web API

MGnify (formerly EBI Metagenomics) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available...

Analysing and visualising microbiome-derived datasets using the MGnify Web API http://tess.elixir-uk.org/materials/analysing-and-visualising-microbiome-derived-datasets-using-the-mgnify-web-api MGnify (formerly EBI Metagenomics) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets drawn from the European Nucleotide Archive (ENA).
Bioinformática con Ñ

"Bioinformática con Ñ" is a project born in 2013 aimed to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The first release, published in 2014 and edited by Álvaro Sebastián and Alberto Pascual-García, consists on more than 500 pages where the following...

Scientific topics: Systems biology, Bioinformatics

Keywords: introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management

Resource type: Book

Bioinformática con Ñ http://tess.elixir-uk.org/materials/bioinformatica-con-n "Bioinformática con Ñ" is a project born in 2013 aimed to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The first release, published in 2014 and edited by Álvaro Sebastián and Alberto Pascual-García, consists on more than 500 pages where the following matters are covered: biomedical databases, sequence analysis, phylogeny and evolution, structural biology, including diverse topics such as docking, virtual screening or molecular dynamics, statistics and R, systems biology, programming skills, data mining, parallel computation, bibliography management and science article writing. Portada: Enrique Sahagún Systems biology Bioinformatics introduction to bioinformatics, structural biology, biomolecular databases, Systems biology, phylogenetics, Programming, Sequence Analysis, DNA RNA, Virtual Screening, molecular evolution, molecular dynamics, Molecular docking, normal modes analysis, Proteins, protein folding, protein structure alignment, chromatin structure, intrinsically disordered proteins, data minning, R-programming, parallel computing, bibliography management Anyone interested in bioinformatics
ELIXIR EXCELERATE Train the Trainer

This set of course material was designed in the context of the ELIXIR EXCELERATE Train the Trainer programme. It covers four sessions: * Learning principles and how they apply to training and teaching * Teaching techniques that can be used to enhance learner engagement and participation *...

Keywords: Train the trainer, Pedagogy, Course development, Course design

Resource type: Training materials

ELIXIR EXCELERATE Train the Trainer http://tess.elixir-uk.org/materials/elixir-excelerate-train-the-trainer This set of course material was designed in the context of the ELIXIR EXCELERATE Train the Trainer programme. It covers four sessions: * Learning principles and how they apply to training and teaching * Teaching techniques that can be used to enhance learner engagement and participation * Lesson, course, and materials design * Assessment and feedback in training and teaching Train the trainer, Pedagogy, Course development, Course design Trainers Training instructors Training Designers teachers
RNA - Seq de novo

Practical session on transciptome de novo assembly

Keywords: RNA-seq

RNA - Seq de novo http://tess.elixir-uk.org/materials/rna-seq-de-novo Practical session on transciptome de novo assembly RNA-seq
Galaxy: Initiation II

Galaxy II: common tools, quality control; alignment; data managment

Keywords: Genomics

Galaxy: Initiation II http://tess.elixir-uk.org/materials/galaxy-initiation-ii Galaxy II: common tools, quality control; alignment; data managment Genomics