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
https://sphn.ch/training/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.
Personalized Health Informatics Group
Vasundra Touré
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
https://doi.org/10.5281/zenodo.4610033
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
Esther Plomp
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)
https://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module4.html
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
Frédéric de Lamotte
Paulette Lieby
Lionel Maurel
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)
https://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module3.html
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
Frédéric de Lamotte
Hélène Chiapello
Thomas Denecker
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
https://www.youtube.com/playlist?list=PLD6bAdANKoMX5ntDRlNHAWKrnPdshLVgT
http://tess.elixir-uk.org/materials/cineca-discovery-service-catalog
Description and demonstration of the CINECA service catalog
Jonathan Dursi
Jordi Rambla
Frédéric Haziza
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
https://www.youtube.com/watch?v=oFmgC2upkSU
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
Kirill Tsukanov
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
https://www.youtube.com/watch?v=VEvHBrJlE6M
http://tess.elixir-uk.org/materials/fair-software-tools
CINECA webinar discussing the importance of the FAIR principles for software tools used in research
Carlos Martinez Ortiz
Marta Lloret Llinares
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?
https://www.youtube.com/watch?v=Or3AKpERvrw
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.
Kees van Bochove
Marta Lloret Llinares
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
https://www.youtube.com/watch?v=oiEFnWDVjP8
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
Tony Burdett
Marta Lloret Llinares
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)
https://www.youtube.com/watch?v=jGatQTTp-Dg
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).
Dalia Alghamdi
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
https://www.youtube.com/watch?v=Z20ZOrtQ7Cs
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.
Emma Griffiths
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
https://www.youtube.com/watch?v=7m6xtJEh1WE
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.
Emma Griffiths
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
https://www.youtube.com/watch?v=1HcaQMtppVs
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
Michaela Th. Mayrhofer
Marta Lloret Llinares
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
https://stemangiola.github.io/bioc_2020_tidytranscriptomics/
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.
Maria Doyle
Stefano Mangiola
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
https://www.ebi.ac.uk/training-beta/online/courses/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
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
https://www.ebi.ac.uk/training/online/course/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
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
https://www.ebi.ac.uk/training/online/course/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
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
https://www.ebi.ac.uk/training/online/course/analysing-and-visualising-microbiome-derived-datasets-using-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
https://zenodo.org/communities/bioinfconn
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.
F. Abascal, J. Aguirre, E. Andrés-León, D. Bajic, D. Baú, J. A. Bueren-Calabuig, Á. Cortés-Cabrera, I. Dotu, J. M. Fernández, H. G. D. Santos, B. Garcı́a-Jiménez, R. Guantes, I. Irisarri, N. Jiménez-Lozano, J. Klett, R. Méndez, A. Morreale, A. Pascual-Garcı́a, A. Perona, A. Sebastian, M. Stich, S. Tarazona, I. Yruela y R. Zardoya
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
https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TtT
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
Allegra Via
Patricia Palagi
Pedro Fernandes
Sarah Morgan
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
RNA - Seq de novo
https://www.france-bioinformatique.fr/en/training_material/rna-seq-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
Galaxy: Initiation II
https://www.france-bioinformatique.fr/en/training_material/galaxy-initiation-ii
http://tess.elixir-uk.org/materials/galaxy-initiation-ii
Galaxy II: common tools, quality control; alignment; data managment
Genomics