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
https://sphn.ch/training/protege-training/
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.
Personalized Health Informatics Group
Vasundra Touré
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: Ontology and terminology, Medical informatics, FAIR data, Data management, Computer science
Operations: Data retrieval, Data handling, Database search, Query and retrieval
Keywords: Clinical data, SPARQL, Query data, RDF, Knowledge graph, Triplestore, Ontology
Resource type: Video, Training materials, E-learning
Training Primer (RDF and SPARQL)
https://sphn.ch/training/sphn-rdf-training-primer/
http://tess.elixir-uk.org/materials/training-primer-rdf-and-sparql
This training provides a first introduction to RDF and SPARQL.
Personalized Health Informatics Group
Vasundra Touré
Philip Krauss
Sabine Österle
Ontology and terminology
Medical informatics
FAIR data
Data management
Computer science
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: Computer science, Data management, FAIR data, Medical informatics, Ontology and terminology
Operations: Data handling, Standardisation and normalisation
Keywords: Clinical data, Data semantics, FAIR, Standards, Ontology, SNOMED CT, LOINC, ATC, CHOP, ICD
Resource type: Video, Training materials, E-learning
Semantic Standards
https://sphn.ch/training/semantic-standards-training/
http://tess.elixir-uk.org/materials/semantic-standards
This training module provides an introduction on the key semantic standards used within SPHN.
Personalized Health Informatics Group
Kristin Gnodke
Sabine Österle
Computer science
Data management
FAIR data
Medical informatics
Ontology and terminology
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
https://sphn.ch/training/datavisualization/
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.
Personalized Health Informatics Group
Petar Horki
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: Medical informatics, FAIR data, Data management, Computer science
Operations: Validation, Data handling
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
https://sphn.ch/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.
Personalized Health Informatics Group
Philip Krauss
Martin Zablocki
Sabine Österle
Vasundra Touré
Medical informatics
FAIR data
Data management
Computer science
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
https://sphn.ch/training/pythonandr/
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.
Personalized Health Informatics Group
Petar Horki
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
https://doi.org/10.5281/zenodo.6599750
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.
Ana M. P. Melo
Filipa Pereira
Pedro Príncipe
Celia W.G. van Gelder
Mijke Jetten
Daniel Faria
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
SPHN/BioMedIT Data Privacy and IT Security Training
SPHN/BioMedIT Data Privacy and IT Security Training
https://edu.isb-sib.ch/course/view.php?id=424
http://tess.elixir-uk.org/materials/sphn-biomedit-data-privacy-and-it-security-training
No description provided.
Cellosaurus : A resource on cell lines
Cellosaurus : A resource on cell lines
https://edu.isb-sib.ch/course/view.php?id=585
http://tess.elixir-uk.org/materials/cellosaurus-a-resource-on-cell-lines
No description provided.
Introduction to Workflows with Common Workflow Language
Introduction to workflow thinking for novices, using the Common Workflow Language
Scientific topics: Workflows
Operations: RNA-Seq analysis
Keywords: cwl, commonwl, sciworkflows, workflows
Resource type: Carpentries style curriculum
Introduction to Workflows with Common Workflow Language
https://carpentries-incubator.github.io/cwl-novice-tutorial/
http://tess.elixir-uk.org/materials/introduction-to-workflows-with-common-workflow-language
Introduction to workflow thinking for novices, using the Common Workflow Language
Michael R. Crusoe
Gerard Capes
Douglas Lowe
Anne Luesink
Stian Soiland-Reyes
Toby Hodges
Sehrish Kanwal
Pedro L Fernandes
Workflows
cwl, commonwl, sciworkflows, workflows
esearchers and research software engineers who would like to begin automating their analyses in workflows.
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
PSLS22 Practical Statistics for the Life Sciences
This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data...
PSLS22 Practical Statistics for the Life Sciences
https://gtpb.github.io/PSLS22/
http://tess.elixir-uk.org/materials/psls22-practical-statistics-for-the-life-sciences
This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data exploration. We then move into statistical modeling and data analysis. We will focus on the link between linear regression and analysis of variance. Together, these methods contribute to the study of General Linear Models. The course also introduces the basics of non-parametric testing, and addresses categorical data analysis and logistic regression.
Lieven Clement
Milan Malfait
Jeroen Gilis
Graduate students
All postgraduates
Schema.org, what and why?
In this tutorial you will get an idea on what Schema.org is and how it is useful
Keywords: schemaorg, markup, structured data, schemaorg, markup, structured data
Schema.org, what and why?
http://bioschemas.org/tutorials/what_why_schema
http://tess.elixir-uk.org/materials/schema-org-what-and-why
In this tutorial you will get an idea on what Schema.org is and how it is useful
schemaorg, markup, structured data, schemaorg, markup, structured data
Bioschemas, what and why?
In this tutorial you will learn what Bioschemas is, what the added value to schema.org.is and what the main elements in Bioschemas are
Keywords: schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas
Bioschemas, what and why?
http://bioschemas.org/tutorials/what_why_bioschemas
http://tess.elixir-uk.org/materials/bioschemas-what-and-why
In this tutorial you will learn what Bioschemas is, what the added value to schema.org.is and what the main elements in Bioschemas are
schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas
Schema.org markup examples
With these examples you will get a better understanding of benefits brought by structure data, i.e., schema.org markup
Keywords: schemaorg, markup, structured data, example, schemaorg, markup, structured data, example
Schema.org markup examples
http://bioschemas.org/tutorials/markup_examples
http://tess.elixir-uk.org/materials/schema-org-markup-examples
With these examples you will get a better understanding of benefits brought by structure data, i.e., schema.org markup
schemaorg, markup, structured data, example, schemaorg, markup, structured data, example
How to select the right profile for your resource
In this how-to, we will guide you through the necessary steps for you to select a Bioschemas profile that will be later used to add mark up to your own resources
Keywords: schemaorg, markup, structured data, bioschemas profile, schemaorg, markup, structured data, bioschemas profile
How to select the right profile for your resource
http://bioschemas.org/tutorials/howto/howto_right_profile
http://tess.elixir-uk.org/materials/how-to-select-the-right-profile-for-your-resource
In this how-to, we will guide you through the necessary steps for you to select a Bioschemas profile that will be later used to add mark up to your own resources
schemaorg, markup, structured data, bioschemas profile, schemaorg, markup, structured data, bioschemas profile
How to update a profile
In this how-to, we will guide you through the necessary steps for you to update a profile, i.e.,create and publish a new draft profile, you need some knowledge on spreadsheets, GitHub, git and Jekyll.
Keywords: schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile
How to update a profile
http://bioschemas.org/tutorials/howto/howto_new_profile_version
http://tess.elixir-uk.org/materials/how-to-update-a-profile
In this how-to, we will guide you through the necessary steps for you to update a profile, i.e.,create and publish a new draft profile, you need some knowledge on spreadsheets, GitHub, git and Jekyll.
schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile
How to create a new Bioschemas profile
In this how-to, we will guide you through the necessary steps to create a new Bioschemas profile.
Keywords: schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile
How to create a new Bioschemas profile
http://bioschemas.org/tutorials/howto/howto_create_new_profile
http://tess.elixir-uk.org/materials/how-to-create-a-new-bioschemas-profile
In this how-to, we will guide you through the necessary steps to create a new Bioschemas profile.
schema.org, markup, structured data, bioschemas profile, schema.org, markup, structured data, bioschemas profile
How to check your Bioschemas deployment
This guide will show you how to check your deployed markup, both locally and what is retrieved by external services.
Keywords: schemaorg, JSON-LD, bioschemas
How to check your Bioschemas deployment
http://bioschemas.org/tutorials/howto/howto_check_deploy
http://tess.elixir-uk.org/materials/how-to-check-your-bioschemas-deployment
This guide will show you how to check your deployed markup, both locally and what is retrieved by external services.
schemaorg, JSON-LD, bioschemas
How to mark up your own resource with Bioschemas
In this how-to, we will guide you through the necessary steps in order to get a JSON-LD markup describing your own resource using a Bioschemas profile
Keywords: schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas
How to mark up your own resource with Bioschemas
http://bioschemas.org/tutorials/howto/howto_add_markup
http://tess.elixir-uk.org/materials/how-to-mark-up-your-own-resource-with-bioschemas
In this how-to, we will guide you through the necessary steps in order to get a JSON-LD markup describing your own resource using a Bioschemas profile
schemaorg, markup, structured data, bioschemas, schemaorg, markup, structured data, bioschemas
Adding Schema.org to a GitHub Pages site
This guide will show you how to do add Schema.org markup to a GitHub Pages site.
Keywords: schemaorg, TeSS, GitHub pages, schemaorg, TeSS, GitHub pages
Adding Schema.org to a GitHub Pages site
http://bioschemas.org/tutorials/howto/howto_add_github
http://tess.elixir-uk.org/materials/adding-schema-org-to-a-github-pages-site-deb50140-9274-4c87-9eda-5361cb287e71
This guide will show you how to do add Schema.org markup to a GitHub Pages site.
schemaorg, TeSS, GitHub pages, schemaorg, TeSS, GitHub pages
Tutorial on developing Building Blocks
This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them.
Scientific topics: Personalised medicine, Workflows, Bioinformatics
Keywords: HPC, building blocks
Resource type: Tutorial
Tutorial on developing Building Blocks
https://permedcoe.readthedocs.io/en/latest/04_creating/04_tutorial/tutorial.html
http://tess.elixir-uk.org/materials/tutorial-on-developing-building-blocks
This section provides a step-by-step by tutorial on how to develop Building Blocks using the permedcoe package and an application that uses them.
Javi Conejero
Personalised medicine
Workflows
Bioinformatics
HPC, building blocks
Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities
Tutorial on working with computing clusters
This tutorial provides an introduction to how to access a computing cluster, manage your data and submit jobs using a batch job system.
Keywords: HPC
Resource type: Tutorial
Tutorial on working with computing clusters
https://permedcoe.github.io/cluster-tutorial/
http://tess.elixir-uk.org/materials/tutorial-on-working-with-computing-clusters
This tutorial provides an introduction to how to access a computing cluster, manage your data and submit jobs using a batch job system.
Henrik Nortamo
Jesse Harrison
David Vicente
HPC
Novice users of HPC and anyone who expects to need to use HPC systems at some stage in their research
SARS-CoV-2 : Studying a new virus
In December 2019, a new type of virus of the family Coronaviridae called SARS-CoV-2 (formerly 2019-nCoV) was identified as the cause of an outbreak. In this e-learning course, you will learn to find, use or interpret information about a new virus. Knowledge of the basic molecular biology of...
SARS-CoV-2 : Studying a new virus
https://edu.isb-sib.ch/course/view.php?id=572
http://tess.elixir-uk.org/materials/sars-cov-2-studying-a-new-virus
In December 2019, a new type of virus of the family Coronaviridae called SARS-CoV-2 (formerly 2019-nCoV) was identified as the cause of an outbreak. In this e-learning course, you will learn to find, use or interpret information about a new virus. Knowledge of the basic molecular biology of viruses is presumed.
Machine Learning & BioStatistics Hackathon 2020
Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020.
Scientific topics: Computer science, Statistics and probability, Machine learning
Keywords: machine learning, biostatistics, eLearning, EeLP
Resource type: Training materials
Machine Learning & BioStatistics Hackathon 2020
https://elixir.mf.uni-lj.si/course/view.php?id=53
http://tess.elixir-uk.org/materials/machine-learning-biostatistics-hackathon-2020
Materials created at the Machine Learning and BioStatistics hackathon organised by ELIXIR-GR (CERTH) in October and November 2020.
Fotis Psomopoulos
Computer science
Statistics and probability
Machine learning
machine learning, biostatistics, eLearning, EeLP
Life Science Researchers
statisticians
Training Designers
Training instructors
Trainers
HPC Hackathon Materials
Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021.
Scientific topics: Computer science
Keywords: HPC, high-performance computing, eLearning, EeLP
Resource type: Training materials
HPC Hackathon Materials
https://elixir.mf.uni-lj.si/course/view.php?id=70
http://tess.elixir-uk.org/materials/hpc-hackathon-materials
Materials developed at the HPC hackathon hosted by ELIXIR-SI (UL) in May and June 2021.
Alan O'Cais
Javi Conejero
Leon Kos
Damjan Harisch
Computer science
HPC, high-performance computing, eLearning, EeLP
Life Science Researchers
Training Designers
Training instructors
Trainers
Containers and Workflows training materials hackathon
Materials developed at the Containers and Workflows hackathon organised by ELIXIR-BE (VIB) in February and April 2021.
Scientific topics: Computer science
Keywords: Containers, Workflows, eLearning, EeLP
Resource type: Training materials
Containers and Workflows training materials hackathon
https://elixir.mf.uni-lj.si/course/view.php?id=62
http://tess.elixir-uk.org/materials/containers-and-workflows-training-materials-hackathon
Materials developed at the Containers and Workflows hackathon organised by ELIXIR-BE (VIB) in February and April 2021.
Tuur Muyldermans / Alexander Botzki
Computer science
Containers, Workflows, eLearning, EeLP
Life Science Researchers
Training Designers
Training instructors
Trainers
Explore and visualize your data with Python
In this e-learning course, you will reproduce a typical analysis pipeline using Python, an open-source and general-purpose scripting language which runs on all major operating systems. Basic knowledge of Python programming is required.
Explore and visualize your data with Python
https://edu.isb-sib.ch/course/view.php?id=570
http://tess.elixir-uk.org/materials/explore-and-visualize-your-data-with-python
In this e-learning course, you will reproduce a typical analysis pipeline using Python, an open-source and general-purpose scripting language which runs on all major operating systems. Basic knowledge of Python programming is required.
neXtProt : Exploring human proteins
In this 1-hour e-learning course, you will learn what type of information on human proteins is found in neXtProt, where it comes from and how it is organized in topic-specific entry views. Basic knowledge of biology and proteins is required.
neXtProt : Exploring human proteins
https://edu.isb-sib.ch/course/view.php?id=549
http://tess.elixir-uk.org/materials/nextprot
In this 1-hour e-learning course, you will learn what type of information on human proteins is found in neXtProt, where it comes from and how it is organized in topic-specific entry views. Basic knowledge of biology and proteins is required.