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: 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)
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
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
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
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
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: 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
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
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
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
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
https://f1000research.com/documents/9-1377
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.
Allegra Via
Patricia Palagi
Jessica Lindvall
Rochelle E. Tractenberg
Teresa Attwood
The GOBLET Foundation
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
https://f1000research.com/documents/10-836
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.
Marie-Claude Blatter
Philippe Lemercier
Teresa Attwood
The GOBLET Foundation
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)
https://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module2.html
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
Frédéric de Lamotte
Julien Seiler
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)
https://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module1.html
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.
Frédéric de Lamotte
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
https://python.sdv.univ-paris-diderot.fr/
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.
Patrick Fuchs
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
https://elearning.bits.vib.be/courses/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.
Alexander Botzki
Joost Van Durme
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
https://osf.io/k263z/
http://tess.elixir-uk.org/materials/data-security-and-encryption
1. Data security
2. Encryption
3. Passwords
Jan Lammertyn
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
https://osf.io/syx4m/
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
Alexander Botzki
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
https://osf.io/fpvgy/
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
https://osf.io/wbr7t/
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
Flora D'Anna
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
https://osf.io/c2g9k/
http://tess.elixir-uk.org/materials/data-management-plans
dmponline.be - creating data management plans
why, what to cover, examples and self-assessment grids
Laura Standaert
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
https://osf.io/5xhya/
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
Hanne Elsen
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
https://osf.io/xhp2e/
http://tess.elixir-uk.org/materials/research-data-management-trends-and-requirements
Paula Oset - Research funders and journal policies
Paula Oset
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
https://osf.io/mvrny/
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)
Thomas Van de Velde
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
https://osf.io/fpvgy/
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.
Alexander Botzki
Laura Standaert
Tuur Muyldermans
Hanne Elsen
Paula Oset
Thomas Van de Velde
Flora D'Anna
Nele Pauwels
Griet Den Herder
Jan Lammertyn
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
https://bigcat-um.github.io/SPARQLTutorialBioSB2019/
http://tess.elixir-uk.org/materials/sparqling-biology-a-beginners-course
Course given at BioSB 2019 for biologists about SPARQL.
Denise Slenter
Biology
Sparql queries, Sparql syntax
Biologists
Chemists
runBioSimulations tutorial and help
runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA),...
Scientific topics: Simulation experiment, Computational biology, Systems biology
Operations: Modelling and simulation
Keywords: biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL
Resource type: Tutorial, Documentation
runBioSimulations tutorial and help
https://run.biosimulations.org/help
http://tess.elixir-uk.org/materials/runbiosimulations-tutorial-and-help
runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BNGL, SBML). runBioSimulations also provides a REST API for programmatic access to the same simulation capabilities.
The runBioSimulations tutorial and help describes how to use this web application and web service to execute simulations and visualize their results. This includes instructions on how to create COMBINE/OMEX archives of modeling projects.
Jonathan Karr
Ion Moraru
Bilal Shaikh
Gnaneswara Marupilla
Simulation experiment
Computational biology
Systems biology
biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL
modelers
BioSimulators tutorial and help
BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms,...
Scientific topics: Simulation experiment, Computational biology, Systems biology
Operations: Modelling and simulation
Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL
Resource type: Tutorial, Documentation
BioSimulators tutorial and help
https://biosimulators.org/help
http://tess.elixir-uk.org/materials/biosimulators-help
BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.
The BioSimulators help describes how to use this registry:
- How to find a containerized simulation tools that are capable of executing a modeling study.
- How to use containerized simulation tools to execute modeling studies.
- How to containerize a simulation tool and submit it to the BioSimulators registry.
Jonathan Karr
Ion Moraru
Bilal Shaikh
Simulation experiment
Computational biology
Systems biology
Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL
modelers
Computational biologists
software developers, bioinformaticians
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
https://hub-courses.pages.pasteur.fr/R_pasteur_phd/index.html
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).
Institut Pasteur, Bioinformatics and Biostatistics Hub
Blaise Li
Étienne Kornobis
Sébastien Mella
Vincent Guillemot
R-programming, Descriptive statistics, Statistics, Bioinformatics
PhD students
Post-Doctoral Fellows
Biologists
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
https://www.youtube.com/watch?v=lFqpuZfv_8o
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.
Emma Griffiths
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
https://www.youtube.com/watch?v=mk7LfUIQe6U
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.
Emma Griffiths
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
https://www.youtube.com/watch?v=vW-1w9vnGys
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.
Henriette Harmse
Ontology and terminology
Data submission, annotation, and curation
Data management
CINECA, data harmonization, Annotation, Ontologies
biocurators
software developers, bioinformaticians
How to use V-pipe (SARS-CoV-2 data)
How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data)
Scientific topics: Workflows, Genetic variation, Virology
Operations: Read pre-processing, Alignment, Variant calling
Keywords: coronavirus, NGS bioinformatics, Variant-calling
Resource type: Computer Software, workflow
How to use V-pipe (SARS-CoV-2 data)
https://cbg-ethz.github.io/V-pipe/tutorial/sars-cov2/
http://tess.elixir-uk.org/materials/how-to-use-v-pipe-sars-cov-2-data
How to use V-pipe bioinformatics virus NGS Pipeline - (specifically for SARS-CoV-2 data)
Ivan Topolsky
Workflows
Genetic variation
Virology
coronavirus, NGS bioinformatics, Variant-calling
bioinformaticians
Biologists, Genomicists, Computer Scientists
