GA4GH Passports and ELIXIR AAI
The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API.
Keywords: AAI , GA4GH, Passports, Auhtorisation
Resource type: Training materials, Video
GA4GH Passports and ELIXIR AAI
https://docs.google.com/document/d/1oZdW3TsAv2rd4uAJdh6gP3jTbmLuhflUTCrE4x0pGMc/edit
http://tess.elixir-uk.org/materials/ga4gh-passports-and-elixir-aai
The target group of the training is developers and administrators of services that want to make use of GA4GH Passports to authenticate a user and authorise them to call an API.
Mikael Linden
Stefan Negru
Teemu Kataja
AAI , GA4GH, Passports, Auhtorisation
software developers, bioinformaticians
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
Making cohort data FAIR
CINECA webinar about how to make data from cohort studies FAIR
Scientific topics: Data management, Data integration and warehousing
Keywords: FAIR data, Cohort data, Ontologies, Standards
Resource type: Video
Making cohort data FAIR
https://www.youtube.com/watch?v=NWeffXwRa-U
http://tess.elixir-uk.org/materials/making-cohort-data-fair
CINECA webinar about how to make data from cohort studies FAIR
Will Hsiao
Marta Lloret Llinares
Data management
Data integration and warehousing
FAIR data, Cohort data, Ontologies, Standards
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
Discovering scientific evidence using Europe PMC SciLite annotation
For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find...
Keywords: Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer
Resource type: Life Sciences Literature Database
Discovering scientific evidence using Europe PMC SciLite annotation
https://trainingcontent.embl.org/discovering-scientific-evidence-using-europe-pmc-scilite-annotation
http://tess.elixir-uk.org/materials/discovering-scientific-evidence-using-europe-pmc-scilite-annotation
For readers of life sciences journal articles, annotations make it easier to scan an article and get a quick overview, find key concepts, and discover evidence, such as gene disease associations or molecular interactions. This webinar will demonstrate how to use the power of text mining to find evidence in scientific literature.
Who is this course for?
This webinar is suitable for scientists, database curators or anyone who wishes to learn more about how to use annotations.
Outcomes
By the end of the webinar you will be able to:
Explore Europe PubMed Central
Use text mining for scientific literature searches
Dayane Araujo
Aravind Venkatesan
Biomedical Literature, Annotations, Literature search, SciLite, Protein structure viewer, Chemical viewer
Finding the data behind research publications with Europe PMC
This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis.
Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints,...
Keywords: Biomedical Literature, Data links, databases, External links
Resource type: Life Sciences Literature Database
Finding the data behind research publications with Europe PMC
https://www.ebi.ac.uk/training-beta/events/finding-data-behind-research-articles-europe-pmc/
http://tess.elixir-uk.org/materials/finding-the-data-behind-research-publications-with-europe-pmc
This webinar will explain how to use Europe PMC to find relevant articles in your research field and locate the linked data containing facts and evidence to support your hypothesis.
Europe PMC is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more.
Who is this course for?
This webinar is aimed at scientists with an interest in learning more about the data-rich literature search tools provided by Europe PMC. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.
Dayane Araujo
Michael Parkin
Biomedical Literature, Data links, databases, External links
Using Europe PMC for effective literature research
This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex...
Keywords: Literature search, peer reviewed articles, Europe PMC, Preprints, Data links, Annotations, Europe PMC, ORCID
Resource type: Life Science Literature Database, Life Sciences Literature Database
Using Europe PMC for effective literature research
https://www.ebi.ac.uk/training-beta/events/using-europe-pmc-effective-literature-research/
http://tess.elixir-uk.org/materials/using-europe-pmc-for-effective-literature-research
This webinar will explain how to find and access relevant scientific literature and show how you can follow the latest developments in your scientific field. It will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex queries.
Europe PMC (https://europepmc.org/) is an open biomedical literature database including PubMed indexed articles, preprints, micropublications and more.
This webinar is aimed at scientists who want to optimise their literature searches. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.
Dayane Araujo
Michael Parkin
Literature search, peer reviewed articles, Europe PMC, Preprints, Data links, Annotations, Europe PMC, ORCID
Searching and browsing scientific publications with the new Europe PMC
Literature search is an essential and routine task in scientific research. Following the release of the new Europe PMC website, this webinar will show you the new full-text searching and browsing features built to optimise the literature research. Learn how to find the most recent, most relevant...
Keywords: Literature search, Data links, preprints
Resource type: Life Sciences Literature Database
Searching and browsing scientific publications with the new Europe PMC
https://www.ebi.ac.uk/training-beta/events/searching-and-browsing-scientific-publications-new-europe-pmc/
http://tess.elixir-uk.org/materials/searching-and-browsing-scientific-publications-with-the-new-europe-pmc
Literature search is an essential and routine task in scientific research. Following the release of the new Europe PMC website, this webinar will show you the new full-text searching and browsing features built to optimise the literature research. Learn how to find the most recent, most relevant and most cited articles in a topic of interest. Also, learn how to find and explore the enhanced content available in Europe PMC.
This webinar is aimed at life science scientists who are interested in optimising their literature search skills. No prior knowledge of bioinformatics is required.
Dayane Araujo
Michael Parkin
Literature search, Data links, preprints
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
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).
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 Common Workflow Language
**This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).**
Scientific topics: Workflows
Keywords: commonwl, common workflow language, CWL, Workflows, eLearning, EeLP
Resource type: Installation instructions, Manual
How to use Common Workflow Language
https://elixir.mf.uni-lj.si/course/view.php?id=37
http://tess.elixir-uk.org/materials/how-to-use-common-workflow-language
**This is an online tutorial where you can learn how to use the Common Workflow Language (CWL).**
Rob Finn
Michael Crusoe
Rob Finn
Michael Crusoe
Workflows
commonwl, common workflow language, CWL, Workflows, eLearning, EeLP
bioinformaticians
life scientists
programmers
Literature Searching Skills and Tools
Training slides on literature searching skills and tools. Part of biocurators training for the Postgraduate Certificate in Biocuration, developed by the University of Cambridge and the European Bioinformatics Institute (EMBL-EBI).
Keywords: Medical publications, Curation strategy, PubMed search, Literature database search, Biocuration, Europe PMC
Resource type: Slides
Literature Searching Skills and Tools
https://figshare.com/articles/Literature_Searching_Skills_and_Tools/7228721
http://tess.elixir-uk.org/materials/literature-searching-skills-and-tools
Training slides on literature searching skills and tools. Part of biocurators training for the Postgraduate Certificate in Biocuration, developed by the University of Cambridge and the European Bioinformatics Institute (EMBL-EBI).
Maria Levchenko
Medical publications, Curation strategy, PubMed search, Literature database search, Biocuration, Europe PMC
Integrating publications into bioinformatics analysis
Overview
Research literature contains a wealth of information that can be extracted at scale using text-mining technologies. To make text-mining data available to a wider group of researchers, the publications database, Europe PMC, provides access to millions of text-mined annotations, such as...
Keywords: Europe PMC, REST API, Bioinformatic analysis
Resource type: Webinar
Integrating publications into bioinformatics analysis
https://www.ebi.ac.uk/training/online/course/integrating-publications-bioinformatics-analysis
http://tess.elixir-uk.org/materials/integrating-publications-into-bioinformatics-analysis
Overview
Research literature contains a wealth of information that can be extracted at scale using text-mining technologies. To make text-mining data available to a wider group of researchers, the publications database, Europe PMC, provides access to millions of text-mined annotations, such as genes and proteins, metabolites, species, mutations, phosphorylations, interactions, associations, and many more.
This webinar will demonstrate how to access text-mined literature evidence programmatically, and how to supplement it with bibliographic information for advanced use cases. Two of such use cases, mapping of tropical disease research by author affiliation geoparsing and comparison of applicability of analytical chemistry techniques, will be introduced by invited speaker, Dr. Magnus Palmblad.
This webinar was recorded on 2nd October 2019. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded below.
Audience
This webinar is aimed at individuals who wish to learn about accessing text-mined literature evidence programmatically. No prior knowledge of bioinformatics is required, but undergraduate level knowledge of biology would be useful.
See the EMBL-EBI training pages for a list of upcoming webinars.
No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.
Maria Levchenko
Magnus Palmblad
Europe PMC, REST API, Bioinformatic analysis
Navigating the data-rich literature: finding evidence in biomedical publications
In the age of data‐driven science, discovering all the data associated with a study can be tricky. In this webinar, we will demonstrate how to locate primary data in a publication, find facts and evidence to support your hypothesis, and scan a paper for important biological concepts using tools...
Keywords: Europe PMC, Biomedical Literature, Literature search
Resource type: Webinar
Navigating the data-rich literature: finding evidence in biomedical publications
https://www.ebi.ac.uk/training/online/course/navigating-data-rich-literature-finding-evidence-biomedical-publications
http://tess.elixir-uk.org/materials/navigating-the-data-rich-literature-finding-evidence-in-biomedical-publications
In the age of data‐driven science, discovering all the data associated with a study can be tricky. In this webinar, we will demonstrate how to locate primary data in a publication, find facts and evidence to support your hypothesis, and scan a paper for important biological concepts using tools provided by Europe PMC.
This webinar was recorded on 4th October 2017. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded here.
This webinar is aimed at scientists with an interest in learning more about the literature search tools provided by Europe PMC.
No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful.
If you would like to learn more about Europe PMC have a look at our other webinar on Europe PMC: get the most from literature searches and our Europe PMC: Quick tour.
See the EMBL-EBI training pages for a list of upcoming webinars.
Maria Levchenko
Europe PMC, Biomedical Literature, Literature search
Preprint discovery 101: Tips & tricks for authors and readers
Preprints - research articles that are publicly posted before undergoing formal peer review - provide a rapid means to share research results. In this webinar, we will demonstrate how to follow hot-off-the-press research by incorporating preprints in your literature search routine using discovery...
Keywords: Europe PMC, Preprints
Resource type: Webinar
Preprint discovery 101: Tips & tricks for authors and readers
https://www.ebi.ac.uk/training/online/course/preprint-discovery-101-tips-tricks-authors-and-readers
http://tess.elixir-uk.org/materials/preprint-discovery-101-tips-tricks-for-authors-and-readers
Preprints - research articles that are publicly posted before undergoing formal peer review - provide a rapid means to share research results. In this webinar, we will demonstrate how to follow hot-off-the-press research by incorporating preprints in your literature search routine using discovery tools developed by Europe PMC. We will also share some useful tips for those of you posting preprints, including how to claim a preprint to your ORCID or check if your preprint has been cited, reviewed or recommended by others.
To learn more about using Europe PMC in your research try our Europe PMC: Quick tour or our webinar Effective Literature Research with Europe PMC.
This webinar was recorded on 17 October 2018. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded below.
See the EMBL-EBI training pages for a list of upcoming webinars.
This webinar is aimed at biological researchers who wish to learn more about incorporating pre-prints into their research. No prior knowledge is required.
Maria Levchenko
Europe PMC, Preprints
How to Share Text Mining Results in Biology
Overview
Though text mining becomes more widespread in biology, an average researcher can rarely use it to their advantage. In this webinar, Europe PMC presents a tool to easily share annotated biological entities and relations with the research community. Europe PMC Annotation Submission...
Keywords: Europe PMC, Text mining, Literature search
Resource type: Webinar
How to Share Text Mining Results in Biology
https://ebi.ac.uk/training/online/course/how-share-text-mining-results-biology
http://tess.elixir-uk.org/materials/how-to-share-text-mining-results-in-biology
Overview
Though text mining becomes more widespread in biology, an average researcher can rarely use it to their advantage. In this webinar, Europe PMC presents a tool to easily share annotated biological entities and relations with the research community. Europe PMC Annotation Submission System allows text miners and curators in the field of life sciences to make their results available to the public. Annotated concepts can be browsed and searched for both on Europe PMC website as a part of SciLite tool and Advanced search, as well as via the Annotations API.
This webinar was recorded on 9th of July 2019. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded below.
Audience
This webinar is aimed at individuals who wish to learn more about sharing and reusing results of biomedical text-mining. No prior knowledge of bioinformatics is required, but an undergraduate level knowledge of biology would be useful.
See the EMBL-EBI training pages for a list of upcoming webinars.
No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful.
Dayane Araujo
Aravind Venkatesan
Francesco Talo
Europe PMC, Text mining, Literature search
Extracting gene-disease evidence from literature, genetics, genomics and more
Do you want to identify and prioritise new therapeutic targets? Are you looking for associations of your gene of interest with a specific disease? Do you work in the area of drug repurposing? Are you interested in disease biology? If you said yes to any of these questions, this webinar is for...
Keywords: Europe PMC, Open Targets, gene-disease relationship, Text mining
Resource type: Webinar
Extracting gene-disease evidence from literature, genetics, genomics and more
https://www.ebi.ac.uk/training/online/course/extracting-gene-disease-evidence-literature-genetics-genomics-and-more
http://tess.elixir-uk.org/materials/extracting-gene-disease-evidence-from-literature-genetics-genomics-and-more
Do you want to identify and prioritise new therapeutic targets? Are you looking for associations of your gene of interest with a specific disease? Do you work in the area of drug repurposing? Are you interested in disease biology? If you said yes to any of these questions, this webinar is for you. Watch to explore gene-disease relations using freely available tools from Europe PMC and Open Targets. Maria and Denise will show you how to access evidence from research literature, genetics, genomics and chemical data to obtain information at drug targets and disease levels.
This webinar was recorded on 7th June 2018. It is best viewed in full screen mode using Google Chrome. The slides from this webinar can be downloaded below.
Denise Carvalho-Silva
Maria Levchenko
Europe PMC, Open Targets, gene-disease relationship, Text mining
Scientists
Europe PMC: Services for academic authors
Researchers are often asked to maintain an up-to-date publication list, whether for job applications, tenure evaluations, or grant proposals. An easy way to do this is by using your ORCID iD and linking it to your published papers. An ORCID is a unique identifier - personalised number that is...
Keywords: Europe PMC, ORCID, Biomedical Literature
Resource type: Webinar
Europe PMC: Services for academic authors
https://www.ebi.ac.uk/training/online/course/europe-pmc-services-academic-authors
http://tess.elixir-uk.org/materials/europe-pmc-services-for-academic-authors
Researchers are often asked to maintain an up-to-date publication list, whether for job applications, tenure evaluations, or grant proposals. An easy way to do this is by using your ORCID iD and linking it to your published papers. An ORCID is a unique identifier - personalised number that is assigned to you when you register. By using your ORCID in addition to your name you can make sure that you are easily distinguishable from other researchers with the same name, keep track of your work through name changes, and even pull together different kinds of achievements, like grant awards, training, etc.
This video shows how you can register for an ORCID, add your publications in three easy steps to build your digital CV, and how to get a personal author profile page that showcases your publications and citations.
This webinar was recorded on 7th of August 2017. It is best viewed in full-screen mode using Google Chrome.
No prior knowledge of bioinformatics is required, but an undergraduate-level understanding of biology would be useful.
Maria Levchenko
Europe PMC, ORCID, Biomedical Literature