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Keywords: Europe PMC  or RNA-seq 

A Tidy Transcriptomics introduction to RNA-Seq analyses

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

Scientific topics: RNA-Seq

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

Resource type: Tutorial

A Tidy Transcriptomics introduction to RNA-Seq analyses http://tess.elixir-uk.org/materials/a-tidy-transcriptomics-introduction-to-rna-seq-analyses This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages. RNA-Seq Differential Expression, Gene Expression, RNA-seq, Transcriptomics Biologists
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 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). 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 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. 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 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. Europe PMC, Biomedical Literature, Literature search
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 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. 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 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. 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 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. Europe PMC, ORCID, Biomedical Literature
Effective Literature Research with Europe PMC

Following the latest developments in your scientific field requires thorough and frequent literature research. In this webinar, we will show how to find and access relevant scientific literature using Europe PMC, an open biomedical literature database, part of PubMed Central International. We...

Keywords: Europe PMC, Biomedical Literature, Literature search

Resource type: Webinar

Effective Literature Research with Europe PMC http://tess.elixir-uk.org/materials/effective-literature-research-with-europe-pmc Following the latest developments in your scientific field requires thorough and frequent literature research. In this webinar, we will show how to find and access relevant scientific literature using Europe PMC, an open biomedical literature database, part of PubMed Central International. We will cover searches by topic and author, searches for associated research data, as well as advanced options for building complex queries. This webinar was recorded on 30 May 2018. It is best viewed in full-screen mode using Google Chrome. The slides from this webinar can be downloaded here. To learn more about searching grant information and on managing, exporting and saving searches you can watch our previous webinar Europe PMC: get the most from literature searches. You will find more information about Europe PMCs API service in our webinar Europe PMC, programmatically. You can also try our Europe PMC: Quick Tour. See the EMBL-EBI training pages for a list of upcoming webinars. 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. Europe PMC, Biomedical Literature, Literature search Scientists who want to optimise their literature searches
Text mining: Key concepts and applications

EMBL-EBI presents this talk on an introduction to text mining and its applications in service provision. The 1st part of this talk focuses on what text mining is and some of the methods and available tools. The 2nd part looks at how to find articles on Europe PMC - a free literature resource for...

Keywords: Literature search, Text mining, Europe PMC, Biomedical Literature

Resource type: Webinar

Text mining: Key concepts and applications http://tess.elixir-uk.org/materials/text-mining-key-concepts-and-applications EMBL-EBI presents this talk on an introduction to text mining and its applications in service provision. The 1st part of this talk focuses on what text mining is and some of the methods and available tools. The 2nd part looks at how to find articles on Europe PMC - a free literature resource for biomedical and health researchers - and how to build your own text mining pipeline. The final part gives a nice case study showing how Europe PMC's pipeline was integrated into a new drug target validation platform called Open Targets (previously CTTV). Literature search, Text mining, Europe PMC, Biomedical Literature
Extracting research evidence from publications

Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature...

Keywords: Literature search, Biomedical Literature, Europe PMC, Text mining

Resource type: Webinar

Extracting research evidence from publications http://tess.elixir-uk.org/materials/extracting-research-evidence-from-publications Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature evidence using Europe PMC Annotations API. We highlight several use cases, including linking diseases with potential treatment targets, or identifying which protein structures are cited along with a gene mutation. Literature search, Biomedical Literature, Europe PMC, Text mining Wet-lab researchers and bioinformaticians who want to access scientific literature and data programmatically.
Europe PMC, programmatically

Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, books, patents, and clinical guidelines. More than 32 million abstracts (27 million from PubMed) and 4 million full-text articles can be freely accessed through Europe PMC in a single...

Keywords: Literature search, Programmatic Access, Europe PMC, REST API, Biomedical Literature

Resource type: Webinar

Europe PMC, programmatically http://tess.elixir-uk.org/materials/europe-pmc-programmatically Europe PMC is an open repository, providing access to worldwide biomedical literature, including articles, books, patents, and clinical guidelines. More than 32 million abstracts (27 million from PubMed) and 4 million full-text articles can be freely accessed through Europe PMC in a single search. The mission of Europe PMC is to build open access, full-text scientific literature resources and deliver world-class literature services. This webinar will introduce the Europe PMC Articles RESTful API and show you how to access publications and related information, such as citations, data links, or text-mined terms, programmatically. Francesco Talo Yogmatee Rochun Literature search, Programmatic Access, Europe PMC, REST API, Biomedical Literature
Europe PMC: get the most from literature searches

With Europe PMC, a free biomedical repository and partner in PubMed Central International, you can search worldwide, life-sciences literature, including articles, books, patents, and clinical guidelines. In this webinar, we will show how to use Europe PMC for effective literature research. We...

Keywords: Literature search, Life sciences publications, Europe PMC

Resource type: Webinar

Europe PMC: get the most from literature searches http://tess.elixir-uk.org/materials/europe-pmc-get-the-most-from-literature-searches With Europe PMC, a free biomedical repository and partner in PubMed Central International, you can search worldwide, life-sciences literature, including articles, books, patents, and clinical guidelines. In this webinar, we will show how to use Europe PMC for effective literature research. We will cover searches by topic and author, advanced search options for building complex queries, and setting alerts for your topic to stay on top of the published literature. Literature search, Life sciences publications, Europe PMC This webinar is aimed at scientists with an interest in learning more about the Europe PMC and optimising their literature searches.