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Keywords: Europe PMC  or Information visualisation 


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.
Keynote on Visual Analytics & Human/Computer Interfaces

Sara Irina Fabrikant discusses how analysis of scientific data can be enhanced using information visualization, visual analytics, cognition principles, and graphical user interface design. She focuses on the use of evaluation to valid visualization approaches. This talk was presented at VIZBI...

Keywords: Information visualisation

Resource type: Video

Keynote on Visual Analytics & Human/Computer Interfaces http://tess.elixir-uk.org/materials/keynote-on-visual-analytics-amp-human-computer-interfaces Sara Irina Fabrikant discusses how analysis of scientific data can be enhanced using information visualization, visual analytics, cognition principles, and graphical user interface design. She focuses on the use of evaluation to valid visualization approaches. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Information visualisation 2017-01-31
Keynote on Visual Design Principles

Martin Krzywinski (http://mkweb.bcgsc.ca/) gives a great primer on the key principles of effective visual design in biological sciences. During the talk he highlights the principles with examples from various peer-reviewed publications and discusses the practical aspects of effective figure...

Keywords: Genome, HCI, Information visualisation, Communication

Resource type: Video

Keynote on Visual Design Principles http://tess.elixir-uk.org/materials/keynote-on-visual-design-principles Martin Krzywinski (http://mkweb.bcgsc.ca/) gives a great primer on the key principles of effective visual design in biological sciences. During the talk he highlights the principles with examples from various peer-reviewed publications and discusses the practical aspects of effective figure design.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Martin Krzywinski Genome, HCI, Information visualisation, Communication 2017-01-31
BBSRC: Data and Data Visualisation

Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation

Resource type: Video

BBSRC: Data and Data Visualisation http://tess.elixir-uk.org/materials/bbsrc-data-and-data-visualisation Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Michael Ball Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation 2017-02-01
MARender: A Simple JavaScript Library for Biomedical Visualisation

Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015.  Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Information visualisation

Resource type: Slideshow

MARender: A Simple JavaScript Library for Biomedical Visualisation http://tess.elixir-uk.org/materials/marender-a-simple-javascript-library-for-biomedical-visualisation Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015.  Created at: 2nd BiVi Annual Meeting. Mr. William Edward Hill Anatomy Physiology and Atlases, Information visualisation 2017-02-03
Visualization of Biomolecular Structures: State of the Art

Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on...

Keywords: Molecular, Information visualisation

Resource type: Slideshow

Visualization of Biomolecular Structures: State of the Art http://tess.elixir-uk.org/materials/visualization-of-biomolecular-structures-state-of-the-art Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling-Curve, surface, solid, and object representations Created at: EuroVis 2015. Barbara Kozlikova Michael Krone Molecular, Information visualisation 2017-02-28
Art and Science: A partnership catalyzing discovery in biomedicine

A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our...

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation

Resource type: Video

Art and Science: A partnership catalyzing discovery in biomedicine http://tess.elixir-uk.org/materials/art-and-science-a-partnership-catalyzing-discovery-in-biomedicine A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our understanding and treatment of disease. The challenge is to ensure that technical and non-technical researchers can access, use and learn from this wealth of data and analytical resources. Bang will present examples of solutions developed at the Broad Institute that draw on art and design to enable scientific discovery.Bang Wong is the creative director of the Broad Institute of MIT & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at the Johns Hopkins University School of Medicine. His work focuses on the design and development of computation-visualization tools to meet the analytical challenges of research data. He leads the data visualization initiative at the Broad and is the founding author of Points of View published by Nature Methods, a series of articles that focus on the fundamental aspects of data presentation in science. Created at: 3rd BiVi Annual Meeting (2017). Bang Wong Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation 2017-05-12
From Visual Exploration of Biomedical Data to Storytelling and Back Again

A 3rd BiVi 2017 Keynote Presentation by Marc Streit who discusses visual exploration and sharing discoveries with examples from the Caleydo project.Chaired by Tom FreemanThe primary goal of visual data exploration tools is to enable the discovery of new insights. To justify and reproduce...

Keywords: Communication, Information visualisation

Resource type: Video

From Visual Exploration of Biomedical Data to Storytelling and Back Again http://tess.elixir-uk.org/materials/from-visual-exploration-of-biomedical-data-to-storytelling-and-back-again A 3rd BiVi 2017 Keynote Presentation by Marc Streit who discusses visual exploration and sharing discoveries with examples from the Caleydo project.Chaired by Tom FreemanThe primary goal of visual data exploration tools is to enable the discovery of new insights. To justify and reproduce insights, the discovery process needs to be documented and communicated. A common approach to documenting and presenting findings is to capture visualizations as images or videos. Images, however, are insufficient for telling the story of a visual discovery, as they lack full provenance information and context. Videos are difficult to produce and edit, particularly due to the nonlinear nature of the exploration process. Most importantly, however, neither approach provides the opportunity to return to any point in the exploration in order to review the state of the visualization in detail or to conduct additional analyses.In this talk, Marc introduces their efforts to more tightly integrate biomedical data exploration with the presentation of discoveries. Based on provenance data captured during the exploration process, users can extract key steps, add annotations, and author 'Vistories', visual stories based on the history of the exploration. These Vistories can be shared for others to view, but also to retrace and extend the original analysis. Marc demonstrates how such methods can increase the reproducibility of cancer research and drug discovery.The presented work is part of the Caleydo project, which is a long-running collaboration between JKU Linz, Harvard University and the University of Utah.Marc Streit is a tenured Associate Professor at the Institute of Computer Graphics at Johannes Kepler University Linz where he leads the Visual Data Science group. He finished his PhD at the Institute for Computer Graphics and Vision at Graz University of Technology in early 2011 and moved to Linz later that year. In 2012 he was a visiting researcher at the Center for Biomedical Informatics (CBMI) at Harvard Medical School. As part of a Fulbright scholarship for research and lecturing he was a visiting professor at the Visual Computing Group at Harvard Paulson School in 2014. Marc also teaches courses at the Imperial College Business School and Salzburg University of Applied Sciences.His scientific areas of interest include visualization, visual analytics, and biological data visualization, where he is particularly interested in the integrated analysis of large heterogeneous data. Together with his team he develops novel visual analysis tools for cancer research, drug discovery, and other biomedical applications. Most of his research is embedded in the open-source project Caleydo, where he is one of the project leaders and founding-members. Since 2016 he is a CEO of the JKU spin-off company datavisyn.Marc won Best Paper Awards at InfoVis'13, BioVis’12, InfoVis’11, GI’10 and Honorable Mention Awards at EuroVis'16, CHI'14, InfoVis'14 and EuroVis’12. He is a co-author of the Nature Methods Points of View column. In 2013 he co-edited the Special Issue on Visual Analytics in the IEEE Computer journal. Additionally, he actively contributes to the scientific community by serving on the organizing and program committee of several scientific events as well as by acting as a reviewer for high-quality journals and conferences. He was program chair of the IEEE Visualization in Data Science Symposium and papers and now general chair of BioVis, the Symposium on Biological Data Visualization. Created at: 3rd BiVi Annual Meeting (2017). Prof. Marc Streit Communication, Information visualisation 2017-05-15