FAIR Data Principles
Overview of Interdisciplinary Earth Data Alliance (IEDA) Data Management Resources
In the digital era, documenting and sharing our scientific data is growing increasingly important as an integral part of the scientific process. Data Management not only makes our data resources available for others to build upon, but it also enables data syntheses and new analyses that hold the potential for significant scientific advancement. Effective data management begins during the planning stages of a project and continues throughout the research process from field and/or laboratory work, through analysis, and culminating with scientific literature and data publication. By planning ahead, and following some best practices along the way, the process of data management can be simple and relatively low-effort, enabling rapid contribution and publication of data in the appropriate data systems at the conclusion of a project.
IEDA offers a variety of tools to support investigators along the full continuum of their data management efforts: Links to these tools and resources are available from the landing page for this resource.
- IEDA Data Discovery Tools
- IEDA Data Management Plan (DMP) Tool
Research & Analysis
- Register sample-based data sets and samples
- Register sample metadata and get a unique sample identifier (IGSN)
- Download Templates for Analytical Data
- Learn about contributing Analytical Data to the EarthChem Library
- Register sensor-based data sets and samples
- Contribute sensor data files (e.g. geophysical data) and supporting metadata to MGDS
- IEDA Analysis Tools
- GeoMapApp earth science exploration and visualization application
- Analyze your own geospatial data within the context of other available datasets
- GeoMapApp earth science exploration and visualization application
Synthesis & Publication
- Register final data sets with IEDA
- Publish your data
- Publishing your data with a DOI ensures that it can be directly referenced in your paper and cited by others.
- IEDA Data Compliance Reporting (DCR) Tool
- Rapidly generate a Data Compliance Report (DCR) based on your NSF award number to demonstrate that your data are registered with IEDA systems and you are compliant with NSF Data Policies.
Simplifying the Reuse and Interoperability of Hydrologic Data Sets and Models with Semantic Metadata that is Human-Readable & Machine-Actionable
This slide set discusses the big, generic problem facing geoscientists today that stems from lack of interoperability across a huge number of heterogeneous resources, and how to solve it. Practical solutions to tame the inherent heterogeneity involve the collection of standardized, "deep-description" metadata for resources that are then wrapped with standardized APIs that provide callers wtih access to both the data and the metadata.
EarthChem Library: How to Complete a Data Submission Template
A brief tutorial that shows how to upload, preview, and publish from iData. To use the accompanying My Geo Hub tutorial exercises, go to https://mygeohub.org/resources/1217. Note that the number before each step is the time on the YouTube video where it shows how each step is done. Also, note that the video does not contain audio content.
How to Manage Your Samples in MySESAR
The System for Earth Sample Registration (SESAR) operates a registry that distributes the International Geo Sample Number IGSN. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search.
MySESAR provides a private working space in the System for Earth Sample Registration. This tutorial will introduce you to how to manage samples in MySESAR, including how to search the sample catalog, how to view and edit samples, how to print labels, how to group samples and how to transfer ownership of samples. For details relating to sample registration, please see tutorials for individual sample and batch sample registration here: http://www.geosamples.org/help/registration.
MySESAR allows you to:
- obtain IGSNs for your samples by registering them with SESAR.
- register samples one at a time by entering metadata into a web form.
- register multiple samples by uploading metadata in a SESAR spreadsheet form.
- generate customized SESAR spreadsheet forms.
- view lists of samples that you registered.
- edit sample metadata profiles.
- upload images and other documents such as field notes, maps, or links to publications to a sample profile.
- restrict access to metadata profiles of your samples.
- transfer ownership of a sample to another SESAR user.
GeoBuilder for Exploring Geospatial Data
A step-by-step tutorial for GeoBuilder. The GeoBuilder tool provides a wizard type interface that guides users through several steps for loading, selecting, configuring and analyzing geo-referenced tabular data. As a result, the data is presented on an Open Street Map with customized annotation, station/site popup, and dynamic filtering and plotting. The tool can be used in two ways: first, an end user can use it to dynamically load and explore a csv file of interest. Second, a data owner can use it to build a customized view of the data he wants to share, save the configuration, and publish the data, configuration, and viewer as a new “tool” specifically for his data. With this, any scientist can easily develop an interactive web-enabled GIS interface to share their data within minutes, as compared to the past where they needed to hire a web developer and spent months to get the same done.
Note that My Geo Hub registration is required to access the GeoBuilder tool.
GeoBuilder - How to Share My Session
A brief tutorial that shows how to share a GeoBuilder session. The GeoBuilder tool provides a wizard type interface that guides users through several steps for loading, selecting, configuring and analyzing geo-referenced tabular data. To use the accompanying My Geo Hub tutorial exercises, go to https://mygeohub.org/resources/1219. Note that the number before each step is the time on the YouTube video where it shows how each step is done. Also, note that the video does not contain audio content.
For more information about GeoBuilder, go to https://mygeohub.org/resources/geobuilder.
The focus of this workshop is on working with genomics data and data management and analysis for genomics research. It covers data management and analysis for genomics research including best practices for the organization of bioinformatics projects and data, use of command line utilities, use of command line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing.
- Project organization and management
- Introduction to the command line
- Data wrangling and processing
- Introduction to cloud computing for genomics
- Data analysis and visualization in R *beta*
Sustaining Science Gateways—Finding your "best fit" model
Digital projects – science gateways, data repositories, educational websites, and others—have a few things in common. They can deliver a great deal of value to users – by sharing widely sophisticated tools, large data sets, or access to computing capacity among those in the academic sector who really need them to advance their work. But they share something else in common, too: They are devilishly hard to run in a way that permits ongoing growth and expansion.
In this webinar, Nancy Maron, a lead instructor in the Science Gateways Bootcamp, introduces participants to the key elements of sustainability planning – the building blocks for developing Science Gateways that have the best chance for ongoing growth.
The webinar will introduce sustainability models and share some key tactics for identifying the models that are most likely to work for your gateway. We will touch upon funding models, the competitive environment, and audience assessment, to show how these need to be considered in tandem with any plan.
Working in the R Ecosystem: Building Applications & Content for Your Gateway
The R programming language first appeared on the scene in the 1990's as an open source environment for statistical modeling and data analysis. Throughout the last decade, interest in the language has grown alongside researcher's abilities to collect and store larger amounts of data. Today, scientific and business decisions increasingly rely on the interpretation of this data. New libraries for processing data and communicating results are being debuted in ways that break down traditional language silos. Technologies like interactive documents, HTML based applications, and RESTful APIs have exposed capability gaps between R's interfaces for numerical analysis libraries and its built-in ability for graphical display. In this webinar, Derrick Kearney will survey several R libraries that are helping people bridge the gap between their R-based analysis and the numerous ways people are representing results today, all of which can be published on your science gateway, thus extending your research impact to others in a reproducible way.
Webinar: National Data Service (NDS) Labs Workbench
The growing size and complexity of high-value scientific datasets are pushing the boundaries of traditional models of data access and discovery. Many large datasets are only accessible through the systems on which they were created or require specialized software or computational resources for re-use. In response to this growing need, the National Data Service (NDS) consortium is developing the Labs Workbench platform, a scalable, web-based system intended to support turn-key deployment of encapsulated data management and analysis tools to support exploratory analysis and development on cloud resources that are physically "near" the data and associated high-performance computing (HPC) systems. The Labs Workbench may complement existing science gateways by enabling exploratory analysis of data and the ability for users to deploy and share their own tools. The Labs Workbench platform has also been used to support a variety training and workshop environments.
This webinar includes a demonstration of the Labs Workbench platform and a discussion of several key use cases. A presentation of findings from the recent Workshop on Container Based Analysis Environments for Research Data Access and Computing further highlight compatibilities between science gateways and interactive analysis platforms such as Labs Workbench.
Facing the data challenge: Developing data policy and services
Overview of research data management (RDM), who is responsible for RDM, the components of a researh data service, and policy and research activity roadmap development in compliance with Engineering and Physical Sciences Research Council (EPSRC) funding expectations in the UK.
Research Data Management and Sharing MOOC
This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management plans and be familiar with best practices for working with data including the organization, documentation, and storage and security of data. Learners will also understand the impetus and importance of archiving and sharing data as well as how to assess the trustworthiness of repositories.
Note: The course is free to access. However, if you pay for the course, you will have access to all of the features and content you need to earn a Course Certificate from Coursera. If you complete the course successfully, your electronic Certificate will be added to your Coursera Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. Note that the Course Certificate does not represent official academic credit from the partner institution offering the course.
Also, note that the course is offered on a regular basis. For information about the next enrollment, go to the provided URL.
DataONE Data Management Module 03: Data Management Planning
Data management planning is the starting point in the data life cycle. Creating a formal document that outlines what you will do with the data during and after the completion of research helps to ensure that the data is safe for current and future use. This 30-40 minute lesson describes the benefits of a data management plan (DMP), outlines the components of a DMP, details tools for creating a DMP, provides NSF DMP information, and demonstrates the use of an example DMP and includes a downloadable presentation (PPT or PDF) with supporting hands-on exercise and handout.
DataONE Data Management Module 05: Data Quality Control and Assurance
Quality assurance and quality control are phrases used to describe activities that prevent errors from entering or staying in a data set. These activities ensure the quality of the data before it is collected, entered, or analyzed, as well as actively monitoring and maintaining the quality of data throughout the study. In this lesson, we define and provide examples of quality assurance, quality control, data contamination and types of errors that may be found in data sets. After completing this lesson, participants will be able to describe best practices in quality assurance and quality control and relate them to different phases of data collection and entry. This 30-40 minute lesson includes a downloadable presentation (PPT or PDF) with supporting hands-on exercise and handout.
DataONE Data Management Module 06: Data Protection and Backups
There are several important elements to digital preservation, including data protection, backup and archiving. In this lesson, these concepts are introduced and best practices are highlighted with case study examples of how things can go wrong. Exploring the logistical, technical and policy implications of data preservation, participants will be able to identify their preservation needs and be ready to implement good data preservation practices by the end of the module. This 30-40 minute lesson includes a downloadable presentation (PPT or PDF) with supporting hands-on exercise and handout.
DataONE Data Management Module 07: Metadata
What is metadata? Metadata is data (or documentation) that describes and provides context for data and it is everywhere around us. Metadata allows us to understand the details of a dataset, including: where it was collected, how it was collected, what gaps in the data mean, what the units of measurement are, who collected the data, how it should be attributed etc. By creating and providing good descriptive metadata for our own data, we enable others to efficiently discover and use the data products from our research. This lesson explores the importance of metadata to data authors, users of the data and organizations, and highlights the utility of metadata. It provides an overview of the different metadata standards that exist, and the core elements that are consistent across them; guiding users in selecting a metadata standard to work with and introduces the best practices needed for writing a high quality metadata record.
This 30-40 minute lesson includes a downloadable presentation (PPT or PDF) with supporting hands-on exercise, handout, and supporting data files.
DataONE Data Management Module 08: Data Citation
Data citation is a key practice that supports the recognition of data creation as a primary research output rather than as a mere byproduct of research. Providing reliable access to research data should be a routine practice, similar to the practice of linking researchers to bibliographic references. After completing this lesson, participants should be able to define data citation and describe its benefits; to identify the roles of various actors in supporting data citation; to recognize common metadata elements and persistent data locators and describe the process for obtaining one, and to summarize best practices for supporting data citation. This 30-40 minute lesson includes a downloadable presentation (PPT or PDF) with supporting hands-on exercise and handout.
DataONE Data Management Module 09: Analysis and Workflows
Understanding the types, processes, and frameworks of workflows and analyses is helpful for researchers seeking to understand more about research, how it was created, and what it may be used for. This lesson uses a subset of data analysis types to introduce reproducibility, iterative analysis, documentation, provenance and different types of processes. Described in more detail are the benefits of documenting and establishing informal (conceptual) and formal (executable) workflows. This 30-40 minute lesson includes a downloadable presentation (PPT or PDF) with supporting hands-on exercise and handout.
DataONE Data Management Module 10: Legal and Policy Issues
Conversations regarding research data often intersect with questions related to ethical, legal, and policy issues for managing research data. This lesson will define copyrights, licenses, and waivers, discuss ownership and intellectual property, and describe some reasons for data restriction. After completing this lesson, participants will be able to identify ethical, legal, and policy considerations that surround the use and management of research data. The 30-40 minute lesson includes a downloadable presentation (PPT or PDF) with supporting hands-on exercise and handout.
NASA Earthdata Webinar Series
Monthly webinars on discovery and access to NASA Earth science data sets, services and tools. Webinars are archived on YouTube from 2013 to the present. Presenters are experts in different domains within NASA's Earth science research areas and are usually affiliated with NASA data centers and / or data archives. Specific titles for the current year's webinars can be found from the main page, but can also be found from separate pages for each year. These webinars are available to assist those wishing to learn or teach how to obtain and view these data.
NASA Earthdata Video Tutorials
Short video tutorials on topics related to available NASA EOSDIS data products, various types of data discovery, data access, and data tool demonstrations such as the Panoply tool for creating line plots. Videos accessible on YouTube from listing on main webinars and tutorials page. These tutorials are available to assist those wishing to learn or teach how to obtain and view these data.
Introduction to Data Documentation - DISL Data Management Metadata Training Webinar Series - Part 1
Introduction to data documentation (metadata) for science datasets. Includes basic concepts about metadata and a few words about data accessibility. Video is about 23 minutes.
An overview of the EDI data repository and data portal
The Environmental Data Initiative (EDI) data repository is a metadata-driven archive for environmental and ecological research data described by the Ecological Metadata Language (EML). This webinar will provide an overview of the PASTA software used by the repository and demonstrate the essentials of uploading a data package to the repository through the EDI Data Portal.
FAIR Self-Assessment Tool
The FAIR Data Principles are a set of guiding principles in order to make data findable, accessible, interoperable and reusable (Wilkinson et al., 2016). Using this tool you will be able to assess the 'FAIRness' of a dataset and determine how to enhance its FAIRness (where applicable).
This self-assessment tool has been designed predominantly for data librarians and IT staff but could be used by software engineers developing FAIR Data tools and services, and researchers provided they have assistance from research support staff.
You will be asked questions related to the principles underpinning Findable, Accessible, Interoperable and Reusable. Once you have answered all the questions in each section you will be given a ‘green bar’ indicator based on your answers in that section, and when all sections are completed, an overall 'FAIRness' indicator is provided.
Webinar: Jupyter as a Gateway for Scientific Collaboration and Education
Project Jupyter, evolved from the IPython environment, provides a platform for interactive computing that is widely used today in research, education, journalism, and industry. The core premise of the Jupyter architecture is to design tools around the experience of interactive computing, building an environment, protocol, file format and libraries optimized for the computational process when there is a human in the loop, in a live iteration with ideas and data assisted by the computer.
The Jupyter Notebook, a system that allows users to compose rich documents that combine narrative text and mathematics together with live code and the output of computations in any format compatible with a web browser (plots, animations, audio, video, etc.), provides a foundation for scientific collaboration. The next generation of the Jupyter web interface, JupyterLab, will combine in a single user interface not only the notebook but multiple other tools to access Jupyter services and remote computational resources and data. A flexible and responsive UI allows the user to mix Notebooks, terminals, text editors, graphical consoles and more, presenting in a single, unified environment the tools needed to work with a remote environment. Furthermore, the entire design is extensible and based on plugins that interoperate via open APIs, making it possible to design new plugins tailored to specific types of data or user needs.
JupyterHub enables Jupyter Notebook and JupyterLab to be used by groups of users for research collaboration and education. We believe JupyterHub provides a foundation on which to build modern scientific gateways that support a wide range of user scenarios, from interactive data exploration in high-level languages like Python, Julia or R, to the education of researchers and students whose work relies on traditional HPC resources.
The presenter discusses the benefits and applications of Jupyter Notebooks.
Scroll to the bottom of the page to view the webinar. Presentation slides are also available on the same page.
R Class for Seismologists
The IRIS Data Management Center (DMC) archives and distributes data to support the seismological research community. The class described here introduces DMC and other seismologists to the R statistical programming language and its use with seismological data available from DMC web services. The capabilities of the seismicRoll, IRISSeismic and IRISMustangMetrics packages developed as part of the MUSTANG project will be demonstrated.
Class materials are broken up into nine separate lessons that assume some experience coding but not necessarily any familiarity with R. Lessons are presented in sequential order and assume the student already has R and RStudio installed on their computer. Autodidacts new to R should take about 20-30 hrs to complete the course. The target audience for these materials consists of IRIS DMC employees or graduate students with a degree in the natural sciences and some experience using scientific software such as MATLAB or Python.
Research Lifecycle at University of Central Florida
Short video discussing the "Research Lifecycle at University of Central Florida," a useful diagram for understanding the typical flow of a research project.
Introduction to R
Learn the basics of reproducible workflows in R using a USGS National Water Information System (NWIS) dataset.
Instructions for accessing the dataset are provided within the tutorial.
Clean your taxonomy data with the taxonomyCleanr R package
Taxonomic data can be messy and challenging to work with. Incorrect spelling, the use of common names, unaccepted names, and synonyms, contribute to ambiguity in what a taxon actually is. The taxonomyCleanr R package helps you resolve taxonomic data to a taxonomic authority, get accepted names and taxonomic serial numbers, as well as create metadata for your taxa in the Ecological Metadata Language (EML) format.
Postgres, EML and R in a data management workflow
Metadata storage and creation of Ecological Metadata Language (EML) can be a challenge for people and organizations who want to archive their data. A workflow was developed to combine efficient EML record generation (using the package developed by the R community) with centrally-controlled metadata in a relational database. The webinar has two components: 1) a demonstration of metadata storage and management using a relational database, and 2) discussion of an example EML file generation workflow using pre-defined R functions.
Experimental Design Assistant
The Experimental Design Assistant (EDA) (https://eda.nc3rs.org.uk) is a free web-based tool that was developed by the NC3Rs (https://www.nc3rs.org.uk). It guides researchers through the design and analysis of in vivo experiments. The EDA allows users to build a stepwise visual representation of their experiment, providing feedback and dedicated support for randomization, blinding and sample size calculation. This demonstration will provide an introduction to the tool and provide guidance on getting started. Ultimately, the use of a tool such as the EDA will lead to carefully designed experiments that yield robust and reproducible data using the minimum number of animals consistent with scientific objectives.
Open Science and Innovation
This course helps you to understand open business models and responsible research and innovation (RRI) and illustrates how these can foster innovation. By the end of the course, you will:
- Understand key concepts and values of open business models and responsible research and innovation
- Know how to plan your innovation activities
- Be able to use Creative Commons licenses in business
- Understand new technology transfer policies with the ethos of Open Science
- Learn how to get things to market faster
Licensing your research outputs is an important part of practicing Open Science. After completing this course, you will:
- Know what licenses are, how they work, and how to apply them
- Understand how different types of licenses can affect research output reuse
- Know how to select the appropriate license for your research
Make EML with R and share on GitHub
Introduction to the Ecological Metadata Language (EML). Topics include:
- Use R to build EML for a mock dataset
- Validate EML and write to file
- Install Git and configure to track file versioning in RStudio
- Set up GitHub account and repository
- Push local content to GitHub for sharing and collaboration
Access the rendered version of this tutorial here:https://cdn.rawgit.com/EDIorg/tutorials/2002b911/make_eml_with_r/make_em...
Florilege, a new database of habitats and phenotypes of food microbe flora
This tutorial explains how to use the “Habitat-Phenotype Relation Extractor for Microbes” application available from the OpenMinTeD platform. It also explains the scientific issues it addresses, and how the results of the TDM process can be queried and exploited by researchers through the Florilège application.
In recent years, developments in molecular technologies have led to an exponential growth of experimental data and publications, many of which are open, however accessible separately. Therefore, it is now crucial for researchers to have bioinformatics infrastructures at their disposal, that propose unified access to both data and related scientific articles. With the right text mining infrastructures and tools, application developers and data managers can rapidly access and process textual data, link them with other data and make the results available for scientists.
The text-mining process behind Florilege has been set up by INRA using the OpenMinTeD environment. It consists in extracting the relevant information, mostly textual, from scientific literature and databases. Words or word groups are identified and assigned a type, like “habitat” or “taxon”.
Sections of the tutorial:
1. Biological motivation of the Florilege database
2. Florilège Use-Case on OpenMinTeD (includes a description of how to access the Habitat-Phenotype Relation Extractor for Microbes application)
3. Florilege backstage: how is it build?
4. Florilège description
5. How to use Florilege ?
Best Practice in Open Research
This course introduces some practical steps toward making your research more open. We begin by exploring the practical implications of open research, and the benefits it can deliver for research integrity and public trust, as well as benefits you will accrue in your own work. After a short elaboration of some useful rules of thumb, we move quickly onto some more practical steps towards meeting contemporary best practice in open research and introduce some useful discipline-specific resources. Upon completing this course, you will:
- Understand the practical implications of taking a more open approach to research
- Be prepared to meet expectations relating to openness from funders, publishers, and peers
- Be able to reap the benefits of working openly
- Have an understanding of the guiding principles to follow when building openness into your research workflow
- Know about some useful tools and resources to help you embed Open Science into work research practices
Managing and Sharing Research Data
Data-driven research is becoming increasingly common in a wide range of academic disciplines, from Archaeology to Zoology, and spanning Arts and Science subject areas alike. To support good research, we need to ensure that researchers have access to good data. Upon completing this course, you will:
- Understand which data you can make open and which need to be protected
- Know how to go about writing a data management plan
- Understand the FAIR principles
- Be able to select which data to keep and find an appropriate repository for them
- Learn tips on how to get maximum impact from your research data