This dataset compiles the top 2500 datasets from Kaggle, encompassing a diverse range of topics and contributors. It provides insights into dataset creation, usability, popularity, and more, offering valuable information for researchers, analysts, and data enthusiasts.

Research Analysis: Researchers can utilize this dataset to analyze trends in dataset creation, popularity, and usability scores across various categories.

Contributor Insights: Kaggle contributors can explore the dataset to gain insights into factors influencing the success and engagement of their datasets, aiding in optimizing future submissions.

Machine Learning Training: Data scientists and machine learning enthusiasts can use this dataset to train models for predicting dataset popularity or usability based on features such as creator, category, and file types.

Market Analysis: Analysts can leverage the dataset to conduct market analysis, identifying emerging trends and popular topics within the data science community on Kaggle.

Educational Purposes: Educators and students can use this dataset to teach and learn about data analysis, visualization, and interpretation within the context of real-world datasets and community-driven platforms like Kaggle.

Column Definitions:

Dataset Name: Name of the dataset. Created By: Creator(s) of the dataset. Last Updated in number of days: Time elapsed since last update. Usability Score: Score indicating the ease of use. Number of File: Quantity of files included. Type of file: Format of files (e.g., CSV, JSON). Size: Size of the dataset. Total Votes: Number of votes received. Category: Categorization of the dataset's subject matter.

Company Datasets for valuable business insights!

Discover new business prospects, identify investment opportunities, track competitor performance, and streamline your sales efforts with comprehensive Company Datasets.

These datasets are sourced from top industry providers, ensuring you have access to high-quality information:

• Owler: Gain valuable business insights and competitive intelligence. -AngelList: Receive fresh startup data transformed into actionable insights. -CrunchBase: Access clean, parsed, and ready-to-use business data from private and public companies. -Craft.co: Make data-informed business decisions with Craft.co's company datasets. -Product Hunt: Harness the Product Hunt dataset, a leader in curating the best new products.

We provide fresh and ready-to-use company data, eliminating the need for complex scraping and parsing. Our data includes crucial details such as:

• Company name;
• Size;
• Founding date;
• Location;
• Industry;
• Revenue;
• Employee count;
• Competitors.

You can choose your preferred data delivery method, including various storage options, delivery frequency, and input/output formats.

Receive datasets in CSV, JSON, and other formats, with storage options like AWS S3 and Google Cloud Storage. Opt for one-time, monthly, quarterly, or bi-annual data delivery.

With Oxylabs Datasets, you can count on:

• Fresh and accurate data collected and parsed by our expert web scraping team.
• Time and resource savings, allowing you to focus on data analysis and achieving your business goals.
• A customized approach tailored to your specific business needs.
• Legal compliance in line with GDPR and CCPA standards, thanks to our membership in the Ethical Web Data Collection Initiative.

Pricing Options:

Standard Datasets: choose from various ready-to-use datasets with standardized data schemas, priced from $1,000/month.

Custom Datasets: Tailor datasets from any public web domain to your unique business needs. Contact our sales team for custom pricing.

Experience a seamless journey with Oxylabs:

• Understanding your data needs: We work closely to understand your business nature and daily operations, defining your unique data requirements.
• Developing a customized solution: Our experts create a custom framework to extract public data using our in-house web scraping infrastructure.
• Delivering data sample: We provide a sample for your feedback on data quality and the entire delivery process.
• Continuous data delivery: We continuously collect public data and deliver custom datasets per the agreed frequency.

Unlock the power of data with Oxylabs' Company Datasets and supercharge your business insights today!

Context

Kaggle is one of the largest communities of data scientists and machine learning practitioners in the world, and its platform hosts thousands of datasets covering a wide range of topics and industries. With so many options to choose from, it can be difficult to know where to start or what datasets are worth exploring. That's where this dataset comes in. By scraping information about the top 10,000 datasets on Kaggle, we have created a single source of truth for the most popular and useful datasets on the platform. This dataset is not just a list of names and numbers, but a valuable tool for data enthusiasts and professionals alike, providing insights into the latest trends and techniques in data science and machine learning

Column description - Dataset_name - Name of the dataset - Author_name - Name of the author - Author_id - Kaggle id of the author - No_of_files - Number of files the author has uploaded - size - Size of all the files - Type_of_file - Type of the files such as csv, json etc. - Upvotes - Total upvotes of the dataset - Medals - Medal of the dataset - Usability - Usability of the dataset - Date - Date in which the dataset is uploaded - Day - Day in which the dataset is uploaded - Time - Time in which the dataset is uploaded - Dataset_link - Kaggle link of the dataset

Acknowledgements The data has been scraped from the official Kaggle Website and is available under the Creative Common License.

Enjoy & Keep Learning !!!

This book is written for statisticians, data analysts, programmers, researchers, teachers, students, professionals, and general consumers on how to perform different types of statistical data analysis for research purposes using the R programming language. R is an open-source software and object-oriented programming language with a development environment (IDE) called RStudio for computing statistics and graphical displays through data manipulation, modelling, and calculation. R packages and supported libraries provides a wide range of functions for programming and analyzing of data. Unlike many of the existing statistical softwares, R has the added benefit of allowing the users to write more efficient codes by using command-line scripting and vectors. It has several built-in functions and libraries that are extensible and allows the users to define their own (customized) functions on how they expect the program to behave while handling the data, which can also be stored in the simple object system.For all intents and purposes, this book serves as both textbook and manual for R statistics particularly in academic research, data analytics, and computer programming targeted to help inform and guide the work of the R users or statisticians. It provides information about different types of statistical data analysis and methods, and the best scenarios for use of each case in R. It gives a hands-on step-by-step practical guide on how to identify and conduct the different parametric and non-parametric procedures. This includes a description of the different conditions or assumptions that are necessary for performing the various statistical methods or tests, and how to understand the results of the methods. The book also covers the different data formats and sources, and how to test for reliability and validity of the available datasets. Different research experiments, case scenarios and examples are explained in this book. It is the first book to provide a comprehensive description and step-by-step practical hands-on guide to carrying out the different types of statistical analysis in R particularly for research purposes with examples. Ranging from how to import and store datasets in R as Objects, how to code and call the methods or functions for manipulating the datasets or objects, factorization, and vectorization, to better reasoning, interpretation, and storage of the results for future use, and graphical visualizations and representations. Thus, congruence of Statistics and Computer programming for Research.

This repository was created for my Master's thesis in Computational Intelligence and Internet of Things at the University of Córdoba, Spain. The purpose of this repository is to store the datasets found that were used in some of the studies that served as research material for this Master's thesis. Also, the datasets used in the experimental part of this work are included.

Below are the datasets specified, along with the details of their references, authors, and download sources.

----------- STS-Gold Dataset ----------------

The dataset consists of 2026 tweets. The file consists of 3 columns: id, polarity, and tweet. The three columns denote the unique id, polarity index of the text and the tweet text respectively.

Reference: Saif, H., Fernandez, M., He, Y., & Alani, H. (2013). Evaluation datasets for Twitter sentiment analysis: a survey and a new dataset, the STS-Gold.

File name: sts_gold_tweet.csv

----------- Amazon Sales Dataset ----------------

This dataset is having the data of 1K+ Amazon Product's Ratings and Reviews as per their details listed on the official website of Amazon. The data was scraped in the month of January 2023 from the Official Website of Amazon.

Owner: Karkavelraja J., Postgraduate student at Puducherry Technological University (Puducherry, Puducherry, India)

Features:

• product_id - Product ID
• product_name - Name of the Product
• category - Category of the Product
• discounted_price - Discounted Price of the Product
• actual_price - Actual Price of the Product
• discount_percentage - Percentage of Discount for the Product
• rating - Rating of the Product
• rating_count - Number of people who voted for the Amazon rating
• about_product - Description about the Product
• user_id - ID of the user who wrote review for the Product
• user_name - Name of the user who wrote review for the Product
• review_id - ID of the user review
• review_title - Short review
• review_content - Long review
• img_link - Image Link of the Product
• product_link - Official Website Link of the Product

License: CC BY-NC-SA 4.0

File name: amazon.csv

----------- Rotten Tomatoes Reviews Dataset ----------------

This rating inference dataset is a sentiment classification dataset, containing 5,331 positive and 5,331 negative processed sentences from Rotten Tomatoes movie reviews. On average, these reviews consist of 21 words. The first 5331 rows contains only negative samples and the last 5331 rows contain only positive samples, thus the data should be shuffled before usage.

This data is collected from https://www.cs.cornell.edu/people/pabo/movie-review-data/ as a txt file and converted into a csv file. The file consists of 2 columns: reviews and labels (1 for fresh (good) and 0 for rotten (bad)).

Reference: Bo Pang and Lillian Lee. Seeing stars: Exploiting class relationships for sentiment categorization with respect to rating scales. In Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pages 115–124, Ann Arbor, Michigan, June 2005. Association for Computational Linguistics

File name: data_rt.csv

----------- Preprocessed Dataset Sentiment Analysis ----------------

Preprocessed amazon product review data of Gen3EcoDot (Alexa) scrapped entirely from amazon.in
Stemmed and lemmatized using nltk.
Sentiment labels are generated using TextBlob polarity scores.

The file consists of 4 columns: index, review (stemmed and lemmatized review using nltk), polarity (score) and division (categorical label generated using polarity score).

DOI: 10.34740/kaggle/dsv/3877817

Citation: @misc{pradeesh arumadi_2022, title={Preprocessed Dataset Sentiment Analysis}, url={https://www.kaggle.com/dsv/3877817}, DOI={10.34740/KAGGLE/DSV/3877817}, publisher={Kaggle}, author={Pradeesh Arumadi}, year={2022} }

This dataset was used in the experimental phase of my research.

File name: EcoPreprocessed.csv

----------- Amazon Earphones Reviews ----------------

This dataset consists of a 9930 Amazon reviews, star ratings, for 10 latest (as of mid-2019) bluetooth earphone devices for learning how to train Machine for sentiment analysis.

This dataset was employed in the experimental phase of my research. To align it with the objectives of my study, certain reviews were excluded from the original dataset, and an additional column was incorporated into this dataset.

The file consists of 5 columns: ReviewTitle, ReviewBody, ReviewStar, Product and division (manually added - categorical label generated using ReviewStar score)

License: U.S. Government Works

Source: www.amazon.in

File name (original): AllProductReviews.csv (contains 14337 reviews)

File name (edited - used for my research) : AllProductReviews2.csv (contains 9930 reviews)

----------- Amazon Musical Instruments Reviews ----------------

This dataset contains 7137 comments/reviews of different musical instruments coming from Amazon.

This dataset was employed in the experimental phase of my research. To align it with the objectives of my study, certain reviews were excluded from the original dataset, and an additional column was incorporated into this dataset.

The file consists of 10 columns: reviewerID, asin (ID of the product), reviewerName, helpful (helpfulness rating of the review), reviewText, overall (rating of the product), summary (summary of the review), unixReviewTime (time of the review - unix time), reviewTime (time of the review (raw) and division (manually added - categorical label generated using overall score).

Source: http://jmcauley.ucsd.edu/data/amazon/

File name (original): Musical_instruments_reviews.csv (contains 10261 reviews)

File name (edited - used for my research) : Musical_instruments_reviews2.csv (contains 7137 reviews)

Description: - This dataset includes all 22 built-in datasets from the Seaborn library, a widely used Python data visualization tool. Seaborn's built-in datasets are essential resources for anyone interested in practicing data analysis, visualization, and machine learning. They span a wide range of topics, from classic datasets like the Iris flower classification to real-world data such as Titanic survival records and diamond characteristics.

• Included Datasets:
  • Anagrams: Analysis of word anagram patterns.
  • Anscombe: Anscombe's quartet demonstrating the importance of data visualization.
  • Attention: Data on attention span variations in different scenarios.
  • Brain Networks: Connectivity data within brain networks.
  • Car Crashes: US car crash statistics.
  • Diamonds: Data on diamond properties including price, cut, and clarity.
  • Dots: Randomly generated data for scatter plot visualization.
  • Dow Jones: Historical records of the Dow Jones Industrial Average.
  • Exercise: The relationship between exercise and health metrics.
  • Flights: Monthly passenger numbers on flights.
  • FMRI: Functional MRI data capturing brain activity.
  • Geyser: Eruption times of the Old Faithful geyser.
  • Glue: Strength of glue under different conditions.
  • Health Expenditure: Health expenditure statistics across countries.
  • Iris: Famous dataset for classifying Iris species.
  • MPG: Miles per gallon for various vehicles.
  • Penguins: Data on penguin species and their features.
  • Planets: Characteristics of discovered exoplanets.
  • Sea Ice: Measurements of sea ice extent.
  • Taxis: Taxi trips data in a city.
  • Tips: Tipping data collected from a restaurant.
  • Titanic: Survival data from the Titanic disaster.

This complete collection serves as an excellent starting point for anyone looking to improve their data science skills, offering a wide array of datasets suitable for both beginners and advanced users.

The benchmarking datasets used for deepBlink. The npz files contain train/valid/test splits inside and can be used directly. The files belong to the following challenges / classes:- ISBI Particle tracking challenge: microtubule, vesicle, receptor- Custom synthetic (based on http://smal.ws): particle- Custom fixed cell: smfish- Custom live cell: suntagThe csv files are to determine which image in the test splits correspond to which original image, SNR, and density.

Looking for a free Walmart product dataset? The Walmart Products Free Dataset delivers a ready-to-use ecommerce product data CSV containing ~2,100 verified product records from Walmart.com. It includes vital details like product titles, prices, categories, brand info, availability, and descriptions — perfect for data analysis, price comparison, market research, or building machine-learning models.

Key Features

Complete Product Metadata: Each entry includes URL, title, brand, SKU, price, currency, description, availability, delivery method, average rating, total ratings, image links, unique ID, and timestamp.

CSV Format, Ready to Use: Download instantly - no need for scraping, cleaning or formatting.

Good for E-commerce Research & ML: Ideal for product cataloging, price tracking, demand forecasting, recommendation systems, or data-driven projects.

Free & Easy Access: Priced at USD $0.0, making it a great starting point for developers, data analysts or students.

Who Benefits?

• Data analysts & researchers exploring e-commerce trends or product catalog data.
• Developers & data scientists building price-comparison tools, recommendation engines or ML models.
• E-commerce strategists/marketers need product metadata for competitive analysis or market research.
• Students/hobbyists needing a free dataset for learning or demo projects.

Why Use This Dataset Instead of Manual Scraping?

• Time-saving: No need to write scrapers or deal with rate limits.
• Clean, structured data: All records are verified and already formatted in CSV, saving hours of cleaning.
• Risk-free: Avoid Terms-of-Service issues or IP blocks that come with manual scraping.
  Instant access: Free and immediately downloadable.

Each R script replicates all of the example code from one chapter from the book. All required data for each script are also uploaded, as are all data used in the practice problems at the end of each chapter. The data are drawn from a wide array of sources, so please cite the original work if you ever use any of these data sets for research purposes.

A diverse selection of 1000 empirical time series, along with results of an hctsa feature extraction, using v1.06 of hctsa and Matlab 2019b, computed on a server at The University of Sydney.

The EPA GitHub repository PAU4ChemAs as described in the README.md file, contains Python scripts written to build the PAU dataset modules (technologies, capital and operating costs, and chemical prices) for tracking chemical flows transfers, releases estimation, and identification of potential occupation exposure scenarios in pollution abatement units (PAUs). These PAUs are employed for on-site chemical end-of-life management. The folder datasets contains the outputs for each framework step. The Chemicals_in_categories.csv contains the chemicals for the TRI chemical categories. The EPA GitHub repository PAU_case_study as described in its readme.md entry, contains the Python scripts to run the manuscript case study for designing the PAUs, the data-driven models, and the decision-making module for chemicals of concern and tracking flow transfers at the end-of-life stage. The data was obtained by means of data engineering using different publicly-available databases. The properties of chemicals were obtained using the GitHub repository Properties_Scraper, while the PAU dataset using the repository PAU4Chem. Finally, the EPA GitHub repository Properties_Scraper contains a Python script to massively gather information about exposure limits and physical properties from different publicly-available sources: EPA, NOAA, OSHA, and the institute for Occupational Safety and Health of the German Social Accident Insurance (IFA). Also, all GitHub repositories describe the Python libraries required for running their code, how to use them, the obtained outputs files after running the Python script modules, and the corresponding EPA Disclaimer. This dataset is associated with the following publication: Hernandez-Betancur, J.D., M. Martin, and G.J. Ruiz-Mercado. A data engineering framework for on-site end-of-life industrial operations. JOURNAL OF CLEANER PRODUCTION. Elsevier Science Ltd, New York, NY, USA, 327: 129514, (2021).

Stay ahead with our comprehensive News Dataset, designed for businesses, analysts, and researchers to track global events, monitor media trends, and extract valuable insights from news sources worldwide.

Dataset Features

News Articles: Access structured news data, including headlines, summaries, full articles, publication dates, and source details. Ideal for media monitoring and sentiment analysis. Publisher & Source Information: Extract details about news publishers, including domain, region, and credibility indicators. Sentiment & Topic Classification: Analyze news sentiment, categorize articles by topic, and track emerging trends in real time. Historical & Real-Time Data: Retrieve historical archives or access continuously updated news feeds for up-to-date insights.

Customizable Subsets for Specific Needs Our News Dataset is fully customizable, allowing you to filter data based on publication date, region, topic, sentiment, or specific news sources. Whether you need broad coverage for trend analysis or focused data for competitive intelligence, we tailor the dataset to your needs.

Popular Use Cases

Media Monitoring & Reputation Management: Track brand mentions, analyze media coverage, and assess public sentiment. Market & Competitive Intelligence: Monitor industry trends, competitor activity, and emerging market opportunities. AI & Machine Learning Training: Use structured news data to train AI models for sentiment analysis, topic classification, and predictive analytics. Financial & Investment Research: Analyze news impact on stock markets, commodities, and economic indicators. Policy & Risk Analysis: Track regulatory changes, geopolitical events, and crisis developments in real time.

Whether you're analyzing market trends, monitoring brand reputation, or training AI models, our News Dataset provides the structured data you need. Get started today and customize your dataset to fit your business objectives.

Dataset

This dataset was created by Abhishek Ranjan

Released under Database: Open Database, Contents: Database Contents

Contents

Public health-related decision-making on policies aimed at controlling the COVID-19 pandemic outbreak depends on complex epidemiological models that are compelled to be robust and use all relevant available data. This data article provides a new combined worldwide COVID-19 dataset obtained from official data sources with improved systematic measurement errors and a dedicated dashboard for online data visualization and summary. The dataset adds new measures and attributes to the normal attributes of official data sources, such as daily mortality, and fatality rates. We used comparative statistical analysis to evaluate the measurement errors of COVID-19 official data collections from the Chinese Center for Disease Control and Prevention (Chinese CDC), World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC). The data is collected by using text mining techniques and reviewing pdf reports, metadata, and reference data. The combined dataset includes complete spatial data such as countries area, international number of countries, Alpha-2 code, Alpha-3 code, latitude, longitude, and some additional attributes such as population. The improved dataset benefits from major corrections on the referenced data sets and official reports such as adjustments in the reporting dates, which suffered from a one to two days lag, removing negative values, detecting unreasonable changes in historical data in new reports and corrections on systematic measurement errors, which have been increasing as the pandemic outbreak spreads and more countries contribute data for the official repositories. Additionally, the root mean square error of attributes in the paired comparison of datasets was used to identify the main data problems. The data for China is presented separately and in more detail, and it has been extracted from the attached reports available on the main page of the CCDC website. This dataset is a comprehensive and reliable source of worldwide COVID-19 data that can be used in epidemiological models assessing the magnitude and timeline for confirmed cases, long-term predictions of deaths or hospital utilization, the effects of quarantine, stay-at-home orders and other social distancing measures, the pandemic’s turning point or in economic and social impact analysis, helping to inform national and local authorities on how to implement an adaptive response approach to re-opening the economy, re-open schools, alleviate business and social distancing restrictions, design economic programs or allow sports events to resume.

Product Review Datasets: Uncover user sentiment

Harness the power of Product Review Datasets to understand user sentiment and insights deeply. These datasets are designed to elevate your brand and product feature analysis, help you evaluate your competitive stance, and assess investment risks.

Data sources:

• Trustpilot: datasets encompassing general consumer reviews and ratings across various businesses, products, and services.

Leave the data collection challenges to us and dive straight into market insights with clean, structured, and actionable data, including:

• Product name;
• Product category;
• Number of ratings;
• Ratings average;
• Review title;
• Review body;

Choose from multiple data delivery options to suit your needs:

1. Receive data in easy-to-read formats like spreadsheets or structured JSON files.
2. Select your preferred data storage solutions, including SFTP, Webhooks, Google Cloud Storage, AWS S3, and Microsoft Azure Storage.
3. Tailor data delivery frequencies, whether on-demand or per your agreed schedule.

Why choose Oxylabs?

1. Fresh and accurate data: Access organized, structured, and comprehensive data collected by our leading web scraping professionals.

2. Time and resource savings: Concentrate on your core business goals while we efficiently handle the data extraction process at an affordable cost.

3. Adaptable solutions: Share your specific data requirements, and we'll craft a customized data collection approach to meet your objectives.

4. Legal compliance: Partner with a trusted leader in ethical data collection. Oxylabs is a founding member of the Ethical Web Data Collection Initiative, aligning with GDPR and CCPA standards.

Pricing Options:

Standard Datasets: choose from various ready-to-use datasets with standardized data schemas, priced from $1,000/month.

Custom Datasets: Tailor datasets from any public web domain to your unique business needs. Contact our sales team for custom pricing.

Experience a seamless journey with Oxylabs:

• Understanding your data needs: We work closely to understand your business nature and daily operations, defining your unique data requirements.
• Developing a customized solution: Our experts create a custom framework to extract public data using our in-house web scraping infrastructure.
• Delivering data sample: We provide a sample for your feedback on data quality and the entire delivery process.
• Continuous data delivery: We continuously collect public data and deliver custom datasets per the agreed frequency.

Join the ranks of satisfied customers who appreciate our meticulous attention to detail and personalized support. Experience the power of Product Review Datasets today to uncover valuable insights and enhance decision-making.

A collection of 22 data set of 50+ requirements each, expressed as user stories.

The dataset has been created by gathering data from web sources and we are not aware of license agreements or intellectual property rights on the requirements / user stories. The curator took utmost diligence in minimizing the risks of copyright infringement by using non-recent data that is less likely to be critical, by sampling a subset of the original requirements collection, and by qualitatively analyzing the requirements. In case of copyright infringement, please contact the dataset curator (Fabiano Dalpiaz, f.dalpiaz@uu.nl) to discuss the possibility of removal of that dataset [see Zenodo's policies]

The data sets have been originally used to conduct experiments about ambiguity detection with the REVV-Light tool: https://github.com/RELabUU/revv-light

This collection has been originally published in Mendeley data: https://data.mendeley.com/datasets/7zbk8zsd8y/1

Overview of the datasets [data and links added in December 2024]

The following text provides a description of the datasets, including links to the systems and websites, when available. The datasets are organized by macro-category and then by identifier.

Public administration and transparency

g02-federalspending.txt (2018) originates from early data in the Federal Spending Transparency project, which pertain to the website that is used to share publicly the spending data for the U.S. government. The website was created because of the Digital Accountability and Transparency Act of 2014 (DATA Act). The specific dataset pertains a system called DAIMS or Data Broker, which stands for DATA Act Information Model Schema. The sample that was gathered refers to a sub-project related to allowing the government to act as a data broker, thereby providing data to third parties. The data for the Data Broker project is currently not available online, although the backend seems to be hosted in GitHub under a CC0 1.0 Universal license. Current and recent snapshots of federal spending related websites, including many more projects than the one described in the shared collection, can be found here.

g03-loudoun.txt (2018) is a set of extracted requirements from a document, by the Loudoun County Virginia, that describes the to-be user stories and use cases about a system for land management readiness assessment called Loudoun County LandMARC. The source document can be found here and it is part of the Electronic Land Management System and EPlan Review Project - RFP RFQ issued in March 2018. More information about the overall LandMARC system and services can be found here.

g04-recycling.txt(2017) concerns a web application where recycling and waste disposal facilities can be searched and located. The application operates through the visualization of a map that the user can interact with. The dataset has obtained from a GitHub website and it is at the basis of a students' project on web site design; the code is available (no license).

g05-openspending.txt (2018) is about the OpenSpending project (www), a project of the Open Knowledge foundation which aims at transparency about how local governments spend money. At the time of the collection, the data was retrieved from a Trello board that is currently unavailable. The sample focuses on publishing, importing and editing datasets, and how the data should be presented. Currently, OpenSpending is managed via a GitHub repository which contains multiple sub-projects with unknown license.

g11-nsf.txt (2018) refers to a collection of user stories referring to the NSF Site Redesign & Content Discovery project, which originates from a publicly accessible GitHub repository (GPL 2.0 license). In particular, the user stories refer to an early version of the NSF's website. The user stories can be found as closed Issues.

(Research) data and meta-data management

g08-frictionless.txt (2016) regards the Frictionless Data project, which offers an open source dataset for building data infrastructures, to be used by researchers, data scientists, and data engineers. Links to the many projects within the Frictionless Data project are on GitHub (with a mix of Unlicense and MIT license) and web. The specific set of user stories has been collected in 2016 by GitHub user @danfowler and are stored in a Trello board.

g14-datahub.txt (2013) concerns the open source project DataHub, which is currently developed via a GitHub repository (the code has Apache License 2.0). DataHub is a data discovery platform which has been developed over multiple years. The specific data set is an initial set of user stories, which we can date back to 2013 thanks to a comment therein.

g16-mis.txt (2015) is a collection of user stories that pertains a repository for researchers and archivists. The source of the dataset is a public Trello repository. Although the user stories do not have explicit links to projects, it can be inferred that the stories originate from some project related to the library of Duke University.

g17-cask.txt (2016) refers to the Cask Data Application Platform (CDAP). CDAP is an open source application platform (GitHub, under Apache License 2.0) that can be used to develop applications within the Apache Hadoop ecosystem, an open-source framework which can be used for distributed processing of large datasets. The user stories are extracted from a document that includes requirements regarding dataset management for Cask 4.0, which includes the scenarios, user stories and a design for the implementation of these user stories. The raw data is available in the following environment.

g18-neurohub.txt (2012) is concerned with the NeuroHub platform, a neuroscience data management, analysis and collaboration platform for researchers in neuroscience to collect, store, and share data with colleagues or with the research community. The user stories were collected at a time NeuroHub was still a research project sponsored by the UK Joint Information Systems Committee (JISC). For information about the research project from which the requirements were collected, see the following record.

g22-rdadmp.txt (2018) is a collection of user stories from the Research Data Alliance's working group on DMP Common Standards. Their GitHub repository contains a collection of user stories that were created by asking the community to suggest functionality that should part of a website that manages data management plans. Each user story is stored as an issue on the GitHub's page.

g23-archivesspace.txt (2012-2013) refers to ArchivesSpace: an open source, web application for managing archives information. The application is designed to support core functions in archives administration such as accessioning; description and arrangement of processed materials including analog, hybrid, and
born digital content; management of authorities and rights; and reference service. The application supports collection management through collection management records, tracking of events, and a growing number of administrative reports. ArchivesSpace is open source and its

Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies. Methods This serves as an overview of the analysis performed on PacBio sequence data that is summarized in Analysis Flowchart.pdf and was used as primary data for the paper by Westfall et al. "Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies" Five different PacBio sequencing datasets were used for this analysis: M027, M2199, M1567, M004, and M005 For the datasets which were indexed (M027, M2199), CCS reads from PacBio sequencing files and the chunked_demux_config files were used as input for the chunked_demux pipeline. Each config file lists the different Index primers added during PCR to each sample. The pipeline produces one fastq file for each Index primer combination in the config. For example, in dataset M027 there were 3–4 samples using each Index combination. The fastq files from each demultiplexed read set were moved to the sUMI_dUMI_comparison pipeline fastq folder for further demultiplexing by sample and consensus generation with that pipeline. More information about the chunked_demux pipeline can be found in the README.md file on GitHub. The demultiplexed read collections from the chunked_demux pipeline or CCS read files from datasets which were not indexed (M1567, M004, M005) were each used as input for the sUMI_dUMI_comparison pipeline along with each dataset's config file. Each config file contains the primer sequences for each sample (including the sample ID block in the cDNA primer) and further demultiplexes the reads to prepare data tables summarizing all of the UMI sequences and counts for each family (tagged.tar.gz) as well as consensus sequences from each sUMI and rank 1 dUMI family (consensus.tar.gz). More information about the sUMI_dUMI_comparison pipeline can be found in the paper and the README.md file on GitHub. The consensus.tar.gz and tagged.tar.gz files were moved from sUMI_dUMI_comparison pipeline directory on the server to the Pipeline_Outputs folder in this analysis directory for each dataset and appended with the dataset name (e.g. consensus_M027.tar.gz). Also in this analysis directory is a Sample_Info_Table.csv containing information about how each of the samples was prepared, such as purification methods and number of PCRs. There are also three other folders: Sequence_Analysis, Indentifying_Recombinant_Reads, and Figures. Each has an .Rmd file with the same name inside which is used to collect, summarize, and analyze the data. All of these collections of code were written and executed in RStudio to track notes and summarize results. Sequence_Analysis.Rmd has instructions to decompress all of the consensus.tar.gz files, combine them, and create two fasta files, one with all sUMI and one with all dUMI sequences. Using these as input, two data tables were created, that summarize all sequences and read counts for each sample that pass various criteria. These are used to help create Table 2 and as input for Indentifying_Recombinant_Reads.Rmd and Figures.Rmd. Next, 2 fasta files containing all of the rank 1 dUMI sequences and the matching sUMI sequences were created. These were used as input for the python script compare_seqs.py which identifies any matched sequences that are different between sUMI and dUMI read collections. This information was also used to help create Table 2. Finally, to populate the table with the number of sequences and bases in each sequence subset of interest, different sequence collections were saved and viewed in the Geneious program. To investigate the cause of sequences where the sUMI and dUMI sequences do not match, tagged.tar.gz was decompressed and for each family with discordant sUMI and dUMI sequences the reads from the UMI1_keeping directory were aligned using geneious. Reads from dUMI families failing the 0.7 filter were also aligned in Genious. The uncompressed tagged folder was then removed to save space. These read collections contain all of the reads in a UMI1 family and still include the UMI2 sequence. By examining the alignment and specifically the UMI2 sequences, the site of the discordance and its case were identified for each family as described in the paper. These alignments were saved as "Sequence Alignments.geneious". The counts of how many families were the result of PCR recombination were used in the body of the paper. Using Identifying_Recombinant_Reads.Rmd, the dUMI_ranked.csv file from each sample was extracted from all of the tagged.tar.gz files, combined and used as input to create a single dataset containing all UMI information from all samples. This file dUMI_df.csv was used as input for Figures.Rmd. Figures.Rmd used dUMI_df.csv, sequence_counts.csv, and read_counts.csv as input to create draft figures and then individual datasets for eachFigure. These were copied into Prism software to create the final figures for the paper.

This data release contains the elemental concentration data for more than 1700 archived stream-sediment samples collected in Alaska. Samples were retrieved from the USGS Mineral Program's sample archive in Denver, CO, and the Alaska Division of Geological and Geophysical Surveys Geologic Materials Center in Anchorage, AK. All samples were analyzed using a multi-element analytical method involving fusion of the sample by sodium peroxide, dissolution of the fusion cake by nitric acid, and elemental analysis by inductively coupled plasma-optical emission spectroscopy (ICP-OES) and inductively coupled plasma-mass spectroscopy (ICP-MS). Additionally, 106 samples from the Nixon Fork area were analyzed by a second multi-element method in which the samples are decomposed by a mixture of hydrochloric, nitric, perchloric, and hydrofluoric acids and the elemental composition is determined by ICP-OES and ICP-MS. New Hg (mercury) concentrations, determined by cold-vapor atomic absorption spectrometry, are reported for 296 samples from southeast Alaska.

Our model is examined based on an extensive data set. Due to the unavailability of real data sets, the values of model parameters are generated randomly using discrete uniform distribution.

This workflow adapts the approach and parameter settings of Trans-Omics for precision Medicine (TOPMed). The RNA-seq pipeline originated from the Broad Institute. There are in total five steps in the workflow starting from:

1. Read alignment using STAR which produces aligned BAM files including the Genome BAM and Transcriptome BAM.
2. The Genome BAM file is processed using Picard MarkDuplicates. producing an updated BAM file containing information on duplicate reads (such reads can indicate biased interpretation).
3. SAMtools index is then employed to generate an index for the BAM file, in preparation for the next step.
4. The indexed BAM file is processed further with RNA-SeQC which takes the BAM file, human genome reference sequence and Gene Transfer Format (GTF) file as inputs to generate transcriptome-level expression quantifications and standard quality control metrics.
5. In parallel with transcript quantification, isoform expression levels are quantified by RSEM. This step depends only on the output of the STAR tool, and additional RSEM reference sequences.

For testing and analysis, the workflow author provided example data created by down-sampling the read files of a TOPMed public access data. Chromosome 12 was extracted from the Homo Sapien Assembly 38 reference sequence and provided by the workflow authors. The required GTF and RSEM reference data files are also provided. The workflow is well-documented with a detailed set of instructions of the steps performed to down-sample the data are also provided for transparency. The availability of example input data, use of containerization for underlying software and detailed documentation are important factors in choosing this specific CWL workflow for CWLProv evaluation.

This dataset folder is a CWLProv Research Object that captures the Common Workflow Language execution provenance, see https://w3id.org/cwl/prov/0.5.0 or use https://pypi.org/project/cwl

Steps to reproduce

To build the research object again, use Python 3 on macOS. Built with:

• Processor 2.8GHz Intel Core i7
• Memory: 16GB
• OS: macOS High Sierra, Version 10.13.3
• Storage: 250GB

1. Install cwltool

   pip3 install cwltool==1.0.20180912090223

2. Install git lfs
   The data download with the git repository requires the installation of Git lfs:
   https://www.atlassian.com/git/tutorials/git-lfs#installing-git-lfs

3. Get the data and make the analysis environment ready:

   git clone https://github.com/FarahZKhan/cwl_workflows.git
   cd cwl_workflows/
   git checkout CWLProvTesting
   ./topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/download_examples.sh

4. Run the following commands to create the CWLProv Research Object:

   cwltool --provenance rnaseqwf_0.6.0_linux --tmp-outdir-prefix=/CWLProv_workflow_testing/intermediate_temp/temp --tmpdir-prefix=/CWLProv_workflow_testing/intermediate_temp/temp topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/Dockstore.json
   
   zip -r rnaseqwf_0.5.0_mac.zip rnaseqwf_0.5.0_mac
   sha256sum rnaseqwf_0.5.0_mac.zip > rnaseqwf_0.5.0_mac_mac.zip.sha256

The https://github.com/FarahZKhan/cwl_workflows repository is a frozen snapshot from https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL commit 027e8af41b906173aafdb791351fb29efc044120