LibGuides: Digital Scholarship & Research Services: Resources & Tools

A Sampling of Open Data Repositories

BioSystics Analytics Platform (BioSystics-AP)
Microphysiology Systems Database (now called the BioSystics Analytics Platform™) captures, manages, analyzes, shares, and computationally models complex data sets from in vitro experimental models, animal studies, and human clinical data, creating actionable knowledge and predicting biological outcomes that optimizes precision medicine, including preclinical trials. Links to internal and external databases provide information on drugs, assays, preclinical and clinical data for model and study design, and to develop computational models. The BioSystics-AP provides a streamlined workflow for selecting in vitro models, implementing studies and capturing data in a central location for efficient review, analyses and computational modeling. The BioSystics-AP facilitates secure data sharing within a lab and organization, with collaborators, government agencies, and the research community.
Data.Gov
The home of the U.S. Government’s open data. Here you will find data, tools, and resources to conduct research, develop web and mobile applications, design data visualizations, and more.
Inter-University Consortium for Political and Social Research
An international consortium of more than 750 academic institutions and research organizations, Inter-university Consortium for Political and Social Research (ICPSR) provides leadership and training in data access, curation, and methods of analysis for the social science research community.

ICPSR maintains a data archive of more than 250,000 files of research in the social and behavioral sciences. It hosts 21 specialized collections of data in education, aging, criminal justice, substance abuse, terrorism, and other fields.
List of domain-specific repositories
To help researchers locate an appropriate repository for sharing or accessing data, BMIC maintains lists of domain-specific and generalist data sharing repositories that are each described by several properties. In general, NIH does not endorse or require sharing in any specific repository and encourages researchers to select the repository that is most appropriate for their data type and discipline (though such specification does exist for particular initiatives).
List of generalist repositories
To help researchers locate an appropriate repository for sharing or accessing data, BMIC maintains lists of domain-specific and generalist data sharing repositories that are each described by several properties. In general, NIH does not endorse or require sharing in any specific repository and encourages researchers to select the repository that is most appropriate for their data type and discipline (though such specification does exist for particular initiatives).
Metabolomics Workbench (MetWB)
The Metabolomics Program's Data Repository and Coordinating Center (DRCC), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego, has developed the Metabolomics Workbench. MetWB will serve as a national and international repository for metabolomics data and metadata and will provide analysis tools and access to metabolite standards, protocols, tutorials, training, and more.
RED
RED is a service of the University of South Dakota University Libraries that promotes and shares the scholarship, creative works, and data created by University of South Dakota faculty, students, and institutional partners.
Stimulating Peripheral Activity to Relieve Conditions Portal (SPARC)
The SPARC Portal provides interactive access to a growing collection of data, maps, and computational studies that focus on the role of the autonomic nervous system in controlling organ function. These resources are made available to the public with the intent of advancing bioelectronic medicine towards more precise treatment of diseases and conditions.

Open Educational Resources (OER)

LibreText: based out of UC Davis, LibreText was recently given a $5 million grant from the Department of Education to further develop their STEM open textbook project. They provide access to hundreds of textbooks and courses, mostly in the sciences and social sciences.
OASIS: an OER search tool with full textbooks, modules, homework sets, A/V materials and more. If you're not ready to commit to a complete course redesign, and instead want to begin using smaller pieces of open content, OASIS is a great search tool to use.
Open Textbook Library: faculty-reviewed, openly licensed college textbooks. This tool is best for instructors looking to find full textbooks for use in a quarter or semester course.
OpenStax: a non-profit organization based out of Rice University, OpenStax provides access to full textbooks, plus ancillary material, primarily for undergraduate courses.
Project Gutenberg: contains thousands of public domain literary works, primarily published prior to 1924.
Wikibooks: managed by the Wikimedia Foundation, this platform contains thousands of open textbooks across all subject areas.

Research tools @ USD

Databases A-Z

Journal Finder

WorldCat

Wegner Library YouTube channel

Research Guides

InterLibrary Loan

Digital Scholarship and Data Tools

AntConc
Constellate
Constellate is the text analytics service from the not-for-profit ITHAKA - the same people who brought you JSTOR and Portico. It is a platform for teaching, learning, and performing text analysis using the world’s leading archival repositories of scholarly and primary source content.
Dedoose
A cross-platform app for analyzing qualitative and mixed methods research with text, photos, audio, videos, spreadsheet data and more
DMPTool
Create data management plans that meet requirements and promote your research.
The Lens
Search, Analyze and Manage Patent and Scholarly Data.
Mallet: MAchine Learning for LanguagE Toolkit
MALLET is a Java-based package for statistical natural language processing, document classification, clustering, topic modeling, information extraction, and other machine learning applications to text.
NVivo
Qualitative analysis tool.
Omeka
Open-source web publishing platforms for sharing digital collections and creating media-rich online exhibits.
OpenRefine
OpenRefine (previously Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data.
Open Science Framework
OSF is a free, open platform to support your research and enable collaboration.
ORCiD
ORCID, which stands for Open Researcher and Contributor ID, is a global, not-for-profit organization sustained by fees from our member organizations. We are community-built and governed by a Board of Directors representative of our membership with wide stakeholder representation. ORCID is supported by a dedicated and knowledgeable professional staff.
Pressbooks
An easy-to-use book production software for open, online chapter-based publications. Pressbooks is used by educational institutions around the world as well as authors and publishers, and is a first choice for publishing and sharing OER (Open Educational Resources) content that can be adapted and reused.
Python
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
R
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.
ReproZip
ReproZip can automatically pack your research along with all necessary data files, libraries, environment variables and options into a self-contained bundle. Then ReproZip can use that bundle to automatically set up the same original environment so anybody can reproduce the research on a different machine, without tracking down and installing the dependencies, or even having to run the same operating system!
Trello
Project manager.
Tropy
Take control of your research photos with Tropy, a tool that shortens the path from finding archival sources to writing about them.
Voyant
Text analysis, open source.

Metadata Creation Tools

CEDAR
CEDAR Workbench is an open source tool to manage metadata for any field of study, using rigorous semantic principles if desired. It allows users to specify templates using a UI (like survey forms in Google Forms or Survey Monkey), then to fill out those forms efficiently using drop-down menus, help tips, and intelligent suggestions. Templates and metadata can be shared with other users and groups. Metadata also can be downloaded in JSON-LD, simple JSON, or RDF, or exported to connected repositories, which can be integrated using the full API suite.
ISA Framework
The open source ISA framework and tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies.

Built around the 'Investigation' (the project context), 'Study' (a unit of research) and 'Assay' (analytical measurement) data model and serializations (tabular, JSON and RDF), the ISA framework helps you to provide rich description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) so that the resulting data and discoveries are reproducible and reusable.
OntoMaton
OntoMaton provides ontology searching and automated tagging via NCBO's Bioportal of biomedical ontologies within Google spreadsheets. This tool is best for biomedical research. OntoMaton is part of the ISA-Tools suite. Annotations are generated within your tabular data file.
RightField
RIghtField is an open source tool that allows searching and selecting of ontology terms for any field of study from within Microsoft Excel. RightField allows you to assign a pre-determined list of options to a particular cell within the spreadsheet. All annotations are embedded within the spreadsheet. The user can select from the NCBO's BioPortal ontologies or import an ontology from a URL or your local machine.

Digital Scholarship Tools for the Health and Natural Sciences

Bioicons
High-quality science illustrations.
Biorender
Create professional science figures.
Canva
Create free flow charts.
Free Health Icons
Labtab
Lab management app for PIs.
Reactome
Reactions, Proteins and Pathways. Visualize and interact with biological pathways.
Scidraw
Repository of high quality drawings of animals, scientific setups. Useful for presentations and posters.
Smart Servier
Free medical images including anatomy and cellular biology.

Free health Sciences Tools

Entrez Programming Utilities (eutils)
Use this resource for text searching in genomic records
MEDLINE/PubMed Data
Use this resource to download MEDLINE and PubMed data. You can access via bulk download or API.
MeSH Headings
Use this resource to download MeSH headings for use in content mining projects or to create search APIs.
National Library of Medicine
Use this guide to search National Library of Medicine (NLM) data.

Tool Indexes

Dirt Directory (archived copy)
The DiRT Directory is a registry of digital research tools for scholarly use. DiRT makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mindmapping software.
TAPoR3
Discover research tools for study texts.

Other useful research tips and tools

How to Make Sense of a Scientific Journal Article

Strategy for Finding Statistics and Data

Publishing

JANE: Journal/Author Name Estimator
Have you recently written a paper, but you're not sure to which journal you should submit it? Or maybe you want to find relevant articles to cite in your paper? Or are you an editor, and do you need to find reviewers for a particular paper? Jane can help!

Just enter the title and/or abstract of the paper in the box, and click on 'Find journals', 'Find authors' or 'Find Articles'. Jane will then compare your document to millions of documents in PubMed to find the best matching journals, authors or articles.
Elsevier Journal Finder
Enter title and abstract of your paper to easily find journals that could be best suited for publishing. JournalFinder uses smart search technology and field-of-research specific vocabularies to match your paper to scientific journals.