Welcome to Open Science Data Repository (OSDR) tutorial documentation!

OSDR is a public science data library for space biology researchers and future space explorers. It pulls data from the https://osdr.nasa.gov/bio/ and offers a simple and intuitive API.

Check out the API usage section for further information, including how to installation the project.

Note

This project is under active development.

Contents

• Home
• Open Science Data Repository (OSDR) Tutorial Introduction
• NASA OSDR home page
  • Explore the OSDR home page
  • About
    • Data & Tools
    • Research & Resources
      • Seminars: The analysis working groups regularly host spacebiology discussions and seminars.
    • Working Groups
    • Help
  • Access data in the OSDR
    • Search Bar
      • Single-word search
      • Multi-word search
      • Multiple-field searches
    • Boolean Operator Options
      • Boolean NOT operator.
      • Boolean AND operator.
      • Boolean * wild card operator.
    • Federating data sources
    • Study Search Filters
  • Data Submission Guide
    • Summary of guidelines for Data Submission to OSDR
      • Step 1: Review a Dataset
      • Step 2: Create an Account
      • Step 3: Review Submission Tutorial
      • Step 4: Create a Study
      • Step 5: Enter Metadata and Upload Data Files
    • Data Submission Portal
      • Instruction on how to create a NASA Guest account to access the BDME
    • OSDR submission console
    • Features of the data submission console:
    • Biological Data Management Environment (BDME) Tutorial
    • How to create a new OSDR repository
      • “Select factor”
      • “Raw data can be uploaded later.”
      • “Create a new OSD-# and DOI”
      • Entering the study description using publication (Option 1)
    • Guided Submission (Option 1)
      • Guided Submission adding assays (Option 2)
      • Unguided Submission (Option 3)
    • Study description
    • Protocols
    • Samples
    • Assays
      • Files in the BDME
    • Associate data with an OSDR archive:
    • My Dashboard & Preview
    • Study Status Review
    • Contact us
  • OSDR Public API
    • OSDR API
    • Making API Requests with Python
    • The requests library
    • Example: Accessing NASA data
    • Summary of Study Metadata API
    • Explanation of the OSDR Study Metadata API
      • Understanding Syntax: The Rules of the Game
      • The API Endpoint: Your Gateway to Study Data
    • Parameters: The Keys that Unlock Information
    • Putting it all Together: A Real-World Example
  • The Power of the Response: Unveiling Study Secrets
  • Remember:
• Summary of Study Data File API
  • Example requests:
• Explanation of the OSDR Study Data File API
  • Understanding the API’s Language: Syntax Breakdown
  • Parameters: The Keys to Specificity
  • Constructing Your Request URL: Examples in Action
  • Study Dataset Search API
  • Crafting Your Search Query: Understanding the Syntax
  • Building Your Search URL: Examples in Action
  • POST and GET requests accept the URL encoded name/value pairs for submission
  • Understanding POST and GET Filter Field Options
  • Alternative Search Interface: Syntax Breakdown
• Base URL: https://osdr.nasa.gov/bio/repo/search?
• Parameters:
• Key Points to Remember:
• Experiments, Missions, Payloads, Hardware, Vehicles, Subjects, Biospecimens
• Tutorial using R Code for Bioinformatics Analysis with NASA OSDR
• This tutorial guides you through leveraging R code to access, analyze, and visualize data from the NASA Open Science Data Repository (OSDR) for differential expression and pathway enrichment analysis.
  • Step 1: Accessing Metadata and Data
  • Step 2: Differential Expression Analysis
  • Step 3: Pathway Enrichment Analysis
• Getting Started with OSDR Data in AWS S3 buckets
• Introduction to OSDR Data on AWG
• Installing the AWS CLI
  • Prerequisites: Equipping Yourself AWS CLI data access.
  • Navigating the OSDR Data Landscape
  • Automating Your Workflow: Scripting with the AWS CLI
  • Exploring OSDR Data
  • Copying Data Locally
• Additional Resources
• AWS S3 bucket GUI setup
  • RadLab API Syntax
  • Key-Value Pairs: A Simpler Approach
  • Data Fields: The Core of Your Query
• Important Considerations:

OSDR Data Visualization Portal

• Metadata Dashboard
• Selecting “processed studies” to find higher-order data.
• Bar charts of factors
• Selecting a study or group of studies for visualization
• Studies Metadata Menu as a Table
• Selecting studies for Multi-study analysis:
• Multi-study Data Normalization:
• Multi-study Sidebar Functions
• Plotly
• PCA Plots
• Selecting groups in PCA plots
• Pair Plots
• Volcano Plots
  • Customizing volcano plots
• Heatmaps
• Ideogram
• DGE Table
  • Multiple study GSEA

Environmental Data for Space Biology Rodent Research

• The Environmental Data Application (EDA App)
  • Key elements of the EDA application:
  • Radiation meta-data
  • Select 1 or more Rodent Research (RR) missions.
  • Scroll down and download tables of radiation metadata
  • Comparison of the environmental measurements on the ISS and Ground.
  • Tables of environmental meta-data with download option.

RadLab Overview

• Data overview page
• RadLab Time series line plots
• Selecting periods for closer inspection
• Data comparison
• Geospatial plots
• Geospatial orthographic projection
• Other Geospatial options
• RadLab sensor color definitions

NASA Biological Institutional Scientific Collection (NBISC)

• What Biospecimens and Materials are available?
• NBISC announces the arrival of the NASA Space Microbial Culture Collection!
• Who can request Biospecimens and Materials?
• How do I request Biospecimens and Materials?
• How do samples get awarded?
• Are there funding opportunities?
• How can I learn more about the knowledge gaps and literature background regarding the field of space biosciences?
  • Contact

Open Science Abbreviations

• Open Science Abbreviations
  • General Abbreviations
  • Data Systems Abbreviations
  • Sample OSDR Abbreviations