Database Commons

a catalog of worldwide biological databases

The mission of NASA's GeneLab database (https://genelab.nasa.gov/) is to collect, curate, and provide access to the genomic, transcriptomic, proteomic and metabolomic (so-called 'omics') data from biospecimens flown in space or exposed to simulated space stressors, maximizing their utilization. This large collection of data enables the exploration of molecular network responses to space environments using a systems biology approach. We review here the various components of the GeneLab platform, including the new data repository web interface, and the GeneLab Online Data Entry (GEODE) web portal, which will support the expansion of the database in the future to include companion non-omics assay data. We discuss our design for GEODE, particularly how it promotes investigators providing more accurate metadata, reducing the curation effort required of GeneLab staff. We also introduce here a new GeneLab Application Programming Interface (API) specifically designed to support tools for the visualization of processed omics data. We review the outreach efforts by GeneLab to utilize the spaceflight data in the repository to generate novel discoveries and develop new hypotheses, including spearheading data analysis working groups, and a high school student training program. All these efforts are aimed ultimately at supporting precision risk management for human space exploration.

Motivation: - To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms.
Results: - The GeneLab Data System (GLDS) is an open access database containing fully coordinated and curated "omics" (genomics, transcriptomics, proteomics, metabolomics) data, detailed metadata and radiation dosimetry for a variety of model organisms. GLDS is supported by an integrated data system allowing federated search across several public bioinformatics repositories. Archived datasets can be queried using full-text search (e.g., keywords, Boolean and wildcards) and results can be sorted in multifactorial manner using assistive filters. GLDS also provides a collaborative platform built on GenomeSpace for sharing files and analyses with collaborators. It currently houses 172 datasets and supports standard guidelines for submission of datasets, MIAME (for microarray), ENCODE Consortium Guidelines (for RNA-seq) and MIAPE Guidelines (for proteomics).
Availability and Implementation: - https://genelab.nasa.gov/.

Accurate assessment of risks of long-term space missions is critical for human space exploration. It is essential to have a detailed understanding of the biological effects on humans living and working in deep space. Ionizing radiation from galactic cosmic rays (GCR) is a major health risk factor for astronauts on extended missions outside the protective effects of the Earth's magnetic field. Currently, there are gaps in our knowledge of the health risks associated with chronic low-dose, low-dose-rate ionizing radiation, specifically ions associated with high (H) atomic number (Z) and energy (E). The NASA GeneLab project ( https://genelab.nasa.gov/ ) aims to provide a detailed library of omics datasets associated with biological samples exposed to HZE. The GeneLab Data System (GLDS) includes datasets from both spaceflight and ground-based studies, a majority of which involve exposure to ionizing radiation. In addition to detailed information on radiation exposure for ground-based studies, GeneLab is adding detailed, curated dosimetry information for spaceflight experiments. GeneLab is the first comprehensive omics database for space-related research from which an investigator can generate hypotheses to direct future experiments, utilizing both ground and space biological radiation data. The GLDS is continually expanding as omics-related data are generated by the space life sciences community. Here we provide a brief summary of the space radiation-related data available at GeneLab.