Access Data in the Open Science Data Repository (OSDR)

Searching for data within the OSDR

The OSDR repository landing page has several different search features as shown below.

1. The OSDR Toolbar: Links out to the “OSDR Home page”, “Data & Tools”, “Research & Resources”, “Working Groups” and “Help” menus.

2. Keyword Search: Allows users to search using keywords (e.g., Leaf) and Boolean operators such as “AND”, “OR”, and “NOT” (e.g., Leaf AND Arabidopsis).

3. Search Filters: Users can select specific Data Source, Data Type, and/or Study Metadata search filters to help target specific datasets. Described in more detail below.

4. Sort Results: Search queries are sorted by “Release Date” by default, but can be adjusted to reflect “Relevance”, “Accession ID”, or “Title”.

5. Results Display: Shows the number of search results. The default number of results per page is 25, but this can be increased to 50 or 100.

6. Results Icon: Each search result displays an icon reflecting the associated organism.

7. Title: Search result titles are shown. Users can click on a result title to navigate to that Study page. Note: The result titles could link to other Data Types (e.g., Experiment, Subject, Payload, etc.) depending on what was selected in the “Data Type” search filter.

General Search Filters

Data Source

Users can specify one or more data sources to search from. Sources include OSDR and federated repositories.

OSDR Data Sources (by default these are both selected):

• GeneLab: Search for omics datasets hosted on OSDR

• ALSDA: Search for physiological and phenotypic datasets hosted on OSDR

Federated Data Sources:

• NIH GEO: Queries datasets hosted on The National Institutes of Health (NIH) Gene Expression Omnibus (GEO)

• EBI PRIDE: Queries datasets hosted on The European Bioinformatics Institute (EBI) Proteomics Identification (PRIDE)

• ANL MG-RAST: Queries datasets hosted on The Argonne National Laboratory (ANL) Metagenomics Rapid Annotations using Subsystems Technology (MG-RAST)

Data Type

Users can specify one or more data types to search from.

Options include:

• Study: Contains omics (GeneLab) and/or physiological/phenotypic (ALSDA) data and associated metadata derived from one tissue type of an organism (non-plants) or from one organism (plants) of an experiment.

• Experiment: Contains one or more studies and associated reference data including Subject, Biospecimen, Payload, Mission, Hardware, and Vehicle.

• Subject: An individual model organism used in an experiment (e.g., Mouse 1 from Rodent Research 4).

• Biospecimen: A sample derived from a subject (e.g., leaf).

• Payload: Identifier for cargo that carried an experiment to a spacecraft.

• Mission: Spaceflight mission carrying one or more experiments.

• Hardware: Equipment/instruments used in an experiment.

• Vehicle: Vessel that carries payloads to a spacecraft.

Study Search Filters

Users can specify one or more types of study metadata to search from.

Options include:

• Project Type: Spaceflight (e.g., ISS, STS), High Altitude (e.g., Parabolic flight, hot air balloon), or Ground (e.g., ground-based cosmic radiation exposure).

• Assay Type: Select from several omics (e.g., RNA sequencing, bisulfite sequencing, mass spectrometry) and physiological/phenotypic (e.g., microscopy, histomorphometry, ultrasonography) assays.

• Organism: Select one or more types of organisms (e.g., Rodent, Human, Plant).

• Tissue: Select one or more tissue types (e.g., liver, seedlings, whole organism).

• Factor: Select from several different experimental factors (e.g., spaceflight, ionizing radiation, light cycle).

Example Search

The example below shows the results from a multiple-term search that applied the GeneLab and ALSDA “Data Source” filters, the Study “Data Type” filter, and the Spaceflight “Study Search Filter”, along with a keyword search of “genome ecotype”.