I am excited to share with you that we released the OSDR Biological Data API earlier this week:
It is a successor to GLOpenAPI that now incorporates both GeneLab and ALSDA datasets from the OSDR data repo (hence the rebranding) and improves access to their metadata and data.
The classic use cases are all there:
- you can select and retrieve sample-level metadata across the entire database with compound queries and filters,
- and then request the matching underlying data.
To that, we added:
- a REST interface (making it easier to traverse the database and find dataset, assay, sample, and file objects);
- retrieval of more deeply nested metadata fields;
- additional sensible output formats;
- and we significantly improved the API’s performance, too.
Also, while it’s primarily intended for programmatic access, interactive in-browser
viewers for JSONs and tables are back and better than ever.
Check it out and let us know what you think!
Here’s some examples:
- file listings for a dataset and for a specific sample
- metadata for spaceflight-related tissue-specific M. musculus samples
- an interactive differential expression table
- merged unnormalized counts across several datasets
- a metadata table with links to image files
- a MultiQC report that you don’t even have to download
P.S. The legacy GLOpenAPI is currently still operational in its original location, so none of your existing scripts will break: https://visualization.genelab.nasa.gov/GLOpenAPI/.
That said, the new Biological Data API has a layer that makes it backwards compatible with GLOpenAPI (just replace https://visualization.genelab.nasa.gov/GLOpenAPI/ with https://visualization.osdr.nasa.gov/biodata/api/ – no “v2”); we encourage people to try it out, or even better, to start transitioning to the new API and the new syntax that is described in the documentation.
@HUMANawg @MultiOmicsAWG @AnimalAWG @AIMLawg @ALSDAawg @PlantAWG @MicrobesAWG @RLWG @FemaleReproAWG
