Metadata retrieval from sequence databases with ffq.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 36610997.
- Also identified by DOI 10.1093/bioinformatics/btac667 and PMC identifier 9883619.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Several genomic databases host data and metadata for an ever-growing collection of sequence datasets. While these databases have a shared hierarchical structure, there are no tools specifically designed to leverage it for metadata extraction. We present a command-line tool, called ffq, for querying user-generated data and metadata from sequence databases. Given an accession or a paper's DOI, ffq efficiently fetches metadata and links to raw data in JSON format. ffq's modularity and simplicity make it extensible to any genomic database exposing its data for programmatic access. ffq is free and open source, and the code can be found here: https://github.com/pachterlab/ffq.
Medical subject headings
- Software
- Metadata