Add metadata column to distinguish patent sequences (e.g. include Genbank division)
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Description
Right now, NCBI datasets downloads for viruses often include sequences of non-natural origin, predominantly patent related sequences.
It would be great if the metadata fields included one that would allow to easily filter those sequences out. For example, you could include the Genbank division the sequence appears in. There is a dedicated patent division PAT: https://www.ncbi.nlm.nih.gov/education/patent_and_ip_faqs/
Unfortunately, it seems this information is lost in the datasets input pipeline. Would be great if it could be kept and surfaced.
The feature would be immediately and immensely useful to Pathoplexus as it would allow us to not ingest patent sequences - those are out of scope for Pathoplexus as they are not useful in pathogen genomic analyses. See https://github.com/loculus-project/loculus/issues/6450
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No files, tests, or entry points are named in the issue. Start by tracing the NCBI datasets input pipeline to find where GenBank division metadata is discarded, then verify that the surfaced field preserves the PAT value so consumers can filter patent sequences.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100