nmdc-target-gene

name

nmdc-target-gene

description

Use this skill to curate amplicon LibraryPreparation records an NCBI ingest left unfinished: write a description (target plus primers) from the SRA DESIGN_DESCRIPTION on every amplicon library, and select a TargetGeneEnum target_gene for single-gene amplicons while leaving whole-operon amplicons unset. Trigger when the run notes or the amplicon_curation sidecar flag amplicon libraries needing a description or target_gene.

Amplicon LibraryPreparation curation (description + target_gene)

The NCBI pipeline carries the SRA library descriptor verbatim but deliberately does not parse the free-text DESIGN_DESCRIPTION — restating it as prose is a natural-language task, not a regex job. Two slots are left for you, the running agent, both read from the same DESIGN_DESCRIPTION and written to the same records:

1. description — set on every amplicon LibraryPreparation, restating what was amplified (target + primers). See Set the description below.
2. target_gene — the pipeline already committed it for designs naming one explicit rRNA gene (e.g. "...amplify bacterial 16S rRNA genes" → 16S_rRNA); you resolve the rest, leaving whole-operon amplicons unset. See How to decide target_gene below.

The decisive distinction is single gene vs. whole operon:

• A design that targets one rRNA gene (the design text or primers name a single SSU or LSU gene) → commit that TargetGeneEnum value.
• A design that targets an rRNA operon → leave target_gene unset. An rRNA operon spans two genes (a bacterial operon covers 16S and 23S; a eukaryotic operon covers 18S and 28S), and target_gene is single-valued with no whole-operon permissible value. There is no honest single value, so the slot is omitted rather than reduced to one of the genes the operon happens to contain. Carry what was amplified in LibraryPreparation.description instead (the pipeline already writes e.g. "Amplicon library preparation targeting bacterial rRNA operons using 8F and 2490R primers" there) — do not invent a target_gene.

This reflects nmdc-schema #3238: the MFD PacBio/Nanopore amplicons sequence the full 16S–ITS–23S (or 18S–ITS–28S) operon, which the schema cannot represent as a target_gene, so those records carry a description and no target_gene.

This is a judgment task delegated to you, the running agent — there is no hardcoded mapping and no LLM API call in the pipeline. Use whatever model you are running; the biology guidance below makes the decision reproducible across models.

Before committing (or deliberately omitting) any value, read nmdc-curation-rules — its evidence-first / omit-rather-than-guess rules govern every commit here.

Inputs

The pipeline writes the work-list to the curation-inputs sidecar results/ncbi_<ACCESSION>_nmdc_curation_inputs.json under the amplicon_curation key — every amplicon LibraryPreparation, grouped by distinct DESIGN_DESCRIPTION:

{
  "design_description": "amplicon sequencing using 3NDF and 21R to amplify eukaryotic rRNA operons",
  "example_library_name": "pb_eukoperon_MFD09597",
  "target_gene": null,
  "library_preparation_ids": ["nmdc:libprp-99-...", "..."],
  "count": 450
}

target_gene is the value the pipeline already set: a gene string (e.g. "16S_rRNA") means it is resolved — leave it as-is and only add the description; null means you must decide it (and, for an operon, deliberately leave it unset).

Work once per design (not per library): derive the description (always) and the target_gene (when null), then apply both to every library_preparation_ids entry for that design.

Set the description

Set LibraryPreparation.description on every amplicon library in the work-list. Read the two facts out of the design_description free text — there is no fixed format across BioProjects, so read for meaning rather than matching a pattern:

• target — what the design says it amplifies, e.g. "bacterial rRNA operons", "bacterial 16S rRNA genes", "eukaryotic rRNA operons".
• primers — the primer pair named in the design, e.g. "8F and 2490R", "8F and 1391R", "3NDF and 21R".

MFD designs follow the shape "amplicon sequencing using <primers> to amplify <target>" (see references/worked-examples.md), but other projects phrase it differently — extract the same two facts however the design is worded. If a design genuinely names no target or no primers, omit description rather than inventing text (omit-rather-than-guess).

Then write the description in this fixed template so phrasing is consistent:

Amplicon library preparation targeting <target> using <primers> primers

For concrete design_description → description worked examples, see references/worked-examples.md.

How to decide target_gene

For each design, weigh three pieces of evidence — the design text, the primer names, and the library name:

1. Operon vs. gene is the first question. If the design text says "rRNA operon(s)", or the library name encodes an operon (pb_bacoperon_*, pb_eukoperon_*), or the primers span both subunits (a forward SSU primer paired with a reverse primer that reads into the LSU — e.g. 8F/2490R, where 2490R reads into the 23S), then the amplicon is a whole operon → leave target_gene unset. Stop here; do not pick a gene.
2. Single-gene amplicons select one TargetGeneEnum value. Only when the design targets a single rRNA gene, pick a permissible value of TargetGeneEnum (16S_rRNA, 18S_rRNA, 23S_rRNA, 28S_rRNA):
   • Domain narrows the choice to a pair and rules out the other domain's pair: prokaryotic (bacterial/archaeal) → 16S_rRNA (SSU) or 23S_rRNA (LSU); eukaryotic → 18S_rRNA (SSU) or 28S_rRNA (LSU).
   • Primer names select within the pair — e.g. 8F/1391R and 8F/27F are bacterial 16S (SSU) primers → 16S_rRNA; 3NDF/21R anchor the eukaryotic 18S → 18S_rRNA. If you are unsure of a primer, check a primer database / the literature rather than guessing.
   • Library name corroborates the domain: npumi_16SrRNA_* names the gene outright (16S_rRNA).

When the evidence does not resolve to exactly one gene — most importantly any whole-operon amplicon — leave it unset (omit-rather-than-guess). Do not assert 16S_rRNA/18S_rRNA/23S_rRNA/28S_rRNA for an operon just because the operon contains that gene.

A concrete per-project outcome (the MFD operon-vs-single-gene split) is in references/worked-examples.md.

Patch the output

Patch the generated results/ncbi_<ACCESSION>_nmdc.json programmatically, keyed on each design's library_preparation_ids — do not hand-edit hundreds of records. Per design:

• description — set it on every listed LibraryPreparation (always).
• target_gene — if the sidecar row's target_gene is already a gene string, leave the record's value as-is. If it is null, set a TargetGeneEnum value for a single-gene design, or leave it absent for an operon (the description carries the target).

Re-validate the file against the schema afterward (see ncbi-to-nmdc § Step 7), then note in the run report, per design, the description set and whether target_gene was set (and to what) or deliberately omitted (operon), with counts.