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NMNH voucher submissions

Source: vignettes/NMNH-Vouchers.Rmd
NMNH-Vouchers.Rmd

This page is for GenBank submissions containing specimens from the Smithsonian National Museum of Natural History (NMNH). Other users can skip it.

NMNH asks that each GenBank record from one of its specimens carry the specimen voucher and the specimen’s EZID in the following format:

[specimen_voucher=USNM:FISH:487075] [voucherURI=http://n2t.net/ark:/65665/30f303846-9d23-4069-881e-e43ff718ef9f]

Not sure how to find the specimen EZIDs for your samples? Consult your department’s data manager.

Steps

  1. Turn it on. In Export Data, tick NMNH user. RiboPilot adds [specimen_voucher={nmnh_specimen_voucher}] [voucherURI={nmnh_voucherURI}] to the FASTA header templates, including the per-marker template. If the template already has either modifier, it asks before replacing it. The switch is remembered when the header template is saved.
  2. Check the status. The NMNH user box shows how many samples need attention, or “All N samples ready”.
  3. Review and fix samples in the voucher report.
  4. Export as usual. Exporting with problems asks first, and an empty [specimen_voucher=] or [voucherURI=] is left out of the header.
NMNH user ticked: where each value comes from and how many samples need attention
NMNH user ticked: where each value comes from and how many samples need attention

Where the values come from

For each sample, RiboPilot takes the first valid value from, in order:

  1. your mapping file (pick the Catalog number column and Specimen link column under Optional: take these from mapping file columns),
  2. the linked GBIF record,
  3. the NCBI BioSample,
  4. the GEOME record.

A voucher with no EZID is looked up in GBIF to find the EZID, and an EZID with no voucher is looked up to find the voucher. Linking the samples first (see Linking records across databases) fills in more values.

What is checked and fixed

  • Voucher: must be USNM:<collection>:<catalog> with an NCBI collection code (FISH, Birds, MAMM, Herp, IZ, ENT, Botany), or US:<catalog> for botany. Letter case and repeated USNM prefixes are fixed. USNM:LAB tissue numbers are rejected.
  • EZID: written as http://n2t.net/ark:/65665/3... and checked against GBIF. A tissue EZID is replaced with its parent specimen’s, and the voucher must match the GBIF record. A media EZID is rejected. GBIF’s answers are cached in the project; Re-check with GBIF asks again.

The voucher report

Review and fix (or Review NMNH values) opens the report. It has two tables: Need attention or marked Not NMNH, and Pass the NMNH check. Each cell shows the value, where it came from, and the result; click its ? for details. The Auto-fixed column marks samples whose values RiboPilot corrected.

To fix a sample:

  • Type a value into the cell. It is checked when you leave the cell and saved in the project; your mapping file is not changed. Clear the cell to go back to the automatic value.
  • Pick a field under the cell to take the value from another mapping-file column or metadata field, or None to leave the modifier out.
  • Tick Not NMNH for samples that are not NMNH specimens. Their values are used as found, without NMNH checks.
  • Click the sample ID to open its metadata; Back to voucher report returns.
  • To easily edit many samples, use Download CSV for bulk edit, edit the file, then Upload edited CSV.
NMNH voucher report with a rejected tissue number, a Not NMNH sample, and a voucher that does not match GBIF
NMNH voucher report with a rejected tissue number, a Not NMNH sample, and a voucher that does not match GBIF