OBIS Quality Control

A very brief look at QC checks before publishing

Elizabeth Lawrence

2026-07-22

Quality control

Before publishing — check for:

• ✅ Taxonomy matched to WoRMS (AphiaID required for marine taxa)
  
• ✅ Coordinates in decimal degrees, in the ocean
  
• ✅ Dates in ISO 8601 format (YYYY-MM-DD)
  
• ✅ Unique, stable occurrenceID and eventID
  
• ✅ Table linkages consistent (eventID, occurrenceID)

Tools:

Tool	What it checks
obistools (R package)	Taxonomy, geography, required fields
GBIF data validator	Darwin Core Archive structure
WoRMS taxon match	Scientific names → AphiaIDs

obistools is an R package from OBIS. The GBIF validator is a web-based tool. WoRMS has a batch taxon match tool at marinespecies.org/aphia.php. For unidentified sequences, assign a high-level taxon if possible (e.g., kingdom Animalia) rather than leaving the field empty.

WoRMS Taxon Matching

Options for taxon matching:

• WoRMS Taxon Match Tool
• Programmatically:
  • obistools::match_taxa
  • worrms::wm_records_taxamatch
  • pyworms

No WoRMS match?

Use highest-rank taxon with a match (e.g. family or order). Keep the sequence — it can be re-identified later as reference databases improve.

Still no match?

Unknown sequences recorded as: scientificName = “Biota incertae sedis” scientificNameID = urn:lsid:marinespecies.org:taxname:12

OBIS DNA Data Management Platform

🔧 OBIS is developing a data management platform for DNA data including:

• Bioinformatics
• QC
• Validation
• Publication to OBIS pipeline

To be offered to OBIS nodes to support local eDNA projects!

🚧