Plant nomenclature standardization

Plant nomenclature standardization

Summary

Standardize sample taxonomy strings (species, genus, family) to currently recognized names using the Open Tree of Life API, producing a cleaned taxonomy table with resolved names and OTOL identifiers for integration into downstream metabolomics analysis.

When to use

When your metadata table contains species, genus, or family names that may be outdated, synonymous, or non-canonical, and you need to integrate them with the Literature Component (which requires standardized taxon identifiers) or cross-reference with external databases like Lotus Database (which uses NPClassifyre ontology tied to current taxonomy).

When NOT to use

• Taxonomy is already validated against a current reference ontology (e.g., NCBI Taxonomy for the current year) with stable IDs.
• Your workflow does not use the Literature Component or Lotus Database cross-reference; taxonomy standardization is unnecessary if you rely only on spectral similarity.
• Sample metadata lacks species, genus, or family information; the skill requires at least one rank to operate meaningfully.

Inputs

• Metadata table (TSV format) with ATTRIBUTE_Species, genus, and family columns
• Species, genus, and family column name specifications

Outputs

• Cleaned metadata TSV table with standardized taxonomy names
• OTOL_ID columns appended for species, genus, and family ranks
• Mapping table linking original taxon names to resolved names and OTOL_IDs

How to apply

Load the metadata table (TSV format) and extract the columns designated as species_column, genus_column, and family_column. For each unique taxon name at each rank, query the Open Tree of Life API to retrieve the current accepted name and corresponding OTOL_ID. Create a bidirectional mapping table linking original names to resolved names and OTOL_IDs for all three ranks. Replace the original taxonomy strings in the metadata with resolved names and append new OTOL_ID columns for each rank. Output a cleaned metadata TSV table suitable for use in subsequent Literature Component calculations and database cross-referencing. Rationale: standardization ensures consistent taxon matching across literature databases and prevents erroneous compound–taxon associations that could bias novelty scoring.

Related tools

• Open Tree of Life API (Query service to retrieve current accepted taxon names and OTOL identifiers for each original species, genus, and family name) — https://opentree.readthedocs.io/en/latest/readme.html
• Inventa (Downstream tool that consumes cleaned metadata to calculate Literature Component based on standardized taxon names) — https://github.com/luigiquiros/inventa
• Lotus Database (External reference resource using NPClassifyre ontology; standardized taxonomy enables accurate cross-referencing of reported compounds per taxon)

Evaluation signals

• All rows in original metadata have corresponding entries in the mapping table (100% coverage).
• No null or empty OTOL_ID values in the output cleaned metadata for any taxon rank that was populated in the input.
• Output taxonomy names are recognized as valid current names when spot-checked against the Open Tree of Life web interface.
• Downstream Literature Component calculation completes without taxon lookup errors, confirming identifiers are resolvable.
• Comparison of original vs. cleaned taxonomy reveals expected synonymies (e.g., deprecated species names mapped to accepted names) rather than random or null replacements.

Limitations

• Open Tree of Life API may not recognize very recently described species or highly localized/vernacular taxon names; query failures require manual curation.
• Ambiguous or misspelled input names (e.g. 'Genus spp.', 'Plantae indet.') may fail resolution or resolve to higher-level taxa, reducing specificity for Literature Component.
• API query rate limits or network outages can interrupt large-scale standardization; no built-in retry logic mentioned in the README.
• The skill assumes the input metadata columns are correctly labeled and formatted; malformed or misaligned columns will propagate errors downstream.

Evidence

• [other] Taxonomy normalization is performed using the Open Tree of Life reference to convert sample taxonomy strings to currently recognized names, producing a cleaned taxonomy table required for Literature Component calculations.: "Taxonomy normalization is performed using the Open Tree of Life reference to convert sample taxonomy strings to currently recognized names, producing a cleaned taxonomy table required for Literature"
• [other] For each unique taxon name in each taxonomic rank, query the Open Tree of Life API to retrieve the current accepted name and taxon Open Tree of Life identifier (OTOL_ID).: "For each unique taxon name in each taxonomic rank, query the Open Tree of Life API to retrieve the current accepted name and taxon Open Tree of Life identifier (OTOL_ID)."
• [other] Replace the original taxonomy strings in the metadata table with resolved names and append OTOL_ID columns for each rank.: "Replace the original taxonomy strings in the metadata table with resolved names and append OTOL_ID columns for each rank."
• [readme] The species should be cleaned to up-to-day recognized names, you can use the Open Tree of Life to do so: "The species should be cleaned to up-to-day recognized names, you can use the Open Tree of Life to do so"
• [other] given that the Lotus Dabase uses the NPClassifyre ontology and Sirius uses the Classifyre ontology, performing this step is absolutley necesary: "given that the Lotus Dabase uses the NPClassifyre ontology and Sirius uses the Classifyre ontology, performing this step is absolutley necesary"