kingdom: Plantae, genus: Plantae

[thompsonmj]

In exploring TOL-200M, it was noticed that there are 223,284 entries that have a resolution path of:

kingdom: Plantae
phylum: null
class: null
order: null
family: null
genus: Plantae
species: null

Example entry resolution:

{'uuid': 'e571a2d3-07f3-45fe-b372-67c0594de0c8',
 'scientific_name': 'Plantae',
 'common_name': 'plants; plants',
 'source_dataset': 'gbif',
 'source_id': '1038946915',
 'resolution_status': 'EXACT_MATCH_PRIMARY_SOURCE_ACCEPTED_AUTHOR_DISAMBIGUATION',
 'kingdom': 'Plantae',
 'phylum': '',
 'class': '',
 'order': '',
 'family': '',
 'genus': 'Plantae',
 'species': '',
 'resolution_path': 'RESOLVED',
 'resolution_strategy': 'ExactMatchPrimarySourceAcceptedAuthorDisambiguation',
 'final_query_term': 'Plantae',
 'final_query_rank': 'scientific_name',
 'final_data_source_id': 11,
 'meta_selected_record_id': None,
 'meta_candidate_count': None,
 'meta_accepted_record_id': None,
 'meta_matched_result_id': '11387779',
 'meta_matched_full_name': 'Plantae',
 'meta_author_disambiguation': 'true',
 'resolution_failure_reason': None,
 'meta_original_status': None,
 'meta_force_failed_to_input': None,
 'meta_original_attempt_key': None,
 'source_file': 'part-00000-3990aff1-4728-49f9-bd76-087ff566f4fc-c000.snappy.resolved.parquet',
 'meta_matched_current_name': None,
 'meta_synonym_matched': None,
 'meta_accepted_name': None,
 'meta_disambiguated_record_id': None}

Corresponding Input:

>>> row_dict
{'source_id': '1038946915', 'uuid': 'e571a2d3-07f3-45fe-b372-67c0594de0c8', 'scientific_name': 'Plantae', 'phylum': None, 'class': None, 'order': None, 'family': None, 'genus': None, 'species': None, 'kingdom': 'Plantae', 'common_name': 'plants; plants'}

(in source_taxa/source=gbif/part-00000-3990aff1-4728-49f9-bd76-087ff566f4fc-c000.snappy.parquet)

GNVerifier query result for "Plantae"

$ docker run --rm -i gnames/gnverifier:v1.2.5 -j 1 --format compact --capitalize --all_matches --sources 11 "Plantae" | jq
{
  "id": "827f5f3d-f332-5d4e-9ec9-6dbf1b07bdd9",
  "name": "Plantae",
  "cardinality": 1,
  "matchType": "Exact",
  "results": [
    {
      "dataSourceId": 11,
      "dataSourceTitleShort": "GBIF Backbone Taxonomy",
      "curation": "AutoCurated",
      "recordId": "11387779",
      "outlink": "https://gbif.org/species/11387779",
      "entryDate": "2024-01-11",
      "sortScore": 9.410739851747246,
      "matchedNameID": "827f5f3d-f332-5d4e-9ec9-6dbf1b07bdd9",
      "matchedName": "Plantae",
      "matchedCardinality": 1,
      "matchedCanonicalSimple": "Plantae",
      "matchedCanonicalFull": "Plantae",
      "currentRecordId": "11387779",
      "currentNameId": "827f5f3d-f332-5d4e-9ec9-6dbf1b07bdd9",
      "currentName": "Plantae",
      "currentCardinality": 1,
      "currentCanonicalSimple": "Plantae",
      "currentCanonicalFull": "Plantae",
      "taxonomicStatus": "Accepted",
      "isSynonym": false,
      "classificationPath": "Plantae|Plantae",
      "classificationRanks": "kingdom|genus",
      "classificationIds": "6|11387779",
      "editDistance": 0,
      "stemEditDistance": 0,
      "matchType": "Exact",
      "scoreDetails": {
        "cardinalityScore": 1,
        "infraSpecificRankScore": 0,
        "fuzzyLessScore": 1,
        "curatedDataScore": 0.33333334,
        "authorMatchScore": 0.14285715,
        "acceptedNameScore": 1,
        "parsingQualityScore": 1
      }
    },
    {
      "dataSourceId": 11,
      "dataSourceTitleShort": "GBIF Backbone Taxonomy",
      "curation": "AutoCurated",
      "recordId": "6",
      "outlink": "https://gbif.org/species/6",
      "entryDate": "2024-01-11",
      "sortScore": 9.410739851747246,
      "matchedNameID": "827f5f3d-f332-5d4e-9ec9-6dbf1b07bdd9",
      "matchedName": "Plantae",
      "matchedCardinality": 1,
      "matchedCanonicalSimple": "Plantae",
      "matchedCanonicalFull": "Plantae",
      "currentRecordId": "6",
      "currentNameId": "827f5f3d-f332-5d4e-9ec9-6dbf1b07bdd9",
      "currentName": "Plantae",
      "currentCardinality": 1,
      "currentCanonicalSimple": "Plantae",
      "currentCanonicalFull": "Plantae",
      "taxonomicStatus": "Accepted",
      "isSynonym": false,
      "classificationPath": "Plantae",
      "classificationRanks": "kingdom",
      "classificationIds": "6",
      "editDistance": 0,
      "stemEditDistance": 0,
      "matchType": "Exact",
      "scoreDetails": {
        "cardinalityScore": 1,
        "infraSpecificRankScore": 0,
        "fuzzyLessScore": 1,
        "curatedDataScore": 0.33333334,
        "authorMatchScore": 0.14285715,
        "acceptedNameScore": 1,
        "parsingQualityScore": 1
      }
    }
  ],
  "curation": "AutoCurated"
}

The exact_match_primary_source_accepted_author_disambiguation.py profile incorrectly matches this case (suspect: step 5 not specific enough).