kingdom: Plantae, genus: Plantae

src/taxonopy/resolution/strategy/profiles/exact_match_primary_source_accepted_author_disambiguation.py から始め、疑わしいステップ 5 に重点を置き、提供された入力と GNVerifier の結果を使って Plantae のケースを再現します。このプロファイルが、曖昧な界／属の解決を著者の曖昧性解消における完全一致として誤って受け入れなくなれば完了です。

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).