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  1. Portal
  2. POR-2989

Too eager basionym merging during nub builds?

    Details

    • Type: Improvement Improvement
    • Status: Closed
    • Priority: Blocker Blocker
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Checklistbank
    • Labels:

      Description

      When building the nub using just the Mantodea checklist we yield more synonymised recombinations of basionyms as in the original, even though it is a very well curated experts dataset with basionym information:

      http://www.gbif.org/dataset/99948a8b-63b2-41bf-9d10-6e007e967789

      SOURCE Mantodea:
      Hymenopodidae [family]
        Galinthias meruensis Sjostedt, 1909 [species]
          *Galinthias usambarica Sjostedt, 1909 [species]
        Oxypiloidea (Catasigerpes) nigericus (Giglio-Tos, 1915) [species]
        Oxypilus (Anoxypilus) meruensis (Sjostedt, 1909) [species]
          *Oxypilus (Anoxypilus) nigericus (Beier, 1930) [species]
        Pseudoharpax nigericus Giglio-Tos, 1915 [species]
      
      
      NUB:
      Hymenopodidae [family]
        $Galinthias meruensis Sjostedt, 1909 [species]
          *Galinthias usambarica Sjostedt, 1909 [species]
          *Oxypilus meruensis (Sjostedt, 1909) [species]
          *Oxypilus nigericus (Beier, 1930) [species]
        $Pseudoharpax nigericus Giglio-Tos, 1915 [species]
          *Oxypiloidea nigericus (Giglio-Tos, 1915) [species]
      

      Investigate whether this additional nub grouping could actually be correct or clearly is an error. If it is an error we need to think about how to avoid them. Currently we detect basionyms within a family which might be too eager

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          Hide
          Markus Döring added a comment - - edited

          Attached the outcome of building a nub with all current backbone names from just Asteraceae, Fabaceae and Aves as input. As the input names used are not marked as synonyms or contain basionym links ALL synonyms in the output come from the implemented rules alone - which is useful to eyeball them for unwanted results.

          Synonyms in this text format are prefixed with an asterisk ( *). Basionyms are also prefixed with a dollar symbol ($)

          The attached logs document the detailed building steps name by name
          ------
          There are far fewer synonymizations. The first basionym group is a correct one:
          Aquila africanus (Cassin, 1865); Aquila africana (Cassin, 1865); Spizaetus africanus (Cassin, 1865)

          All of the above reported casesappear fixed in the sense that they are not synonymized at all now:

          • Achillea millefolium L.; Tanacetum millefolium L.; Anthemis millefolia L.; ...
          • Pueraria montana, Anthyllis montana & Astragalus montanus L.
          • Helianthus atrorubens L. & Hebeclinium atrorubens Lemaire
          • Acacia anceps var. angustifolia Benth. and Monopteryx angustifolia Benth.

          Examples of other verified good groupings:

          Anthyllis montana L. [species]
            Anthyllis montana subsp. atropurpurea (Vuk.) Pignatti [subspecies]
              *$Anthyllis montana f. atropurpurea Vuk. [form]
              *Anthyllis atropurpurea (Vuk.) Schloss. & Vuk. [species]
            Anthyllis montana subsp. hispanica (Degen & Hervier) Cullen [subspecies]
              *$Anthyllis montana var. hispanica Degen & Hervier [variety]
            Anthyllis montana subsp. jacquinii (A.Kern.) Hayek [subspecies]
              *$Anthyllis jacquinii A.Kern. [species]
            Anthyllis montana subsp. montana [subspecies]
            $Anthyllis montana var. jacquinii Rchb. f. [variety]
              *Anthyllis montana subsp. jacquinii (Rchb. f.) Rohlena [subspecies]
            Anthyllis montana var. montana [variety]
            Anthyllis montana var. sericea Jeanb. & Timb.-Lagr., 1879 [variety]
          
          $Anthyllis sampaiona Rothm., 1941 [species]
            *Anthyllis vulneraria subsp. sampaiona (Rothm.) Vasc., 1962 [subspecies]
          
          $Hebeclinium megalophyllum Lemaire [species]
            *Eupatorium megalophyllum (Lem.) Klatt [species]
            *Eupatorium megalophyllum (Lem.) N.E.Br. [species]
          

          See http://www.theplantlist.org/tpl1.1/record/gcc-24280

          $Dolichos lobatus Willd. [species]
            *Pueraria lobata (Willd.) Ohwi [species]
            *Pueraria lobata subsp. chinensis (Ohwi) Ohwi [subspecies]
            *Pueraria lobata subsp. lobata [subspecies]
            *Pueraria lobata subsp. thomsonii (Benth.) H.Ohashi & Tateishi [subspecies]
            *Pueraria lobata var. chinensis Ohwi [variety]
            *Pueraria lobata var. lobata [variety]
            *Pueraria lobata var. montana (Lour.) Maesen [variety]
            *Pueraria lobata var. thomsoni (Benth.) Maesen [variety]
            *Pueraria lobata var. thomsonii (Benth.) Maesen [variety]
            *Pueraria montana var. lobata (Willd.) Sanjappa & Pradeep [variety]
          

          See http://www.theplantlist.org/tpl1.1/record/ild-40432

          $Dolichos luteus Sw. [species]
            *Vigna lutea (Sw.) A.Gray [species]
            *Vigna repens var. lutea (Sw.) Kuntze [variety]
          

          See http://www.theplantlist.org/tpl1.1/record/ild-30245

          $Dolichos maritimus Aubl. [species]
            *Canavalia maritima (Aubl.) Thouars [species]
            *Canavalia maritima (Aubl.) Urb., 1919 [species]
          

          See http://www.theplantlist.org/tpl1.1/record/ild-3633

          $Dolichos miniatus Kunth [species]
            *Canavalia miniata (Kunth) DC. [species]
          

          See http://www.theplantlist.org/tpl1.1/record/ild-3633

          $Dolichos niloticus Delile [species]
            *Vigna nilotica (Delile) Hook.f. [species]
          

          See http://www.theplantlist.org/tpl1.1/record/ild-3509

          Show
          Markus Döring added a comment - - edited Attached the outcome of building a nub with all current backbone names from just Asteraceae, Fabaceae and Aves as input. As the input names used are not marked as synonyms or contain basionym links ALL synonyms in the output come from the implemented rules alone - which is useful to eyeball them for unwanted results. Synonyms in this text format are prefixed with an asterisk ( *). Basionyms are also prefixed with a dollar symbol ($) The attached logs document the detailed building steps name by name ------ There are far fewer synonymizations. The first basionym group is a correct one: Aquila africanus (Cassin, 1865); Aquila africana (Cassin, 1865); Spizaetus africanus (Cassin, 1865) All of the above reported casesappear fixed in the sense that they are not synonymized at all now: Achillea millefolium L.; Tanacetum millefolium L.; Anthemis millefolia L.; ... Pueraria montana, Anthyllis montana & Astragalus montanus L. Helianthus atrorubens L. & Hebeclinium atrorubens Lemaire Acacia anceps var. angustifolia Benth. and Monopteryx angustifolia Benth. Examples of other verified good groupings: Anthyllis montana L. [species] Anthyllis montana subsp. atropurpurea (Vuk.) Pignatti [subspecies] *$Anthyllis montana f. atropurpurea Vuk. [form] *Anthyllis atropurpurea (Vuk.) Schloss. & Vuk. [species] Anthyllis montana subsp. hispanica (Degen & Hervier) Cullen [subspecies] *$Anthyllis montana var. hispanica Degen & Hervier [variety] Anthyllis montana subsp. jacquinii (A.Kern.) Hayek [subspecies] *$Anthyllis jacquinii A.Kern. [species] Anthyllis montana subsp. montana [subspecies] $Anthyllis montana var. jacquinii Rchb. f. [variety] *Anthyllis montana subsp. jacquinii (Rchb. f.) Rohlena [subspecies] Anthyllis montana var. montana [variety] Anthyllis montana var. sericea Jeanb. & Timb.-Lagr., 1879 [variety] $Anthyllis sampaiona Rothm., 1941 [species] *Anthyllis vulneraria subsp. sampaiona (Rothm.) Vasc., 1962 [subspecies] $Hebeclinium megalophyllum Lemaire [species] *Eupatorium megalophyllum (Lem.) Klatt [species] *Eupatorium megalophyllum (Lem.) N.E.Br. [species] See http://www.theplantlist.org/tpl1.1/record/gcc-24280 $Dolichos lobatus Willd. [species] *Pueraria lobata (Willd.) Ohwi [species] *Pueraria lobata subsp. chinensis (Ohwi) Ohwi [subspecies] *Pueraria lobata subsp. lobata [subspecies] *Pueraria lobata subsp. thomsonii (Benth.) H.Ohashi & Tateishi [subspecies] *Pueraria lobata var. chinensis Ohwi [variety] *Pueraria lobata var. lobata [variety] *Pueraria lobata var. montana (Lour.) Maesen [variety] *Pueraria lobata var. thomsoni (Benth.) Maesen [variety] *Pueraria lobata var. thomsonii (Benth.) Maesen [variety] *Pueraria montana var. lobata (Willd.) Sanjappa & Pradeep [variety] See http://www.theplantlist.org/tpl1.1/record/ild-40432 $Dolichos luteus Sw. [species] *Vigna lutea (Sw.) A.Gray [species] *Vigna repens var. lutea (Sw.) Kuntze [variety] See http://www.theplantlist.org/tpl1.1/record/ild-30245 $Dolichos maritimus Aubl. [species] *Canavalia maritima (Aubl.) Thouars [species] *Canavalia maritima (Aubl.) Urb., 1919 [species] See http://www.theplantlist.org/tpl1.1/record/ild-3633 $Dolichos miniatus Kunth [species] *Canavalia miniata (Kunth) DC. [species] See http://www.theplantlist.org/tpl1.1/record/ild-3633 $Dolichos niloticus Delile [species] *Vigna nilotica (Delile) Hook.f. [species] See http://www.theplantlist.org/tpl1.1/record/ild-3509
          Hide
          Roderic D. M. Page added a comment -

          Did I miss the attachment...?

          Show
          Roderic D. M. Page added a comment - Did I miss the attachment...?
          Hide
          Markus Döring added a comment -

          Sorry Rod, I had to replace them with a correct version. Here they are!

          Show
          Markus Döring added a comment - Sorry Rod, I had to replace them with a correct version. Here they are!
          Hide
          Markus Döring added a comment -

          The new, strict grouping appears to be good.

          Show
          Markus Döring added a comment - The new, strict grouping appears to be good.
          Hide
          Markus Döring added a comment -

          Fixed occurrence maps for:
          Monopteryx angustifolia is endemic to Brazil: http://www.gbif-uat.org/species/2945505
          Acacia anceps is Australian again: http://www.gbif-uat.org/species/2979404

          Show
          Markus Döring added a comment - Fixed occurrence maps for: Monopteryx angustifolia is endemic to Brazil: http://www.gbif-uat.org/species/2945505 Acacia anceps is Australian again: http://www.gbif-uat.org/species/2979404

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            • Assignee:
              Markus Döring
              Reporter:
              Markus Döring
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              • Created:
                Updated:
                Resolved: