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  1. Portal Feedback
  2. PF-2387

Hedyotis microphylla homonym results in incorrect distribution map

    Details

    • Type: Feedback Feedback
    • Status: Closed
    • Priority: Unassessed Unassessed
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
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      Description

      The occurrence http://www.gbif.org/occurrence/1252562694 in the Philippines is interpreted as Hedyotis microphylla Kunth, which is a synonym of Arcytophyllum filiforme (Ruiz & Pav.) Standl. found in South America.

      This odd distribution (South American plant found in the Philippines) is because the actual name is Hedyotis microphylla Merr. (see http://www.gbif.org/occurrence/1252562694/verbatim ), described in:

      Merrill, E. D. (1906). New or noteworthy Philippine plants, V. The Philippine journal of science, 1(Supplement 3), 169-246. Retrieved from http://direct.biostor.org/reference/164203 http://biodiversity.org/page/695373

      The status of this name is unclear, but this is not Hedyotis microphylla Kunth. Hedyotis microphylla Merr. is in IPNI, so ideally when matching this name and authors it should be recognised as a distinct name and we wouldn't have this odd distribution.

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          Hide
          Markus Döring added a comment -

          Yes, the old backbone ignored authorship pretty much and required binomial names to be unique (it did cope with genus homonyms).
          This is one of the major goals for the improved backbone.

          http://dev.gbif.org/issues/browse/POR-2467
          http://dev.gbif.org/issues/browse/POR-3022

          We hope to advertise a first public preview of the new backbone at the end of this week.

          Show
          Markus Döring added a comment - Yes, the old backbone ignored authorship pretty much and required binomial names to be unique (it did cope with genus homonyms). This is one of the major goals for the improved backbone. http://dev.gbif.org/issues/browse/POR-2467 http://dev.gbif.org/issues/browse/POR-3022 We hope to advertise a first public preview of the new backbone at the end of this week.
          Hide
          Markus Döring added a comment -

          Luckily this seems to be fixed in the upcoming preview. There are 3 names now with different authors, all of them being synonyms:
          http://www.gbif-uat.org/species/search?q=Hedyotis+microphylla&dataset_key=d7dddbf4-2cf0-4f39-9b2a-bb099caae36c

          With Hedyotis microphylla Merr. being a synonym of Praravinia microphylla (Merr.) Bremek.:
          http://www.gbif-uat.org/species/8171958

          Show
          Markus Döring added a comment - Luckily this seems to be fixed in the upcoming preview. There are 3 names now with different authors, all of them being synonyms: http://www.gbif-uat.org/species/search?q=Hedyotis+microphylla&dataset_key=d7dddbf4-2cf0-4f39-9b2a-bb099caae36c With Hedyotis microphylla Merr. being a synonym of Praravinia microphylla (Merr.) Bremek.: http://www.gbif-uat.org/species/8171958
          Hide
          Markus Döring added a comment -

          ... or in the new nub browser (details page waiting for an index rebult still)
          http://mdoering.github.io/nub-browser/app/#/search/Hedyotis%20microphylla

          Show
          Markus Döring added a comment - ... or in the new nub browser (details page waiting for an index rebult still) http://mdoering.github.io/nub-browser/app/#/search/Hedyotis%20microphylla
          Hide
          Roderic D. M. Page added a comment -

          "There are 3 names now with different authors, all of them being synonyms:" I think it's more complicated than that. For example, http://mdoering.github.io/nub-browser/app/#/taxon/2907578 lists these names as synonyms, but IPNI has:

          Hedyotis microphylla Merr Philipp. J. Sci. 1(Suppl. 3): 239 1906
          Lucinaea microphylla Merr. Mitt. Inst. Bot. Hamburg vii. 286 (1937).
          Urophyllum microphyllum Merr. Philipp. J. Sci., C 12: 161 1917

          These are three different names, and Praravinia microphylla (Merr.) Bremek. has the basionym Urophyllum microphyllum Merr. Philipp. J. Sci., C 12: 161 1917 (see http://biodiversitylibrary.org/page/8370141 ) NOT Lucinaea microphylla Merr. as shown in http://mdoering.github.io/nub-browser/app/#/taxon/2907578 - PS the browser is nice but doesn't work in Safari

          I think we're hitting the limits of matching names, IPNI has most if not all of this as explicit links with IDs which should help avoid these situations.

          Show
          Roderic D. M. Page added a comment - "There are 3 names now with different authors, all of them being synonyms:" I think it's more complicated than that. For example, http://mdoering.github.io/nub-browser/app/#/taxon/2907578 lists these names as synonyms, but IPNI has: Hedyotis microphylla Merr Philipp. J. Sci. 1(Suppl. 3): 239 1906 Lucinaea microphylla Merr. Mitt. Inst. Bot. Hamburg vii. 286 (1937). Urophyllum microphyllum Merr. Philipp. J. Sci., C 12: 161 1917 These are three different names, and Praravinia microphylla (Merr.) Bremek. has the basionym Urophyllum microphyllum Merr. Philipp. J. Sci., C 12: 161 1917 (see http://biodiversitylibrary.org/page/8370141 ) NOT Lucinaea microphylla Merr. as shown in http://mdoering.github.io/nub-browser/app/#/taxon/2907578 - PS the browser is nice but doesn't work in Safari I think we're hitting the limits of matching names, IPNI has most if not all of this as explicit links with IDs which should help avoid these situations.
          Hide
          Markus Döring added a comment -

          That's the hopefully rare case I was waiting for when the same author described several species with the same epithet in the same family.

          The trouble is that the old IPNI copy we have does not provide any basionym information: http://www.gbif-uat.org/species/105568293/verbatim
          So in this case the basionym is derived by looking at the authorship. And because the authorship information particulary of zoological names is often missing brackets, our algorithm considers multiple names with original authors as potential recombinations.

          If there are more cases like this we should probably not create new basionym relations programmatically in such problematic cases. We would then end up with all of those names being accepted as IPNI does not indicate a synonymy.

          The only good solution would be to have IPNI or someone else providing us that information

          Show
          Markus Döring added a comment - That's the hopefully rare case I was waiting for when the same author described several species with the same epithet in the same family. The trouble is that the old IPNI copy we have does not provide any basionym information: http://www.gbif-uat.org/species/105568293/verbatim So in this case the basionym is derived by looking at the authorship. And because the authorship information particulary of zoological names is often missing brackets, our algorithm considers multiple names with original authors as potential recombinations. If there are more cases like this we should probably not create new basionym relations programmatically in such problematic cases. We would then end up with all of those names being accepted as IPNI does not indicate a synonymy. The only good solution would be to have IPNI or someone else providing us that information
          Hide
          Markus Döring added a comment -

          See POR-2989 for ideas about improving a too eager programmatic basionym grouping

          Show
          Markus Döring added a comment - See POR-2989 for ideas about improving a too eager programmatic basionym grouping
          Hide
          Matthew Blissett added a comment -

          @Markus, the old IPNI DWCA does have some basionyms present. For example, urn:lsid:ipni.org:names:360445-1 appears once as a taxonID and once as a BasionymID.

          http://ipni.org/urn:lsid:ipni.org:names:360468-1:1.3.2.1

          There's an original name usage on the record: http://www.gbif.org/species/103257968/verbatim

          However, I don't remember how complete IPNI's basionym links are. It could be that they don't have them in their database. (I really can't remember.)

          Show
          Matthew Blissett added a comment - @Markus, the old IPNI DWCA does have some basionyms present. For example, urn:lsid:ipni.org:names:360445-1 appears once as a taxonID and once as a BasionymID. http://ipni.org/urn:lsid:ipni.org:names:360468-1:1.3.2.1 There's an original name usage on the record: http://www.gbif.org/species/103257968/verbatim However, I don't remember how complete IPNI's basionym links are. It could be that they don't have them in their database. (I really can't remember.)
          Hide
          Markus Döring added a comment - - edited

          The upcoming August 2016 backbone has this fixed:

          • 7713093 Hedyotis microphylla DC. ACCEPTED within Hedyotis L.(Rubiaceae)
          • 2892803 Hedyotis microphylla Kunth SYNONYM of Arcytophyllum filiforme (Ruiz & Pav.) Standl. (Rubiaceae)
          • 7912822 Hedyotis microphylla Merr. DOUBTFUL within Hedyotis L. (Rubiaceae)
          • 2899451 Lucinaea microphylla Merr. SYNONYM of Schradera polysperma (Jack) Puff, R.Buchner & Greimler
          • 5338582 Urophyllum microphyllum Merr. SYNONYM of Praravinia microphylla (Merr.) Bremek.

          Again we are missing any basionym due to an old IPNI copy (http://www.gbif.org/species/105579779) and the less eager basionym grouping. Should be adressed in POR-3160

          Show
          Markus Döring added a comment - - edited The upcoming August 2016 backbone has this fixed: 7713093 Hedyotis microphylla DC. ACCEPTED within Hedyotis L.(Rubiaceae) 2892803 Hedyotis microphylla Kunth SYNONYM of Arcytophyllum filiforme (Ruiz & Pav.) Standl. (Rubiaceae) 7912822 Hedyotis microphylla Merr. DOUBTFUL within Hedyotis L. (Rubiaceae) 2899451 Lucinaea microphylla Merr. SYNONYM of Schradera polysperma (Jack) Puff, R.Buchner & Greimler 5338582 Urophyllum microphyllum Merr. SYNONYM of Praravinia microphylla (Merr.) Bremek. Again we are missing any basionym due to an old IPNI copy ( http://www.gbif.org/species/105579779 ) and the less eager basionym grouping. Should be adressed in POR-3160

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            • Assignee:
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              Reporter:
              Roderic D. M. Page
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