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  1. Portal
  2. POR-398

Merge species by their epithet and authorship

    Details

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

      Description

      To avoid creating multiple accepted taxa based on the same holotype we should try to detect original name relations based on the authorship and the species epithet. Try to spot recombinations of the same original name within a family by looking at the epithet and authorship & year.

      See http://iphylo.blogspot.de/2013/08/cluster-maps-papaya-plots-and-trouble.html#disqus_thread
      and http://gist.neo4j.org/?a91e351279438d2ec1e6

        Gliffy Diagrams

        1. asteraceae.txt
          4.10 MB
          Markus Döring
        2. aves.txt
          936 kB
          Markus Döring
        3. curculionidae.txt
          2.42 MB
          Markus Döring
        4. molossidae.txt
          8 kB
          Markus Döring
        5. muridae.txt
          41 kB
          Markus Döring
        1. CDM_Agoseris_apargioides_synonymy.png
          134 kB
        2. CDM_Agoseris_grandiflora_synonymy.png
          239 kB
        3. CDM_Lactuca_aurea_synonymy.png
          91 kB

        Issue Links

          Activity

          Hide
          Roderic D. M. Page added a comment -

          I'd need to play with an example, but I wonder if there's any way to postpone making a decision? Can we not simply say, these names are associated in some way so that user discovers information associated with related names, but avoids the strong assertion that a name is accepted or not. If we separated names and taxa, this would be a fairly easy thing to do I suspect...

          Show
          Roderic D. M. Page added a comment - I'd need to play with an example, but I wonder if there's any way to postpone making a decision? Can we not simply say, these names are associated in some way so that user discovers information associated with related names, but avoids the strong assertion that a name is accepted or not. If we separated names and taxa, this would be a fairly easy thing to do I suspect...
          Hide
          Markus Döring added a comment -

          We will basically create this discoverable cluster of names by having the basionym relation established. Then one can see the list of all names in such a group from the basionym and potentially vice versa.

          BUT in order to include these names in occurrence searches, on maps or statics these need to by synonyms in our backbone. Thats how the system works and I think it makes sense that way. It actually gives the fuzzy term synonym some concrete meaning in GBIF.

          PS: Note that I keep calling it basionym cause Im coming from the botanical world. Think of it as protonyms, chresonyms if you prefer that.

          Show
          Markus Döring added a comment - We will basically create this discoverable cluster of names by having the basionym relation established. Then one can see the list of all names in such a group from the basionym and potentially vice versa. BUT in order to include these names in occurrence searches, on maps or statics these need to by synonyms in our backbone. Thats how the system works and I think it makes sense that way. It actually gives the fuzzy term synonym some concrete meaning in GBIF. PS: Note that I keep calling it basionym cause Im coming from the botanical world. Think of it as protonyms, chresonyms if you prefer that.
          Hide
          Markus Döring added a comment - - edited

          A good visualization of "homotypical groups" within synonym list is often found in botanical literature. The CDM software of the BBM does a pretty nice job to show which names are all based on the same type. I have attached a few screenshots of extensive synonymies:
          http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/469b48a7-a2c9-4769-bd69-49b68674ba72/synonymy
          http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/209399b6-0d3c-4f5a-9f0d-b49ebe0f9403/synonymy
          http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/ccd1ceaf-c100-44a4-ba36-3f83bfed86e6/synonymy

          This synonymy list is gigantic: http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/7b3f0f40-63f2-44a4-a72b-6a8f49dd430f/synonymy

          Show
          Markus Döring added a comment - - edited A good visualization of "homotypical groups" within synonym list is often found in botanical literature. The CDM software of the BBM does a pretty nice job to show which names are all based on the same type. I have attached a few screenshots of extensive synonymies: http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/469b48a7-a2c9-4769-bd69-49b68674ba72/synonymy http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/209399b6-0d3c-4f5a-9f0d-b49ebe0f9403/synonymy http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/ccd1ceaf-c100-44a4-ba36-3f83bfed86e6/synonymy This synonymy list is gigantic: http://cichorieae.e-taxonomy.net/portal/cdm_dataportal/taxon/7b3f0f40-63f2-44a4-a72b-6a8f49dd430f/synonymy
          Hide
          Markus Döring added a comment -

          If there is an accepted name Cichorium intybus L. with a synonym Cichorium glabratum C. Presl
          If then in another source there is an accepted recombination Cichorium intybus subsp. glabratum (C. Presl) Arcang.

          Should the subspecies be accepted in the backbone or become a synonym as the primary source we trust more does not accept C. glabratum which is the basionym based on the same type for the subspecies? I would think so

          Show
          Markus Döring added a comment - If there is an accepted name Cichorium intybus L. with a synonym Cichorium glabratum C. Presl If then in another source there is an accepted recombination Cichorium intybus subsp. glabratum (C. Presl) Arcang. Should the subspecies be accepted in the backbone or become a synonym as the primary source we trust more does not accept C. glabratum which is the basionym based on the same type for the subspecies? I would think so
          Show
          Markus Döring added a comment - Implemented here: https://github.com/gbif/checklistbank/blob/master/checklistbank-cli/src/main/java/org/gbif/checklistbank/nub/NubBuilder.java#L737 test: https://github.com/gbif/checklistbank/blob/master/checklistbank-cli/src/test/java/org/gbif/checklistbank/nub/NubBuilderTest.java#L106 based on these 2 sources: https://github.com/gbif/checklistbank/blob/master/checklistbank-cli/src/test/resources/nub-sources/dataset25.txt https://github.com/gbif/checklistbank/blob/master/checklistbank-cli/src/test/resources/nub-sources/dataset26.txt

            People

            • Assignee:
              Markus Döring
              Reporter:
              Markus Döring
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              Dates

              • Created:
                Updated:
                Resolved: