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  1. Portal
  2. POR-3071

Over 168.000 species homonyms in the backbone for real?

    Details

    • Type: Bug Bug
    • Status: Open
    • Priority: Critical Critical
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Checklistbank
    • Labels:

      Description

      There are over 168.000 species homonyms in the backbone, accounting for over 98 million ocurrences which seems a lot. Investigate if thats good. key list attached

        Gliffy Diagrams

        1. homonym-ids.txt
          3.63 MB
          Markus Döring

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          Activity

          Hide
          Roderic D. M. Page added a comment -

          Not sure that I follow this, the "homonyms" all seem to have different authors, e.g.

          1 6910 UNRANKED ? apicalis 2

          {7425198,8133285}

          {"? apicalis Enderlein, 1920","? apicalis Szepligeti, 1906"}

          Why would these be considered to be homonyms?

          Show
          Roderic D. M. Page added a comment - Not sure that I follow this, the "homonyms" all seem to have different authors, e.g. 1 6910 UNRANKED ? apicalis 2 {7425198,8133285} {"? apicalis Enderlein, 1920","? apicalis Szepligeti, 1906"} Why would these be considered to be homonyms?
          Hide
          Markus Döring added a comment -

          Maybe I used the term homonym badly, but I was looking into how many names exist more than once if you ignore the authorship. This is currently causing some problem for the occurrence species matching (POR-2768) and I wanted to get an idea how large the problem is. And it is quite large affecting 98 million occurrence records!

          Show
          Markus Döring added a comment - Maybe I used the term homonym badly, but I was looking into how many names exist more than once if you ignore the authorship. This is currently causing some problem for the occurrence species matching ( POR-2768 ) and I wanted to get an idea how large the problem is. And it is quite large affecting 98 million occurrence records!
          Hide
          Markus Döring added a comment - - edited

          probably drastically reduced by https://github.com/gbif/checklistbank/commit/a14506422848bcba7b111b34689f7b1790f8035d

          The family was required to match up which often is not the case

          Show
          Markus Döring added a comment - - edited probably drastically reduced by https://github.com/gbif/checklistbank/commit/a14506422848bcba7b111b34689f7b1790f8035d The family was required to match up which often is not the case
          Hide
          Markus Döring added a comment -

          In the improved nub there are 312.127 homonyms now, 210.202 for species. This includes changed sources, e.g. 32k new names coming from new Plazi sources and an updated CoL. On first glance most of them look correct in the sense that they do differ by the authorship and there is no name without authors anymore.


          Still lots of basionym duplications exist because they are just lonely epithets with different authors.
          For example: "? acuminatus Motschulsky, 1844" and "? acuminatus Emerton, 1913"

          These account for 2229 homonym canonical names


          By far the most seem to be genuine different names. Examples:

          Abgrallaspis flabellata {8384876,2088164}       {"Abgrallaspis flabellata (Ferris, 1938)","Abgrallaspis flabellata Davidson, 1964"}
          Abgrallaspis fraxini    {2088195,8163185}       {"Abgrallaspis fraxini Balachowsky, 1953","Abgrallaspis fraxini (McKenzie, 1944)"}
          Abgrallaspis furcillae  {8271615,2088199}       {"Abgrallaspis furcillae (Brain, 1918)","Abgrallaspis furcillae Balachowsky, 1956"}
          Abgrallaspis ithacae    {8071717,2088170}       {"Abgrallaspis ithacae Davidson, 1964","Abgrallaspis ithacae (Ferris, 1938)"}
          Abgrallaspis latastei   {8115977,2088206}       {"Abgrallaspis latastei (Cockerell, 1894)","Abgrallaspis latastei Komosinska, 1969"}
          
           Acanthoderes curvistriata | 1152354 | SPECIES | Acanthoderes (Psapharochrus) curvistriata Tippmann, 1960
           Acanthoderes curvistriata | 8028112 | SPECIES | Acanthoderes curvistriata Zajciw, 1969
           Acanthoderes curvistriata | 8381622 | SPECIES | Acanthoderes (Psapharochrus) curvistriata Gilmour, 1965
           Acanthoderes curvistriata | 7522158 | SPECIES | Acanthoderes curvistriata Júlio, Giorgi & Monné, 2000
          

          Many of these correct homonyms come from ex or in author citations. Maybe there is something mixed up in the sources sometimes?
          Examples:

           Acacia sentis   | 2979108 | SPECIES | Acacia sentis F.Muell.
           Acacia sentis   | 7536326 | SPECIES | Acacia sentis F. Muell. ex Benth.
          
           Acacia sirissa  | 8170030 | SPECIES | Acacia sirissa Buch.-Ham.
           Acacia sirissa  | 7629537 | SPECIES | Acacia sirissa Buch.-Ham. ex Wall.
           Acacia sirissa  | 3973437 | SPECIES | Acacia sirissa Buch.-Ham. ex Voigt
          

          There are only few suspicous looking names. This is truely the same one:

          Abacetus reflexicollis                       | 8026980 | SPECIES | Abacetus reflexicollis (Fairmaire, 1887)
          Abacetus reflexicollis                       | 8433053 | SPECIES | Abacetus reflexicollis (Fairmaire, 1887)
          

          Then there are a few that look like the author comparison didnt do a good job:

           Abutilon anderssonianum                      | 7879667 | SPECIES | Abutilon anderssonianum Garcke in Andersson
           Abutilon anderssonianum                      | 3940391 | SPECIES | Abutilon anderssonianum Garcke ex Andersson
          
           Abutilon halophilum                          | 3938486 | SPECIES | Abutilon halophilum F.Muell.
           Abutilon halophilum                          | 7930829 | SPECIES | Abutilon halophilum F. Müll.
          

          159 names are found in ranks above genus. With the exception of few these all have at least one genus counterpart:

           KINGDOM | Archaea               
           KINGDOM | Bacteria              
           PHYLUM  | Acanthocephala        
           PHYLUM  | Actinobacteria        
           PHYLUM  | Aquificae             
           PHYLUM  | Bryozoa               
           PHYLUM  | Cephalorhyncha        
           PHYLUM  | Chaetognatha          
           PHYLUM  | Chlamydiae            
           PHYLUM  | Chrysiogenetes        
           PHYLUM  | Ciliophora            
           PHYLUM  | Ctenophora            
           PHYLUM  | Deferribacteres       
           PHYLUM  | Elusimicrobia         
           PHYLUM  | Foraminifera          
           PHYLUM  | Gastrotricha          
           PHYLUM  | Gemmatimonadetes      
           PHYLUM  | Microsporidia         
           PHYLUM  | Mollusca              
           PHYLUM  | Nematoda              
           PHYLUM  | Nitrospira            
           PHYLUM  | Onychophora           
           PHYLUM  | Pteridophyta          
           PHYLUM  | Rotifera              
           PHYLUM  | Thermodesulfobacteria 
           PHYLUM  | Thermotogae           
           CLASS   | Acantharia            
           CLASS   | Actinobacteria        
           CLASS   | Amphibia              
           CLASS   | Appendicularia        
           CLASS   | Aquificae             
           CLASS   | Aves                  
           CLASS   | Chlamydiae            
           CLASS   | Chrysiogenetes        
           CLASS   | Deferribacteres       
           CLASS   | Dothideales           
           CLASS   | Elusimicrobia         
           CLASS   | Euglenida             
           CLASS   | Gemmatimonadetes      
           CLASS   | Lingulata             
           CLASS   | Myxomycetes           
           CLASS   | Nitrospira            
           CLASS   | Oligochaeta           
           CLASS   | Ostracoda             
           CLASS   | Polychaeta            
           CLASS   | Polycystina           
           CLASS   | Reptilia              
           CLASS   | Saccharomycetes       
           CLASS   | Thermodesulfobacteria 
           CLASS   | Thermotogae           
           ORDER   | Amphipoda             
           ORDER   | Antipatharia          
           ORDER   | Anura                 
           ORDER   | Blattodea             
           ORDER   | Brachypoda            
           ORDER   | Cingulata             
           ORDER   | Coccoideaceae         
           ORDER   | Coleoptera            
           ORDER   | Diplura               
           ORDER   | Diptera               
           ORDER   | Dothideales           
           ORDER   | Euglenida             
           ORDER   | Gelidiales            
           ORDER   | Hemiptera             
           ORDER   | Heteropoda            
           ORDER   | Hygrophila            
           ORDER   | Hymenoptera           
           ORDER   | Isopoda               
           ORDER   | Isoptera              
           ORDER   | Laurida               
           ORDER   | Lepidoptera           
           ORDER   | Lobata                
           ORDER   | Mecoptera             
           ORDER   | Medeolariales         
           ORDER   | Megaloptera           
           ORDER   | Mytiloida             
           ORDER   | Neuroptera            
           ORDER   | Octopoda              
           ORDER   | Odonata               
           ORDER   | Parachela             
           ORDER   | Pholidota             
           ORDER   | Phragmophora          
           ORDER   | Pilosa                
           ORDER   | Plecoptera            
           ORDER   | Proboscidea           
           ORDER   | Pygophora             
           ORDER   | Scandentia            
           ORDER   | Scorpiones            
           ORDER   | Silicoflagellida      
           ORDER   | Siphonaptera          
           ORDER   | Squamata              
           ORDER   | Trichoptera           
           FAMILY  | Acrolepidae           
           FAMILY  | Aculeata              
           FAMILY  | Admetidae             
           FAMILY  | Agaricus familia      
           FAMILY  | Amphibia              
           FAMILY  | Amphipoda             
           FAMILY  | Anura                 
           FAMILY  | Aves                  
           FAMILY  | Biporidae             
           FAMILY  | Blattodea             
           FAMILY  | Bryozoa               
           FAMILY  | Calycanthaceae        
           FAMILY  | Candelariella         
           FAMILY  | Caryophyllaceae       
           FAMILY  | Cerylidae             
           FAMILY  | Chimaeridae           
           FAMILY  | Chondrophora          
           FAMILY  | Clavidae              
           FAMILY  | Coccoideaceae         
           FAMILY  | Coleoptera            
           FAMILY  | Cononotidae           
           FAMILY  | Convallariaceae       
           FAMILY  | Cornirostridae        
           FAMILY  | Ctenacaridae          
           FAMILY  | Dasyscypha            
           FAMILY  | Dehalococcoides       
           FAMILY  | Delphinapteridae      
           FAMILY  | Deximorpha            
           FAMILY  | Dichotoma             
           FAMILY  | Diptera               
           FAMILY  | Ephyridae             
           FAMILY  | Esperiopsidae         
           FAMILY  | Gelidiales            
           FAMILY  | Haliplectidae         
           FAMILY  | Hemiptera             
           FAMILY  | Hymenoptera           
           FAMILY  | Hypochthoniidae       
           FAMILY  | Lemnaceae             
           FAMILY  | Lepidoptera           
           FAMILY  | Leptodactyla          
           FAMILY  | Macropoda             
           FAMILY  | Magnosiopsis          
           FAMILY  | Medeolariales         
           FAMILY  | Mollusca              
           FAMILY  | Nematoda              
           FAMILY  | Nephrolepidaceae      
           FAMILY  | Nephthyidae           
           FAMILY  | Odonata               
           FAMILY  | Ostracoda             
           FAMILY  | Palaeacaridae         
           FAMILY  | Pamphagodes           
           FAMILY  | Pandalidae            
           FAMILY  | Poaceae               
           FAMILY  | Polychelidae          
           FAMILY  | Pteridophyllaceae     
           FAMILY  | Pteridophyta          
           FAMILY  | Reptilia              
           FAMILY  | Scaliolidae           
           FAMILY  | Scorpiones            
           FAMILY  | Stoeckeria            
           FAMILY  | Thecaphora            
           FAMILY  | Trichiidae            
           FAMILY  | Tridactylites         
           FAMILY  | Umboniidae            
           FAMILY  | Urnatellidae          
           FAMILY  | Vanellidae            
           FAMILY  | Xylella               
          
          Show
          Markus Döring added a comment - In the improved nub there are 312.127 homonyms now, 210.202 for species. This includes changed sources, e.g. 32k new names coming from new Plazi sources and an updated CoL. On first glance most of them look correct in the sense that they do differ by the authorship and there is no name without authors anymore. Still lots of basionym duplications exist because they are just lonely epithets with different authors. For example: "? acuminatus Motschulsky, 1844" and "? acuminatus Emerton, 1913" These account for 2229 homonym canonical names By far the most seem to be genuine different names. Examples: Abgrallaspis flabellata {8384876,2088164} {"Abgrallaspis flabellata (Ferris, 1938)","Abgrallaspis flabellata Davidson, 1964"} Abgrallaspis fraxini {2088195,8163185} {"Abgrallaspis fraxini Balachowsky, 1953","Abgrallaspis fraxini (McKenzie, 1944)"} Abgrallaspis furcillae {8271615,2088199} {"Abgrallaspis furcillae (Brain, 1918)","Abgrallaspis furcillae Balachowsky, 1956"} Abgrallaspis ithacae {8071717,2088170} {"Abgrallaspis ithacae Davidson, 1964","Abgrallaspis ithacae (Ferris, 1938)"} Abgrallaspis latastei {8115977,2088206} {"Abgrallaspis latastei (Cockerell, 1894)","Abgrallaspis latastei Komosinska, 1969"} Acanthoderes curvistriata | 1152354 | SPECIES | Acanthoderes (Psapharochrus) curvistriata Tippmann, 1960 Acanthoderes curvistriata | 8028112 | SPECIES | Acanthoderes curvistriata Zajciw, 1969 Acanthoderes curvistriata | 8381622 | SPECIES | Acanthoderes (Psapharochrus) curvistriata Gilmour, 1965 Acanthoderes curvistriata | 7522158 | SPECIES | Acanthoderes curvistriata Júlio, Giorgi & Monné, 2000 Many of these correct homonyms come from ex or in author citations. Maybe there is something mixed up in the sources sometimes? Examples: Acacia sentis | 2979108 | SPECIES | Acacia sentis F.Muell. Acacia sentis | 7536326 | SPECIES | Acacia sentis F. Muell. ex Benth. Acacia sirissa | 8170030 | SPECIES | Acacia sirissa Buch.-Ham. Acacia sirissa | 7629537 | SPECIES | Acacia sirissa Buch.-Ham. ex Wall. Acacia sirissa | 3973437 | SPECIES | Acacia sirissa Buch.-Ham. ex Voigt There are only few suspicous looking names. This is truely the same one: Abacetus reflexicollis | 8026980 | SPECIES | Abacetus reflexicollis (Fairmaire, 1887) Abacetus reflexicollis | 8433053 | SPECIES | Abacetus reflexicollis (Fairmaire, 1887) Then there are a few that look like the author comparison didnt do a good job: Abutilon anderssonianum | 7879667 | SPECIES | Abutilon anderssonianum Garcke in Andersson Abutilon anderssonianum | 3940391 | SPECIES | Abutilon anderssonianum Garcke ex Andersson Abutilon halophilum | 3938486 | SPECIES | Abutilon halophilum F.Muell. Abutilon halophilum | 7930829 | SPECIES | Abutilon halophilum F. Müll. 159 names are found in ranks above genus. With the exception of few these all have at least one genus counterpart: KINGDOM | Archaea KINGDOM | Bacteria PHYLUM | Acanthocephala PHYLUM | Actinobacteria PHYLUM | Aquificae PHYLUM | Bryozoa PHYLUM | Cephalorhyncha PHYLUM | Chaetognatha PHYLUM | Chlamydiae PHYLUM | Chrysiogenetes PHYLUM | Ciliophora PHYLUM | Ctenophora PHYLUM | Deferribacteres PHYLUM | Elusimicrobia PHYLUM | Foraminifera PHYLUM | Gastrotricha PHYLUM | Gemmatimonadetes PHYLUM | Microsporidia PHYLUM | Mollusca PHYLUM | Nematoda PHYLUM | Nitrospira PHYLUM | Onychophora PHYLUM | Pteridophyta PHYLUM | Rotifera PHYLUM | Thermodesulfobacteria PHYLUM | Thermotogae CLASS | Acantharia CLASS | Actinobacteria CLASS | Amphibia CLASS | Appendicularia CLASS | Aquificae CLASS | Aves CLASS | Chlamydiae CLASS | Chrysiogenetes CLASS | Deferribacteres CLASS | Dothideales CLASS | Elusimicrobia CLASS | Euglenida CLASS | Gemmatimonadetes CLASS | Lingulata CLASS | Myxomycetes CLASS | Nitrospira CLASS | Oligochaeta CLASS | Ostracoda CLASS | Polychaeta CLASS | Polycystina CLASS | Reptilia CLASS | Saccharomycetes CLASS | Thermodesulfobacteria CLASS | Thermotogae ORDER | Amphipoda ORDER | Antipatharia ORDER | Anura ORDER | Blattodea ORDER | Brachypoda ORDER | Cingulata ORDER | Coccoideaceae ORDER | Coleoptera ORDER | Diplura ORDER | Diptera ORDER | Dothideales ORDER | Euglenida ORDER | Gelidiales ORDER | Hemiptera ORDER | Heteropoda ORDER | Hygrophila ORDER | Hymenoptera ORDER | Isopoda ORDER | Isoptera ORDER | Laurida ORDER | Lepidoptera ORDER | Lobata ORDER | Mecoptera ORDER | Medeolariales ORDER | Megaloptera ORDER | Mytiloida ORDER | Neuroptera ORDER | Octopoda ORDER | Odonata ORDER | Parachela ORDER | Pholidota ORDER | Phragmophora ORDER | Pilosa ORDER | Plecoptera ORDER | Proboscidea ORDER | Pygophora ORDER | Scandentia ORDER | Scorpiones ORDER | Silicoflagellida ORDER | Siphonaptera ORDER | Squamata ORDER | Trichoptera FAMILY | Acrolepidae FAMILY | Aculeata FAMILY | Admetidae FAMILY | Agaricus familia FAMILY | Amphibia FAMILY | Amphipoda FAMILY | Anura FAMILY | Aves FAMILY | Biporidae FAMILY | Blattodea FAMILY | Bryozoa FAMILY | Calycanthaceae FAMILY | Candelariella FAMILY | Caryophyllaceae FAMILY | Cerylidae FAMILY | Chimaeridae FAMILY | Chondrophora FAMILY | Clavidae FAMILY | Coccoideaceae FAMILY | Coleoptera FAMILY | Cononotidae FAMILY | Convallariaceae FAMILY | Cornirostridae FAMILY | Ctenacaridae FAMILY | Dasyscypha FAMILY | Dehalococcoides FAMILY | Delphinapteridae FAMILY | Deximorpha FAMILY | Dichotoma FAMILY | Diptera FAMILY | Ephyridae FAMILY | Esperiopsidae FAMILY | Gelidiales FAMILY | Haliplectidae FAMILY | Hemiptera FAMILY | Hymenoptera FAMILY | Hypochthoniidae FAMILY | Lemnaceae FAMILY | Lepidoptera FAMILY | Leptodactyla FAMILY | Macropoda FAMILY | Magnosiopsis FAMILY | Medeolariales FAMILY | Mollusca FAMILY | Nematoda FAMILY | Nephrolepidaceae FAMILY | Nephthyidae FAMILY | Odonata FAMILY | Ostracoda FAMILY | Palaeacaridae FAMILY | Pamphagodes FAMILY | Pandalidae FAMILY | Poaceae FAMILY | Polychelidae FAMILY | Pteridophyllaceae FAMILY | Pteridophyta FAMILY | Reptilia FAMILY | Scaliolidae FAMILY | Scorpiones FAMILY | Stoeckeria FAMILY | Thecaphora FAMILY | Trichiidae FAMILY | Tridactylites FAMILY | Umboniidae FAMILY | Urnatellidae FAMILY | Vanellidae FAMILY | Xylella

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            • Assignee:
              Markus Döring
              Reporter:
              Markus Döring
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                Updated: