taxon ranks in discoverlife variety and subspecies

[seltmann]

@jhpoelen there are two cases in the discoverlife taxonomy where the taxon rank should not be species

Tri-nomials (without a var) are considered subspecies. These are two examples of subspecies https://www.discoverlife.org/mp/20q?search=Pseudopanurgus+nebrascensis+timberlakei
Pseudopanurgus nebrascensis timberlakei

OR

https://www.discoverlife.org/mp/20q?search=Protandrena+(Pterosarus)+labrosiformis+distractus
Protandrena (Pterosarus) labrosiformis distractus

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Names (with a var) should be variety Here is an example. https://www.discoverlife.org/mp/20q?search=Psithyrus+(Allopsithyrus)+barbutellus+var+bimaculatus
Psithyrus (Allopsithyrus) barbutellus var bimaculatus

[jhpoelen]

@seltmann Thanks for your suggestions. I added the functionality, only to find out that all the pages linked from the main page appears to be species https://www.discoverlife.org/mp/20q?act=x_checklist&guide=Apoidea_species&flags=HAS . I am probably missing something.

See attached output of

$ nomer list discoverlife | gzip > discoverlife.tsv.gz 

Note that I haven't yet release a new version with latest features.

discoverlife.tsv.gz

[jhpoelen]

Also, note that:

$ cat discoverlife.tsv.gz | grep -v "species" | wc -l
0

Also, note that

$ zcat discoverlife.tsv.gz | grep "Psithyrus.*bimaculatus"
https://www.discoverlife.org/mp/20q?search=Psithyrus+(Allopsithyrus)+barbutellus+var+bimaculatus    Psithyrus (Allopsithyrus) barbutellus var bimaculatus   HOMONYM_OF  no:match    no:match                    
https://www.discoverlife.org/mp/20q?search=Psithyrus+(Metapsithyrus)+campestris+var+bimaculatus Psithyrus (Metapsithyrus) campestris var bimaculatus    SYNONYM_OF  https://www.discoverlife.org/mp/20q?search=Bombus+campestris    Bombus campestris   species     Animalia | Arthropoda | Insecta | Hymenoptera | Apidae | Bombus campestris  https://www.discoverlife.org/mp/20q?search=Animalia | https://www.discoverlife.org/mp/20q?search=Arthropoda | https://www.discoverlife.org/mp/20q?search=Insecta | https://www.discoverlife.org/mp/20q?search=Hymenoptera | https://www.discoverlife.org/mp/20q?search=Apidae | https://www.discoverlife.org/mp/20q?search=Bombus+campestris    kingdom | phylum | class | order | family | species https://www.discoverlife.org/mp/20q?search=Bombus+campestris    
https://www.discoverlife.org/mp/20q?search=Psithyrus+sylvestris+f+bimaculatus   Psithyrus sylvestris f bimaculatus  SYNONYM_OF  https://www.discoverlife.org/mp/20q?search=Bombus+sylvestris    Bombus sylvestris   species     Animalia | Arthropoda | Insecta | Hymenoptera | Apidae | Bombus sylvestris  https://www.discoverlife.org/mp/20q?search=Animalia | https://www.discoverlife.org/mp/20q?search=Arthropoda | https://www.discoverlife.org/mp/20q?search=Insecta | https://www.discoverlife.org/mp/20q?search=Hymenoptera | https://www.discoverlife.org/mp/20q?search=Apidae | https://www.discoverlife.org/mp/20q?search=Bombus+sylvestris    kingdom | phylum | class | order | family | species https://www.discoverlife.org/mp/20q?search=Bombus+sylvestris    

suggesting that your example Psithyrus (Allopsithyrus) barbutellus var bimaculatus is only listed as a homonym, with unmatched name.

[seltmann]

@jhpoelen I thought the rank is for the primary name, not the valid name. You are right that all of the valid names in DiscoverLife are species names, but many of the synonyms are not. I could be wrong about the meaning of the TaxonRank column.

[jhpoelen]

Thanks for providing the context that only species are listed as valid names. The vars, subspecies etc. are being parsed, but they don't show up because the left hand side of the (left name) -[:name_relation]-> (right name) only contains (name,id) , the right hand side has more information.

Perhaps a reason to revisit the map format . . . and include more information on the left hand side (e.g., authorship name, rank, path etc.)

[jhpoelen]

Described functionality available in Nomer v0.2.8 . Please close this issue after review, or share review comments below.

[seltmann]

@jhpoelen looks good upon review. Closing issue.