NONE in discoverlife names for name type

globalbioticinteractions / nomer

maps identifiers and names to other identifiers and names

GNU General Public License v3.0

19 stars 3 forks source link

NONE in discoverlife names for name type #53

Closed seltmann closed 3 years ago

seltmann commented 3 years ago

In a few names in the name type field (i.e. HAS_ACCEPTED_NAME, SYNONYM_OF) NONE appears. For example:

jhpoelen commented 3 years ago

Thanks for sharing your observation about the reported NONE name relations.

From the first example, Allodape clypeata , I make the attached screenshots from https://www.discoverlife.org/mp/20q?search=Allodape+clypeata .

Note that the page resolves to: Allodape obscuripennis Strand, 1915 with related names:

Allodape clypeata Strand, 1915
Allodape clypeata_homonym Friese, 1924

So, at first glance, discoverlife notes that Allodape clypeata Strand, 1915 has homonym Allodape clypeata Friese, 1924 .

Screenshot from 2021-11-01 14-56-52

@seltmann how would you like to have this homonym relationship between Allodape clypeata_homonym and their counter parts be represented in the nomer output?

seltmann commented 3 years ago

@jhpoelen please add HAS_HOMONYM or HOMONYM_OF relationship when explicit _homonym

jhpoelen commented 3 years ago

I added HOMONYM_OF name relationship, see attached output of

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

discoverlife.tsv.gz

note that

$ zcat discoverlife.tsv.gz | grep "HOMONYM" | wc -l
874

and

$ zcat discoverlife.tsv.gz | grep "HOMONYM" | grep "no:match" | wc -l
517

with

$ zcat discoverlife.tsv.gz | grep "HOMONYM" | grep "no:match" | head -n2
https://www.discoverlife.org/mp/20q?search=Allodape+longula Allodape longula    HOMONYM_OF  no:match    no:match                            
https://www.discoverlife.org/mp/20q?search=Amegilla+bicincta    Amegilla bicincta   HOMONYM_OF  no:match    no:match

suggesting that the majority of homonyms found do not have an another (accepted) homonym mentioned in the same corpus. Is this expected?

jhpoelen commented 3 years ago

Also, for some positive examples:

$ zcat discoverlife.tsv.gz | grep "HOMONYM" | grep -v "no:match" | head -n2
https://www.discoverlife.org/mp/20q?search=Allodape+friesei Allodape friesei    HOMONYM_OF  https://www.discoverlife.org/mp/20q?search=Allodape+friesei Allodape friesei    species     Animalia | Arthropoda | Insecta | Hymenoptera | Apidae | Allodape friesei   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=Allodape+friesei kingdom | phylum | class | order | family | species https://www.discoverlife.org/mp/20q?search=Allodape+friesei 
https://www.discoverlife.org/mp/20q?search=Allodape+obscuripennis   Allodape obscuripennis  HOMONYM_OF  https://www.discoverlife.org/mp/20q?search=Allodape+obscuripennis   Allodape obscuripennis  species     Animalia | Arthropoda | Insecta | Hymenoptera | Apidae | Allodape obscuripennis 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=Allodape+obscuripennis   kingdom | phylum | class | order | family | species https://www.discoverlife.org/mp/20q?search=Allodape+obscuripennis

jhpoelen commented 3 years ago

Also, please note that the NONE relationship no longer occur:

$ nomer list discoverlife | grep "NONE" | wc -l
using matcher [discoverlife-taxon]
0