globalbioticinteractions / nomer

maps identifiers and names to other identifiers and names
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unexpected _homonym suffixes in [nomer list discoverlife] #63

Closed jhpoelen closed 2 years ago

jhpoelen commented 3 years ago

as reported by @seltmann in https://github.com/globalbioticinteractions/nomer/issues/58#issuecomment-968056591 .

See complete list (63 in total) of attached _homonym matches from the

$ nomer list discoverlife | grep _homonym | gzip > unexpected_homonyms.tsv.gz

unexpected_homonyms.tsv.gz

jhpoelen commented 3 years ago

Note that this affects 63 out of nomer list discoverlife | wc -l 50621 name relations.

jhpoelen commented 3 years ago

@seltmann when discoverlife says:

<tr bgcolor=\"#f0f0f0\">\n" +
                "            <td>\n" +
                "                 \n" +
                "              <i>\n" +
                "                <a href=\"/mp/20q?search=Anthidiellum+boreale_homonym\" target=\"_self\">\n" +
                "                  Anthidiellum boreale_homonym\n" +
                "                </a>\n" +
                "              </i>\n" +
                "              <font size=\"-1\" face=\"sans-serif\">\n" +
                "                Wu, 2004\n" +
                "              </font>\n" +
                "               -- \n" +
                "              <i>\n" +
                "                Anthidiellum (Anthidiellum) borealis_homonym \n" +
                "              </i>\n" +
                "              Wu, 2004\n" +
                "            </td>\n" +
                "          </tr>\n

How would you translate this into the name relations?

Would it look like:

Anthidiellum boreale | has accepted name | Anthidiellum boreale
Anthidiellum boreale | homonym of | ...
Anthidiellum (Anthidiellum) borealis | synonym of | Anthidiellum boreale
Anthidiellum (Anthidiellum) borealis | homonym of | ...

?

seltmann commented 3 years ago

@jhpoelen wow, I am not sure.

Since they are both homonyms, neither are valid and it looks like they are homonyms of each other.

Anthidiellum boreale homonym of Anthidiellum (Anthidiellum) borealis

Anthidiellum (Anthidiellum) borealis homonym of Anthidiellum boreale

jhpoelen commented 3 years ago

Ok, so if two names with _homonym suffixes are related, and they have the same name (not authorship), then they are homonyms of each other.

jhpoelen commented 3 years ago

And they are not accepted names.

jhpoelen commented 3 years ago

Nor are they synonyms.

jhpoelen commented 2 years ago

@seltmann I'd like to better understand you interpretation of this discoverlife homonym business.

@jhpoelen wow, I am not sure.

I'd rather spend a little more time on these remaining issues (63 out of about 50k names), than make some fix that we'll end up changing afterwards.

seltmann commented 2 years ago

@jhpoelen you are correct. They should only be considered homonyms, not synonyms or accepted names.

jhpoelen commented 2 years ago

@seltmann thanks for clarifying. I am assuming that the discoverlife folks added homonyms to say something like: do not use this name, because it is a homonym.

Why not simply ignore all homonyms?

jhpoelen commented 2 years ago

@seltmann I did some more work on these discoverlife homonyms and found that my interpretation (e.g., homonyms cannot be accepted names) does not match with the redirect of

https://www.discoverlife.org/mp/20q?search=Proteriades+similis

to

the Hoplitis similis_homonym page.

Please advise on the interpretation of this redirect and included page.

See attached screenshot.

Screenshot from 2021-11-23 14-48-12

jhpoelen commented 2 years ago

@seltmann Another pass at appropriate homonym handling can be found in Nomer v0.2.9 . Please review.