Problems with Aves:Parulidae in ott2

[josephwb]

A few issues with the New World Warblers (Parulidae) in ott2.

I. Seems like it was split.
GBIF: Parulidae family gbif:5263 (8 taxa)
NCBI: Parulini tribe ncbi:400782 (230 taxa)

The GBIF name and rank is correct. "Parulini" is a synonym.

This is how things are arranged:
GBIF: Parulidae -> Passeriformes
NCBI: Parulini -> Emberizinae -> Fringillidae -> Passeroidea -> Passeriformes

In this case, gbif actually gets it right; the ncbi taxonomy is woefully out of date. Nevertheless, Parulidae and Parulini should be considered the same taxon.

II. Genus Parkesia (with species Parkesia noveboracensis and Parkesia motacilla) are listed with only gbif ids, despite being in ncbi.

III. The remaining 5 gbif taxa appear invalid (and are also "orphans"):
uid parent_uid name rank sourceinfo
4132020 3599390 Hemicocichla genus gbif:4846050
4132024 3599390 Helminthophila genus gbif:4846049
4132025 3599390 Enicocichla genus gbif:4846048
4132026 3599390 Henicocichla genus gbif:4846045
4132027 3599390 Exochocicla genus gbif:4846047

IV. Synonyms:
Oporornis philadelphia species ncbi:245564,gbif:2489607
Geothlypis philadelphia species gbif:5789148

Oporornis formosus species ncbi:182909,gbif:2489606
Geothlypis formosa species gbif:6093586

All "Setophaga" and "Dendroica" taxa sharing species name:
fusca, pityophila, plumbea, tigrina, townsendi.
This is a tricky problem, as very recently it has been suggested that Dendroica be subsumed completely into Setophaga (indeed, ncbi redirects there now).

[jar398]

Is there any general, maintainable solution to this problem, such as downloading a good bird taxonomy from somewhere? Or are we stuck doing a bunch of manual edits?

The Parkesia case is completely baffling. I just loaded a fresh taxonomy dump from NCBI, and the string "Parkesia" doesn't occur in any of the .dmp files. Neither does "Parulidae". The identifier for Parulidae occurs many times, but the id for Parkesia (from the web site) doesn't occur at all.

bash-3.2$ grep "Parkesia" ncbi/.dmp
bash-3.2$ grep "Parulidae" ncbi/.dmp
bash-3.2$ grep " 400782 " ncbi/.dmp | wc
26 625 2081
bash-3.2$ grep 1329414 ncbi/.dmp
bash-3.2$

[jar398]

Oops, ignore that comment, I was looking at an old version of NCBI.

ncbi/names.dmp:400782 | Parulidae | | scientific name |

[josephwb]

For my own interests I am compiling and mapping various bird taxonomies. I
can certainly provide something for you. I prefer to use the IOC World Bird
List (http://www.worldbirdnames.org/) myself; it is complete, up to date,
and includes extinct taxa. Of course, they are just about to update... But
3 days from now, not indeterminate.

Would this be useful to you?

JWB.

On 27 June 2013 13:00, Jonathan A Rees notifications@github.com wrote:

Oops, ignore that comment, I was looking at an old version of NCBI.

ncbi/names.dmp:400782 | Parulidae | | scientific name |

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/34#issuecomment-20137951
.

[jar398]

If you can find a dump of the world bird list I can look into including it. 60 seconds of search didn't turn it up.

I spoke to Markus at GBIF and he says he plans to include it in GBIF.

[jar398]

Found a DCA here:
http://dl.dropbox.com/u/457027/iocwbn.zip
linked from
http://www.gbif.org/dataset/c696e5ee-9088-4d11-bdae-ab88daffab78

[jar398]

I am going to fold this issue into OpenTreeOfLife/reference-taxonomy#41 which is basically "get the bird list".