search

OpenTreeOfLife / reference-taxonomy

Open Tree Reference Taxonomy (OTT) tools
BSD 2-Clause "Simplified" License
11 stars 12 forks source link

Lost taxon? #384

Open snacktavish opened 4 years ago

snacktavish commented 4 years ago

In study 809, tree 1, there is a taxon mapped to 

"otu3260": {
"^ot:originalLabel": "Trichastoma tickelli", 
"^ot:ottId": 3598518, 
"^ot:ottTaxonName": "Trichastoma tickelli"
},

This taxon no longer exists.

Based on this, it looks like used to be named Pellorneum tickelli, which we now have in the taxonomy, https://avibase.bsc-eoc.org/species.jsp?avibaseid=F013EAF41AFB3E4C

https://tree.opentreeoflife.org/taxonomy/browse?id=31193

It shows up in ott3.0/deprecated.tsv 3598518 1 Trichastoma tickelli gbif:5788959 id-retired/name-retired * phylesystem

but it appears we don't package a deprecated id's file with ott3.2?

even if we did - making comparisons form other trees to this tree breaks due to deprecated ids (I'm walking through it, but it looks like there are maybe 35 out of 6668 mapped taxa).

This looks very finicky to fix in the taxon-smashing, as I don't see this synonymy listed in any of our inputs... but I think this problem may be a point in favor of sweeping over existing studies in phylesystem to update forwards, and un-map taxa mapped to deprecated ids.

snacktavish commented 4 years ago

_mostly for my own reference - these are the ottids from the study I am having trouble tracking {'^ot:ottId': 85247, '^ot:originalLabel': 'Vermivora pinus', '^ot:ottTaxonName': 'Vermivora pinus'} {'^ot:ottId': 4130734, '^ot:originalLabel': 'Mesopicos elliotii', '^ot:ottTaxonName': 'Mesopicos elliotii'} {'^ot:ottId': 3598518, '^ot:originalLabel': 'Trichastoma tickelli', '^ot:ottTaxonName': 'Trichastoma tickelli'} {'^ot:ottId': 3598142, '^ot:originalLabel': 'Myrmecocichla cinnamomeiventris', '^ot:ottTaxonName': 'Myrmecocichla cinnamomeiventris'} {'^ot:ottId': 3598144, '^ot:originalLabel': 'Myrmecocichla arnoti', '^ot:ottTaxonName': 'Myrmecocichla arnoti'} {'^ot:ottId': 3597470, '^ot:originalLabel': 'Petronia brachydactyla', '^ot:ottTaxonName': 'Petronia brachydactyla'} {'^ot:ottId': 3599175, '^ot:originalLabel': 'Zimmerius flavidifrons', '^ot:ottTaxonName': 'Zimmerius flavidifrons'} {'^ot:ottId': 3595827, '^ot:originalLabel': 'Collocalia mearnsi', '^ot:ottTaxonName': 'Collocalia mearnsi'} {'^ot:ottId': 5342863, '^ot:originalLabel': 'Collocalia spodiopygia', '^ot:ottTaxonName': 'Collocalia spodiopygia'} {'^ot:ottId': 3595830, '^ot:originalLabel': 'Collocalia papuensis', '^ot:ottTaxonName': 'Collocalia papuensis'} {'^ot:ottId': 4130281, '^ot:originalLabel': 'Phaenicophaeus calyorhynchus', '^ot:ottTaxonName': 'Rhamphococcyx calyorhynchus'} {'^ot:ottId': 3598687, '^ot:originalLabel': 'Parus davidi', '^ot:ottTaxonName': 'Parus davidi'} {'^ot:ottId': 4947596, '^ot:originalLabel': 'Bernieria apperti', '^ot:ottTaxonName': 'Bernieria apperti'} {'^ot:ottId': 4947598, '^ot:originalLabel': 'Bernieria tenebrosa', '^ot:ottTaxonName': 'Bernieria tenebrosa'} {'^ot:ottId': 5857013, '^ot:originalLabel': 'Strigops habroptila', '^ot:ottTaxonName': 'Strigops habroptila'} {'^ot:ottId': 3598428, '^ot:originalLabel': 'Alcippe manipurensis', '^ot:ottTaxonName': 'Alcippe manipurensis'} {'^ot:ottId': 3598430, '^ot:originalLabel': 'Alcippe formosana', '^ot:ottTaxonName': 'Alcippe formosana'} {'^ot:ottId': 4947597, '^ot:originalLabel': 'Bernieria cinereiceps', '^ot:ottTaxonName': 'Bernieria cinereiceps'} {'^ot:ottId': 324663, '^ot:originalLabel': 'Miliaria calandra', '^ot:ottTaxonName': 'Miliaria calandra'} {'^ot:ottId': 4947755, '^ot:originalLabel': 'Monarcha godeffroyi', '^ot:ottTaxonName': 'Monarcha godeffroyi'} {'^ot:ottId': 4131465, '^ot:originalLabel': 'Eremopsaltria mongolicus', '^ot:ottTaxonName': 'Eremopsaltria mongolicus'} {'^ot:ottId': 3597364, '^ot:originalLabel': 'Rhodopechys obsoletus', '^ot:ottTaxonName': 'Rhodopechys obsoletus'} {'^ot:ottId': 3598221, '^ot:originalLabel': 'Oenanthe bifasciata', '^ot:ottTaxonName': 'Oenanthe bifasciata'} {'^ot:ottId': 3598850, '^ot:originalLabel': 'Camaroptera simplex', '^ot:ottTaxonName': 'Camaroptera simplex'} {'^ot:ottId': 4947706, '^ot:originalLabel': 'Turdinus macrodactylus', '^ot:ottTaxonName': 'Turdinus macrodactylus'} {'^ot:ottId': 3600157, '^ot:originalLabel': 'Megalaima faber', '^ot:ottTaxonName': 'Megalaima faber'} {'^ot:ottId': 3600257, '^ot:originalLabel': 'Thripias pyrrhogaster', '^ot:ottTaxonName': 'Thripias pyrrhogaster'} {'^ot:ottId': 3597827, '^ot:originalLabel': 'Eurochelidon sirintarae', '^ot:ottTaxonName': 'Eurochelidon sirintarae'} {'^ot:ottId': 4130271, '^ot:originalLabel': 'Coccycua cinerea', '^ot:ottTaxonName': 'Coccycua cinerea'} {'^ot:ottId': 4130270, '^ot:originalLabel': 'Coccycua pumila', '^ot:ottTaxonName': 'Coccycua pumila'} {'^ot:ottId': 5857032, '^ot:originalLabel': 'Pyrilia pulchra', '^ot:ottTaxonName': 'Pyrilia pulchra'} {'^ot:ottId': 5857031, '^ot:originalLabel': 'Pyrilia haematotis', '^ot:ottTaxonName': 'Pyrilia haematotis'} {'^ot:ottId': 5857029, '^ot:originalLabel': 'Pyrilia pyrilia', '^ot:ottTaxonName': 'Pyrilia pyrilia'} {'^ot:ottId': 3599403, '^ot:originalLabel': 'Amaurocichla bocagei', '^ot:ottTaxonName': 'Amaurocichla bocagei'} {'^ot:ottId': 3600769, '^ot:originalLabel': 'Bucorvus cafer', '^ot:ottTaxonName': 'Bucorvus cafer'}