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Open Tree Reference Taxonomy (OTT) tools
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Ranks out of order #5

Open jar398 opened 10 years ago

jar398 commented 10 years ago

Moving this issue here from opentree repo https://github.com/OpenTreeOfLife/opentree/issues/73

Ideally each one of these should be checked, but at the very least those cases where the two taxa come from different taxonomies need scrutiny, since they probably reflect incorrect mappings from the one taxonomy to the other. Especially look at Foraminifera.

* Ranks out of order: (4948698=ncbi:1338366 Cladistia) genus has child (458427=ncbi:8288 Polypteriformes) order * Ranks out of order: (3655460=gbif:4872229 Ophiurinidae) family has child (258604=ncbi:133711 Ophiurina) suborder * Ranks out of order: (182610=ncbi:351107 Cryptobranchia) genus has child (4958364=gbif:4304694. Calycidorididae) family * Ranks out of order: (2850721=gbif:4587706 Nuculoidea) genus has child (2850730=gbif:4587862 Nucularcidae) family * Ranks out of order: (4969615=gbif:3252101 Rhynchonellidae) family has child (795939=ncbi:151154 Rhynchonelloidea) superfamily * Ranks out of order: (4163996=gbif:4865225 Chonetoidea) genus has child (4163997=gbif:4869637 Chonostrophiidae) family * Ranks out of order: (150283=ncbi:881521 Alydus calcaratus) species has child (5022513=gbif:3265607 Camptopus) genus * Ranks out of order: (639810=ncbi:33353 Leptopodomorpha) genus has child (232685=ncbi:236430 Aepophilidae) family * Ranks out of order: (866089=ncbi:33365 Clypeorrhyncha) genus has child (627449=ncbi:33368 Membracoidea) superfamily * Ranks out of order: (323135=ncbi:153011 Asphondyliidi) genus has child (323134=ncbi:153010 Asphondyliini) tribe * Ranks out of order: (496622=ncbi:52723 Cecidomyiidi) genus has child (318540=ncbi:71814 Cecidomyiini) tribe * Ranks out of order: (36637=ncbi:44543 Nyssorhynchus) subgenus has child (905897=ncbi:874512 Myzorhynchella) genus * Ranks out of order: (557466=ncbi:44534 Cellia) subgenus has child (13908=ncbi:262669 Paramyzomyia) genus * Ranks out of order: (610085=ncbi:71543 Lebiomorpha) genus has child (996666=ncbi:60748 Lachnophorini) tribe * Ranks out of order: (896768=ncbi:96841 Flabellifera) genus has child (704129=ncbi:155695 Corallanidae) family * Ranks out of order: (69277=ncbi:92068 Hydracarina) genus has child (103239=ncbi:257019 Hygrobatoidea) superfamily * Ranks out of order: (1041449=ncbi:6849 Limulus) genus has child (5128446=gbif:3267257 Strabopidae) family * Ranks out of order: (874786=ncbi:166251 Eukalyptorhynchia) genus has child (52264=ncbi:297398 Cicerinidae) family * Ranks out of order: (302424=silva:L26446/#4 Ciliophora) genus has child (940284=silva:L31517/#5 Postciliodesmatophora) subphylum * Ranks out of order: (5246810=silva:AB191418/#4 Protalveolata) class has child (1008711=silva:AB721060/#5 Chromerida) phylum * Ranks out of order: (936399=silva:X86094/#5 Foraminifera) class has child (137898=ncbi:212500 Xenophyophora) phylum * Ranks out of order: (45752=silva:AB178580/#5 Acantharia) genus has child (45760=silva:AB178580/#6 Symphyacanthida) order * Ranks out of order: (4972641=silva:X86094/#4 Retaria) genus has child (936399=silva:X86094/#5 Foraminifera) class * Ranks out of order: (5246154=gbif:232 Haplosporea) class has child (858063=silva:U20320/#6 Haplosporida) phylum * Ranks out of order: (4796811=if:99034 Aconchulinida) genus has child (5157203=gbif:6789158. Paulinellideae) family * Ranks out of order: (547775=silva:AB594754 Salmonella enterica subsp. enterica) subspecies has child (1017410=ncbi:140099 Salmonella enterica subsp. enter\ ica serovar Virginia) species

jar398 commented 10 years ago

In recent builds there are only four cases: * Ranks out of order: (gbif:4865225 Chonetoidea) genus has child (gbif:4869637 Chonostrophiidae) family * Ranks out of order: (gbif:1010609 Limulus) genus has child (gbif:3267257 Strabopidae) family * Ranks out of order: (gbif:2050173 Alydus calcaratus) species has child (gbif:3265607 Camptopus) genus * Ranks out of order: (gbif:4587706 Nuculoidea) genus has child (gbif:4587862 Nucularcidae) family These should probably all get manual scrutiny.