# Tony Rees 2014-01-29
# https://groups.google.com/d/msg/opentreeoflife/SrI7KpPgoPQ/wTeD17GzOGoJ
ott.taxon('Trigonocarpales').extinct()
#Pinophyta and daughters need to be deleted; - Bryan 2014-01-28
#Lycopsida and daughters need to be deleted;
#Pteridophyta and daughters need to be deleted;
#Gymnospermophyta and daughters need to be deleted;
ott.taxon('Pinophyta', 'Chloroplastida').incertaeSedis()
ott.taxon('Pteridophyta', 'Chloroplastida').incertaeSedis()
ott.taxon('Gymnospermophyta', 'Chloroplastida').incertaeSedis()
# Patches from the Katz lab to give decent parents to taxa classified
# as Chromista or Protozoa
print '-- Chromista/Protozoa spreadsheet from Katz lab --'
fixChromista(ott)
print '-- more patches --'
# From Laura and Dail on 5 Feb 2014
# https://groups.google.com/d/msg/opentreeoflife/a69fdC-N6pY/y9QLqdqACawJ
ott.taxon('Chlamydiae/Verrucomicrobia group').rename('Verrucomicrobia group')
ott.taxon('Heterolobosea',
'Discicristata').absorb(ott.taxon('Heterolobosea', 'Percolozoa'))
ott.taxon('Excavata', 'Eukaryota').take(ott.taxon('Oxymonadida', 'Eukaryota'))
# Work in progress - Joseph
ott.taxon('Reptilia').hide()
# Chris Owen patches 2014-01-30, attachment to email to JAR and SAS
ott.taxon('Protostomia').take(ott.taxon('Chaetognatha', 'Deuterostomia'))
def patch_ott(ott):
# 2014-01-27 Joseph: Quiscalus is incorrectly in
# Fringillidae instead of Icteridae. NCBI is wrong, GBIF is correct.
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/87
ott.taxon('Icteridae').take(ott.taxon('Quiscalus', 'Fringillidae'))
# Misspelling in GBIF... seems to already be known
# Stephen email to JAR 2014-01-26
# ott.taxon("Torricelliaceae").synonym("Toricelliaceae")
# Joseph 2014-01-27 https://code.google.com/p/gbif-ecat/issues/detail?id=104
ott.taxon('Parulidae').take(ott.taxon('Myiothlypis', 'Passeriformes'))
# I don't get why this one isn't a major_rank_conflict !? - bug. (so to speak.)
ott.taxon('Blattodea').take(ott.taxon('Phyllodromiidae'))
# See above (occurs in both IF and GBIF). Also see issue #67
ott.taxon('Chlamydotomus').incertaeSedis()
# Joseph Brown 2014-01-27
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/87
# Occurs as Sakesphorus bernardi in ncbi, gbif, irmng, as Thamnophilus bernardi in bgif
ott.taxon('Thamnophilus bernardi').absorb(ott.taxon('Sakesphorus bernardi'))
ott.taxon('Thamnophilus melanonotus').absorb(ott.taxon('Sakesphorus melanonotus'))
ott.taxon('Thamnophilus melanothorax').absorb(ott.taxon('Sakesphorus melanothorax'))
ott.taxon('Thamnophilus bernardi').synonym('Sakesphorus bernardi')
ott.taxon('Thamnophilus melanonotus').synonym('Sakesphorus melanonotus')
ott.taxon('Thamnophilus melanothorax').synonym('Sakesphorus melanothorax')
# Mammals - groups cluttering basal part of tree
ott.taxon('Litopterna').extinct()
ott.taxon('Notoungulata').extinct()
# Artiodactyls
ott.taxon('Boreameryx').extinct()
ott.taxon('Thandaungia').extinct()
ott.taxon('Limeryx').extinct()
ott.taxon('Delahomeryx').extinct()
ott.taxon('Krabitherium').extinct()
ott.taxon('Discritochoerus').extinct()
ott.taxon('Brachyhyops').extinct()
# Not fungi - Romina 2014-01-28
# ott.taxon('Adlerocystis').show() - it's Chromista ...
# Index Fungorum says Adlerocystis is Chromista, but I don't believe it
# ott.taxon('Chromista').take(ott.taxon('Adlerocystis','Fungi'))
# Adlerocystis seems to be a fungus, but unclassified - JAR 2014-03-10
ott.taxon('Adlerocystis').incertaeSedis()
# "No clear identity has emerged"
# http://forestis.rsvs.ulaval.ca/REFERENCES_X/phylogeny.arizona.edu/tree/eukaryotes/accessory/parasitic.html
# Need to hide it because it clutters base of Fungi
if ott.maybeTaxon('Amylophagus','Fungi') != None:
ott.taxon('Amylophagus','Fungi').incertaeSedis()
# Bad synonym - Tony Rees 2014-01-28
# https://groups.google.com/d/msg/opentreeoflife/SrI7KpPgoPQ/ihooRUSayXkJ
if ott.maybeTaxon('Lemania pluvialis') != None:
ott.taxon('Lemania pluvialis').prune("make-ott.py")
# Tony Rees 2014-01-29
# https://groups.google.com/d/msg/opentreeoflife/SrI7KpPgoPQ/wTeD17GzOGoJ
trigo = ott.maybeTaxon('Trigonocarpales')
if trigo != None: trigo.extinct()
#Pinophyta and daughters need to be deleted; - Bryan 2014-01-28
#Lycopsida and daughters need to be deleted;
#Pteridophyta and daughters need to be deleted;
#Gymnospermophyta and daughters need to be deleted;
for name in ['Pinophyta', 'Pteridophyta', 'Gymnospermophyta']:
if ott.maybeTaxon(name,'Chloroplastida'):
ott.taxon(name,'Chloroplastida').incertaeSedis()
# Patches from the Katz lab to give decent parents to taxa classified
# as Chromista or Protozoa
print '-- Chromista/Protozoa spreadsheet from Katz lab --'
fixChromista(ott)
print '-- more patches --'
# From Laura and Dail on 5 Feb 2014
# https://groups.google.com/d/msg/opentreeoflife/a69fdC-N6pY/y9QLqdqACawJ
tax = ott.maybeTaxon('Chlamydiae/Verrucomicrobia group')
if tax != None and tax.name != 'Bacteria':
tax.rename('Verrucomicrobia group')
ott.taxon('Heterolobosea','Discicristata').absorb(ott.taxon('Heterolobosea','Percolozoa'))
ott.taxon('Excavata','Eukaryota').take(ott.taxon('Oxymonadida','Eukaryota'))
# There is no Reptilia in OTT 2.9, so this can probably be deleted
if ott.maybeTaxon('Reptilia') != None:
ott.taxon('Reptilia').hide()
# Chris Owen patches 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/88
ott.taxon('Protostomia').take(ott.taxon('Chaetognatha','Deuterostomia'))
ott.taxon('Lophotrochozoa').take(ott.taxon('Platyhelminthes'))
ott.taxon('Polychaeta','Annelida').take(ott.taxon('Myzostomida'))
ott.taxon('Lophotrochozoa').take(ott.taxon('Gnathostomulida'))
# https://dx.doi.org/10.1007/s13127-011-0044-4
# Not in deuterostomes
ott.taxon('Bilateria').take(ott.taxon('Xenacoelomorpha'))
# 8) Stauromedusae should be a class (Staurozoa; Marques and Collins 2004) and should be removed from Scyphozoa
ott.taxon('Cnidaria').take(ott.taxon('Stauromedusae'))
ott.taxon('Copepoda').take(ott.taxon('Prionodiaptomus'))
# Bryan Drew patches 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/89
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90
ott.taxon('Scapaniaceae').absorb(ott.taxon('Lophoziaceae'))
ott.taxon('Salazaria mexicana').rename('Scutellaria mexicana')
# One Scutellaria is in Lamiaceae; the other is a fungus.
# IRMNG's Salazaria 1288740 is in Lamiales, and is a synonym of Scutellaria.
##### RECOVER THIS SOMEHOW --
# ott.taxon('Scutellaria','Lamiaceae').absorb(ott.image(gbif.taxon('Salazaria')))
# IRMNG 1288740 not in newer IRMNG
if False:
sal = irmng.maybeTaxon('1288740')
if sal != None:
ott.taxon('Scutellaria','Lamiaceae').absorb(ott.image(sal)) #Salazaria
# Make an order Boraginales that contains Boraginaceae + Hydrophyllaceae
# http://dx.doi.org/10.1111/cla.12061
# Bryan Drew 2013-09-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/91
ott.taxon('Boraginaceae').absorb(ott.taxon('Hydrophyllaceae'))
ott.taxon('Boraginales').take(ott.taxon('Boraginaceae'))
ott.taxon('lamiids').take(ott.taxon('Boraginales'))
# Bryan Drew 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90
# Vahlia 26024 <- Vahliaceae 23372 <- lammids 596112 (was incertae sedis)
ott.taxon('lamiids').take(ott.taxon('Vahliaceae'))
# Bryan Drew 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90
# http://www.sciencedirect.com/science/article/pii/S0034666703000927
ott.taxon('Araripia').extinct()
# Bryan Drew 2014-02-05
# http://www.mobot.org/mobot/research/apweb/
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/92
ott.taxon('Viscaceae').rename('Visceae')
ott.taxon('Amphorogynaceae').rename('Amphorogyneae')
ott.taxon('Thesiaceae').rename('Thesieae')
ott.taxon('Santalaceae').take(ott.taxon('Visceae'))
ott.taxon('Santalaceae').take(ott.taxon('Amphorogyneae'))
ott.taxon('Santalaceae').take(ott.taxon('Thesieae'))
ott.taxon('Santalaceae').absorb(ott.taxon('Cervantesiaceae'))
ott.taxon('Santalaceae').absorb(ott.taxon('Comandraceae'))
# Bryan Drew 2014-01-30
# http://dx.doi.org/10.1126/science.282.5394.1692
ott.taxon('Magnoliophyta').take(ott.taxon('Archaefructus'))
# Bryan Drew 2014-01-30
# http://deepblue.lib.umich.edu/bitstream/handle/2027.42/48219/ID058.pdf
ott.taxon('eudicotyledons').take(ott.taxon('Phyllites'))
# Bryan Drew 2014-02-13
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/93
# http://dx.doi.org/10.1007/978-3-540-31051-8_2
ott.taxon('Alseuosmiaceae').take(ott.taxon('Platyspermation'))
# JAR 2014-02-24. We are getting extinctness information for genus
# and above from IRMNG, but not for species.
# There's a similar problem in Equus.
for name in ['H**o sapiens neanderthalensis',
'H**o sapiens ssp. Denisova',
'H**o habilis',
'H**o erectus',
'H**o cepranensis',
'H**o georgicus',
'H**o floresiensis',
'H**o kenyaensis',
'H**o rudolfensis',
'H**o antecessor',
'H**o ergaster',
'H**o okotensis']:
tax = ott.maybeTaxon(name)
if tax != None:
tax.extinct()
# JAR 2014-03-07 hack to prevent H.s. from being extinct due to all of
# its subspecies being extinct.
# I wish I knew what the authority for the H.s.s. name was.
hss = ott.newTaxon('H**o sapiens sapiens', 'subspecies', 'https://en.wikipedia.org/wiki/Homo_sapiens_sapiens')
ott.taxon('H**o sapiens').take(hss)
hss.hide()
# Raised by Joseph Brown 2014-03-09, solution proposed by JAR
# Tribolium is incertae sedis in NCBI but we want it to not be hidden,
# since it's a model organism.
# Placement in Tenebrioninae is according to http://bugguide.net/node/view/152 .
# Is this cheating?
ott.taxon('Tenebrioninae').take(ott.taxon('Tribolium','Coleoptera'))
# Bryan Drew 2014-03-20 http://dx.doi.org/10.1186/1471-2148-14-23
ott.taxon('Pentapetalae').take(ott.taxon('Vitales'))
# Bryan Drew 2014-03-14 http://dx.doi.org/10.1186/1471-2148-14-23
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/24
ott.taxon('Streptophytina').elide()
# Dail 2014-03-20
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/29
# Note misspelling in SILVA
ott.taxon('Freshwayer Opisthokonta').rename('Freshwater Microbial Opisthokonta')
# JAR 2014-03-31 just poking around
# Many of these would be handled by major_rank_conflict if it worked
for name in [
'Temnospondyli', # http://tolweb.org/tree?group=Temnospondyli
'Eobatrachus', # https://en.wikipedia.org/wiki/Eobatrachus
'Vulcanobatrachus', # https://en.wikipedia.org/wiki/Vulcanobatrachus
'Beelzebufo', # https://en.wikipedia.org/wiki/Beelzebufo
'Iridotriton', # https://en.wikipedia.org/wiki/Iridotriton
'Baurubatrachus', # https://en.wikipedia.org/wiki/Baurubatrachus
'Acritarcha', # # JAR 2014-04-26
]:
tax = ott.maybeTaxon(name)
if tax != None: tax.extinct()
# Dail 2014-03-31 https://github.com/OpenTreeOfLife/feedback/issues/4
# no evidence given
ott.taxonThatContains('Bacteria', 'Lentisphaerae').take(ott.taxon('Lentisphaerae'))
# David Hibbett 2014-04-02 misspelling in h2007 file
# (Dacrymecetales is 'no rank', Dacrymycetes is a class)
if ott.maybeTaxon('Dacrymecetales') != None:
ott.taxon('Dacrymecetales').rename('Dacrymycetes')
# Dail https://github.com/OpenTreeOfLife/feedback/issues/6
ott.taxon('Telonema').synonym('Teleonema')
# Joseph https://github.com/OpenTreeOfLife/reference-taxonomy/issues/43
ott.taxon('Lorisiformes').take(ott.taxon('Lorisidae'))
# Romina https://github.com/OpenTreeOfLife/reference-taxonomy/issues/42
# As of 2014-04-23 IF synonymizes Cyphellopsis to Merismodes
cyph = ott.maybeTaxon('Cyphellopsis','Cyphellaceae')
if cyph != None:
cyph.unhide()
if ott.maybeTaxon('Cyphellopsis','Niaceae') != None:
cyph.absorb(ott.taxon('Cyphellopsis','Niaceae'))
ott.taxon('Diaporthaceae').take(ott.taxon('Phomopsis'))
ott.taxon('Valsaceae').take(ott.taxon('Valsa', 'Fungi'))
ott.taxon('Agaricaceae').take(ott.taxon('Cystoderma','Fungi'))
# Invert the synonym relationship
ott.taxon('Hypocrea lutea').absorb(ott.taxon('Trichoderma deliquescens'))
# Fold Norops into Anolis
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/31
# TBD: Change species names from Norops X to Anolis X for all X
ott.taxon('Anolis').absorb(ott.maybeTaxon('Norops', 'Iguanidae'))
for (name, super) in [
# JAR 2014-04-08 - these are in study OTUs - see IRMNG
('Inseliellum', None),
('Conus', 'Gastropoda'),
('Patelloida', None),
('Phyllanthus', 'Phyllanthaceae'),
('Stelis','Orchidaceae'),
('Chloris', 'Poaceae'),
('Acropora', 'Acroporidae'),
('Diadasia', None),
# JAR 2014-04-24
# grep "ncbi:.*extinct_inherited" tax/ott/taxonomy.tsv | head
('Tarsius', None),
('Odontesthes', None),
('Leiognathus', 'Chordata'),
('Oscheius', None),
('Cicindela', None),
('Leucothoe', 'Ericales'),
('Hydrornis', None),
('Bostrychia harveyi', None), #fungus
('Agaricia', None), #coral
('Dischidia', None), #eudicot
# JAR 2014-05-13
('Saurischia', None),
# there are two of these, maybe should be merged.
# 'Myoxidae', 'Rodentia'),
# JAR 2014-05-13 These are marked extinct by IRMNG but are all in NCBI
# and have necleotide sequences
('Zemetallina', None),
('Nullibrotheas', None),
('Fissiphallius', None),
('Nullibrotheas', None),
('Sinelater', None),
('Phanerothecium', None),
('Cephalotaxaceae', None),
('Vittaria elongata', None),
('Neogymnocrinus', None),
]:
if super == None:
tax = ott.maybeTaxon(name)
else:
tax = ott.maybeTaxon(name, super)
if tax != None: tax.extant()
# JAR 2014-05-08 while looking at the deprecated ids file.
# http://www.theplantlist.org/tpl/record/kew-2674785
ott.taxon('Berendtiella rugosa').synonym('Berendtia rugosa')
# JAR 2014-05-13 weird problem
# NCBI incorrectly has both Cycadidae and Cycadophyta as children of Acrogymnospermae.
# Cycadophyta (class, with daughter Cycadopsida) has no sequences.
# The net effect is a bunch of extinct IRMNG genera showing up in
# Cycadophyta, with Cycadophyta entirely extinct.
#
# NCBI has subclass Cycadidae = order Cycadales
# GBIF has phylum Cycadophyta = class Cycadopsida = order Cycadales
# IRMNG has class Cycadopsida = order Cycadales
if ott.maybeTaxon('Cycadidae') != None:
ott.taxon('Cycadidae').absorb(ott.taxon('Cycadopsida'))
ott.taxon('Cycadidae').absorb(ott.taxon('Cycadophyta'))
# Similar problem with Gnetidae and Ginkgoidae
# Dail 2014-03-31
# https://github.com/OpenTreeOfLife/feedback/issues/6
ott.taxon('Telonema').synonym('Teleonema')
# JAR noticed 2015-02-17 used in pg_2460
# http://reptile-database.reptarium.cz/species?genus=Parasuta&species=spectabilis
ott.taxon('Parasuta spectabilis').synonym('Rhinoplocephalus spectabilis')
# Bryan Drew 2015-02-17 http://dx.doi.org/10.1016/j.ympev.2014.11.011
sax = ott.taxon('Saxifragella bicuspidata')
ott.taxon('Saxifraga').take(sax)
sax.rename('Saxifraga bicuspidata')
# JAR 2015-07-21 noticed, obviously wrong
ott.taxonThatContains('Ophiurina', 'Acrocnida brachiata').extant()
# straightening out an awful mess
ott.taxon('Saccharomycetes', 'Saccharomycotina').extant() # foo. don't know who sets this
ott.taxonThatContains('Rhynchonelloidea', 'Sphenarina').extant() # NCBI
# "Old" patch system
ott.edit('feed/ott/edits/')
# This is a randomly chosen bivalve to force Bivalvia to not be extinct
ott.taxon('Corculum cardissa', 'Bivalvia').extant()
# Similarly for roaches
ott.taxon('Periplaneta americana', 'Blattodea').extant()
# https://groups.google.com/d/msg/opentreeoflife/SrI7KpPgoPQ/wTeD17GzOGoJ
trigo = ott.maybeTaxon('Trigonocarpales')
if trigo != None: trigo.extinct()
#Pinophyta and daughters need to be deleted; - Bryan 2014-01-28
#Lycopsida and daughters need to be deleted;
#Pteridophyta and daughters need to be deleted;
#Gymnospermophyta and daughters need to be deleted;
ott.taxon('Pinophyta','Chloroplastida').incertaeSedis()
ott.taxon('Pteridophyta','Chloroplastida').incertaeSedis()
ott.taxon('Gymnospermophyta','Chloroplastida').incertaeSedis()
# Patches from the Katz lab to give decent parents to taxa classified
# as Chromista or Protozoa
print '-- Chromista/Protozoa spreadsheet from Katz lab --'
fixChromista(ott)
print '-- more patches --'
# From Laura and Dail on 5 Feb 2014
# https://groups.google.com/d/msg/opentreeoflife/a69fdC-N6pY/y9QLqdqACawJ
ott.taxon('Chlamydiae/Verrucomicrobia group').rename('Verrucomicrobia group')
ott.taxon('Heterolobosea','Discicristata').absorb(ott.taxon('Heterolobosea','Percolozoa'))
ott.taxon('Excavata','Eukaryota').take(ott.taxon('Oxymonadida','Eukaryota'))
# Work in progress - Joseph
ott.taxon('Reptilia').hide()
# Chris Owen patches 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/88
ott.taxon('Protostomia').take(ott.taxon('Chaetognatha','Deuterostomia'))
def patch_ott(ott):
# 2014-01-27 Joseph: Quiscalus is incorrectly in
# Fringillidae instead of Icteridae. NCBI is wrong, GBIF is correct.
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/87
ott.taxon('Icteridae').take(ott.taxon('Quiscalus', 'Fringillidae'))
# Misspelling in GBIF... seems to already be known
# Stephen email to JAR 2014-01-26
# ott.taxon("Torricelliaceae").synonym("Toricelliaceae")
# Joseph 2014-01-27 https://code.google.com/p/gbif-ecat/issues/detail?id=104
ott.taxon('Parulidae').take(ott.taxon('Myiothlypis', 'Passeriformes'))
# I don't get why this one isn't a major_rank_conflict !? - bug. (so to speak.)
ott.taxon('Blattodea').take(ott.taxon('Phyllodromiidae'))
# See above (occurs in both IF and GBIF). Also see issue #67
ott.taxon('Chlamydotomus').incertaeSedis()
# Joseph Brown 2014-01-27
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/87
# Occurs as Sakesphorus bernardi in ncbi, gbif, irmng, as Thamnophilus bernardi in bgif
ott.taxon('Thamnophilus bernardi').absorb(
ott.taxon('Sakesphorus bernardi'))
ott.taxon('Thamnophilus melanonotus').absorb(
ott.taxon('Sakesphorus melanonotus'))
ott.taxon('Thamnophilus melanothorax').absorb(
ott.taxon('Sakesphorus melanothorax'))
ott.taxon('Thamnophilus bernardi').synonym('Sakesphorus bernardi')
ott.taxon('Thamnophilus melanonotus').synonym('Sakesphorus melanonotus')
ott.taxon('Thamnophilus melanothorax').synonym('Sakesphorus melanothorax')
# Mammals - groups cluttering basal part of tree
ott.taxon('Litopterna').extinct()
ott.taxon('Notoungulata').extinct()
# Artiodactyls
ott.taxon('Boreameryx').extinct()
ott.taxon('Thandaungia').extinct()
ott.taxon('Limeryx').extinct()
ott.taxon('Delahomeryx').extinct()
ott.taxon('Krabitherium').extinct()
ott.taxon('Discritochoerus').extinct()
ott.taxon('Brachyhyops').extinct()
# Not fungi - Romina 2014-01-28
# ott.taxon('Adlerocystis').show() - it's Chromista ...
# Index Fungorum says Adlerocystis is Chromista, but I don't believe it
# ott.taxon('Chromista').take(ott.taxon('Adlerocystis','Fungi'))
# Adlerocystis seems to be a fungus, but unclassified - JAR 2014-03-10
ott.taxon('Adlerocystis').incertaeSedis()
# "No clear identity has emerged"
# http://forestis.rsvs.ulaval.ca/REFERENCES_X/phylogeny.arizona.edu/tree/eukaryotes/accessory/parasitic.html
# Need to hide it because it clutters base of Fungi
if ott.maybeTaxon('Amylophagus', 'Fungi') != None:
ott.taxon('Amylophagus', 'Fungi').incertaeSedis()
# Bad synonym - Tony Rees 2014-01-28
# https://groups.google.com/d/msg/opentreeoflife/SrI7KpPgoPQ/ihooRUSayXkJ
if ott.maybeTaxon('Lemania pluvialis') != None:
ott.taxon('Lemania pluvialis').prune("make-ott.py")
# Tony Rees 2014-01-29
# https://groups.google.com/d/msg/opentreeoflife/SrI7KpPgoPQ/wTeD17GzOGoJ
trigo = ott.maybeTaxon('Trigonocarpales')
if trigo != None: trigo.extinct()
#Pinophyta and daughters need to be deleted; - Bryan 2014-01-28
#Lycopsida and daughters need to be deleted;
#Pteridophyta and daughters need to be deleted;
#Gymnospermophyta and daughters need to be deleted;
for name in ['Pinophyta', 'Pteridophyta', 'Gymnospermophyta']:
if ott.maybeTaxon(name, 'Chloroplastida'):
ott.taxon(name, 'Chloroplastida').incertaeSedis()
# Patches from the Katz lab to give decent parents to taxa classified
# as Chromista or Protozoa
print '-- Chromista/Protozoa spreadsheet from Katz lab --'
fixChromista(ott)
print '-- more patches --'
# From Laura and Dail on 5 Feb 2014
# https://groups.google.com/d/msg/opentreeoflife/a69fdC-N6pY/y9QLqdqACawJ
tax = ott.maybeTaxon('Chlamydiae/Verrucomicrobia group')
if tax != None and tax.name != 'Bacteria':
tax.rename('Verrucomicrobia group')
ott.taxon('Heterolobosea',
'Discicristata').absorb(ott.taxon('Heterolobosea', 'Percolozoa'))
ott.taxon('Excavata',
'Eukaryota').take(ott.taxon('Oxymonadida', 'Eukaryota'))
# Work in progress - Joseph
if ott.maybeTaxon('Reptilia') != None:
ott.taxon('Reptilia').hide()
# Chris Owen patches 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/88
ott.taxon('Protostomia').take(ott.taxon('Chaetognatha', 'Deuterostomia'))
ott.taxon('Lophotrochozoa').take(ott.taxon('Platyhelminthes'))
ott.taxon('Polychaeta', 'Annelida').take(ott.taxon('Myzostomida'))
ott.taxon('Lophotrochozoa').take(ott.taxon('Gnathostomulida'))
ott.taxon('Bilateria').take(ott.taxon('Acoela'))
ott.taxon('Bilateria').take(ott.taxon('Xenoturbella'))
ott.taxon('Bilateria').take(ott.taxon('Nemertodermatida'))
# 8) Stauromedusae should be a class (Staurozoa; Marques and Collins 2004) and should be removed from Scyphozoa
ott.taxon('Cnidaria').take(ott.taxon('Stauromedusae'))
ott.taxon('Copepoda').take(ott.taxon('Prionodiaptomus'))
# Bryan Drew patches 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/89
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90
ott.taxon('Scapaniaceae').absorb(ott.taxon('Lophoziaceae'))
ott.taxon('Salazaria mexicana').rename('Scutellaria mexicana')
# One Scutellaria is in Lamiaceae; the other is a fungus.
# IRMNG's Salazaria 1288740 is in Lamiales, and is a synonym of Scutellaria.
##### RECOVER THIS SOMEHOW --
# ott.taxon('Scutellaria','Lamiaceae').absorb(ott.image(gbif.taxon('Salazaria')))
# IRMNG 1288740 not in newer IRMNG
if False:
sal = irmng.maybeTaxon('1288740')
if sal != None:
ott.taxon('Scutellaria',
'Lamiaceae').absorb(ott.image(sal)) #Salazaria
# Make an order Boraginales that contains Boraginaceae + Hydrophyllaceae
# http://dx.doi.org/10.1111/cla.12061
# Bryan Drew 2013-09-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/91
ott.taxon('Boraginaceae').absorb(ott.taxon('Hydrophyllaceae'))
ott.taxon('Boraginales').take(ott.taxon('Boraginaceae'))
ott.taxon('lamiids').take(ott.taxon('Boraginales'))
# Bryan Drew 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90
# Vahlia 26024 <- Vahliaceae 23372 <- lammids 596112 (was incertae sedis)
ott.taxon('lamiids').take(ott.taxon('Vahliaceae'))
# Bryan Drew 2014-01-30
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/90
# http://www.sciencedirect.com/science/article/pii/S0034666703000927
ott.taxon('Araripia').extinct()
# Bryan Drew 2014-02-05
# http://www.mobot.org/mobot/research/apweb/
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/92
ott.taxon('Viscaceae').rename('Visceae')
ott.taxon('Amphorogynaceae').rename('Amphorogyneae')
ott.taxon('Thesiaceae').rename('Thesieae')
ott.taxon('Santalaceae').take(ott.taxon('Visceae'))
ott.taxon('Santalaceae').take(ott.taxon('Amphorogyneae'))
ott.taxon('Santalaceae').take(ott.taxon('Thesieae'))
ott.taxon('Santalaceae').absorb(ott.taxon('Cervantesiaceae'))
ott.taxon('Santalaceae').absorb(ott.taxon('Comandraceae'))
# Bryan Drew 2014-01-30
# http://dx.doi.org/10.1126/science.282.5394.1692
ott.taxon('Magnoliophyta').take(ott.taxon('Archaefructus'))
# Bryan Drew 2014-01-30
# http://deepblue.lib.umich.edu/bitstream/handle/2027.42/48219/ID058.pdf
ott.taxon('eudicotyledons').take(ott.taxon('Phyllites'))
# Bryan Drew 2014-02-13
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/93
# http://dx.doi.org/10.1007/978-3-540-31051-8_2
ott.taxon('Alseuosmiaceae').take(ott.taxon('Platyspermation'))
# JAR 2014-02-24. We are getting extinctness information for genus
# and above from IRMNG, but not for species.
# There's a similar problem in Equus.
for name in [
'H**o sapiens neanderthalensis', 'H**o sapiens ssp. Denisova',
'H**o habilis', 'H**o erectus', 'H**o cepranensis',
'H**o georgicus', 'H**o floresiensis', 'H**o kenyaensis',
'H**o rudolfensis', 'H**o antecessor', 'H**o ergaster',
'H**o okotensis'
]:
tax = ott.maybeTaxon(name)
if tax != None:
tax.extinct()
# JAR 2014-03-07 hack to prevent H.s. from being extinct due to all of
# its subspecies being extinct.
# I wish I knew what the authority for the H.s.s. name was.
hss = ott.newTaxon('H**o sapiens sapiens', 'subspecies',
'https://en.wikipedia.org/wiki/Homo_sapiens_sapiens')
ott.taxon('H**o sapiens').take(hss)
hss.hide()
# Raised by Joseph Brown 2014-03-09, solution proposed by JAR
# Tribolium is incertae sedis in NCBI but we want it to not be hidden,
# since it's a model organism.
# Placement in Tenebrioninae is according to http://bugguide.net/node/view/152 .
# Is this cheating?
ott.taxon('Tenebrioninae').take(ott.taxon('Tribolium', 'Coleoptera'))
# Bryan Drew 2014-03-20 http://dx.doi.org/10.1186/1471-2148-14-23
ott.taxon('Pentapetalae').take(ott.taxon('Vitales'))
# Bryan Drew 2014-03-14 http://dx.doi.org/10.1186/1471-2148-14-23
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/24
ott.taxon('Streptophytina').elide()
# Dail 2014-03-20
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/29
# Note misspelling in SILVA
ott.taxon('Freshwayer Opisthokonta').rename(
'Freshwater Microbial Opisthokonta')
# JAR 2014-03-31 just poking around
# Many of these would be handled by major_rank_conflict if it worked
for name in [
'Temnospondyli', # http://tolweb.org/tree?group=Temnospondyli
'Eobatrachus', # https://en.wikipedia.org/wiki/Eobatrachus
'Vulcanobatrachus', # https://en.wikipedia.org/wiki/Vulcanobatrachus
'Beelzebufo', # https://en.wikipedia.org/wiki/Beelzebufo
'Iridotriton', # https://en.wikipedia.org/wiki/Iridotriton
'Baurubatrachus', # https://en.wikipedia.org/wiki/Baurubatrachus
'Acritarcha', # # JAR 2014-04-26
]:
tax = ott.maybeTaxon(name)
if tax != None: tax.extinct()
# Dail 2014-03-31 https://github.com/OpenTreeOfLife/feedback/issues/4
# no evidence given
ott.taxonThatContains('Bacteria',
'Lentisphaerae').take(ott.taxon('Lentisphaerae'))
# David Hibbett 2014-04-02 misspelling in h2007 file
# (Dacrymecetales is 'no rank', Dacrymycetes is a class)
if ott.maybeTaxon('Dacrymecetales') != None:
ott.taxon('Dacrymecetales').rename('Dacrymycetes')
# Dail https://github.com/OpenTreeOfLife/feedback/issues/6
ott.taxon('Telonema').synonym('Teleonema')
# Joseph https://github.com/OpenTreeOfLife/reference-taxonomy/issues/43
ott.taxon('Lorisiformes').take(ott.taxon('Lorisidae'))
# Romina https://github.com/OpenTreeOfLife/reference-taxonomy/issues/42
# As of 2014-04-23 IF synonymizes Cyphellopsis to Merismodes
cyph = ott.maybeTaxon('Cyphellopsis', 'Cyphellaceae')
if cyph != None:
cyph.unhide()
if ott.maybeTaxon('Cyphellopsis', 'Niaceae') != None:
cyph.absorb(ott.taxon('Cyphellopsis', 'Niaceae'))
ott.taxon('Diaporthaceae').take(ott.taxon('Phomopsis'))
ott.taxon('Valsaceae').take(ott.taxon('Valsa', 'Fungi'))
ott.taxon('Agaricaceae').take(ott.taxon('Cystoderma', 'Fungi'))
# Invert the synonym relationship
ott.taxon('Hypocrea lutea').absorb(ott.taxon('Trichoderma deliquescens'))
# Fold Norops into Anolis
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/31
# TBD: Change species names from Norops X to Anolis X for all X
ott.taxon('Anolis').absorb(ott.maybeTaxon('Norops', 'Iguanidae'))
for (name, super) in [
# JAR 2014-04-08 - these are in study OTUs - see IRMNG
('Inseliellum', None),
('Conus', 'Gastropoda'),
('Patelloida', None),
('Phyllanthus', 'Phyllanthaceae'),
('Stelis', 'Orchidaceae'),
('Chloris', 'Poaceae'),
('Acropora', 'Acroporidae'),
('Diadasia', None),
# JAR 2014-04-24
# grep "ncbi:.*extinct_inherited" tax/ott/taxonomy.tsv | head
('Tarsius', None),
('Odontesthes', None),
('Leiognathus', 'Chordata'),
('Oscheius', None),
('Cicindela', None),
('Leucothoe', 'Ericales'),
('Hydrornis', None),
('Bostrychia harveyi', None), #fungus
('Agaricia', None), #coral
('Dischidia', None), #eudicot
# JAR 2014-05-13
('Saurischia', None),
# there are two of these, maybe should be merged.
# 'Myoxidae', 'Rodentia'),
# JAR 2014-05-13 These are marked extinct by IRMNG but are all in NCBI
# and have necleotide sequences
('Zemetallina', None),
('Nullibrotheas', None),
('Fissiphallius', None),
('Nullibrotheas', None),
('Sinelater', None),
('Phanerothecium', None),
('Cephalotaxaceae', None),
('Vittaria elongata', None),
('Neogymnocrinus', None),
]:
if super == None:
tax = ott.maybeTaxon(name)
else:
tax = ott.maybeTaxon(name, super)
if tax != None: tax.extant()
# JAR 2014-05-08 while looking at the deprecated ids file.
# http://www.theplantlist.org/tpl/record/kew-2674785
ott.taxon('Berendtiella rugosa').synonym('Berendtia rugosa')
# JAR 2014-05-13 weird problem
# NCBI incorrectly has both Cycadidae and Cycadophyta as children of Acrogymnospermae.
# Cycadophyta (class, with daughter Cycadopsida) has no sequences.
# The net effect is a bunch of extinct IRMNG genera showing up in
# Cycadophyta, with Cycadophyta entirely extinct.
#
# NCBI has subclass Cycadidae = order Cycadales
# GBIF has phylum Cycadophyta = class Cycadopsida = order Cycadales
# IRMNG has class Cycadopsida = order Cycadales
if ott.maybeTaxon('Cycadidae') != None:
ott.taxon('Cycadidae').absorb(ott.taxon('Cycadopsida'))
ott.taxon('Cycadidae').absorb(ott.taxon('Cycadophyta'))
# Similar problem with Gnetidae and Ginkgoidae
# Dail 2014-03-31
# https://github.com/OpenTreeOfLife/feedback/issues/6
ott.taxon('Telonema').synonym('Teleonema')
# JAR noticed 2015-02-17 used in pg_2460
# http://reptile-database.reptarium.cz/species?genus=Parasuta&species=spectabilis
ott.taxon('Parasuta spectabilis').synonym('Rhinoplocephalus spectabilis')
# Bryan Drew 2015-02-17 http://dx.doi.org/10.1016/j.ympev.2014.11.011
sax = ott.taxon('Saxifragella bicuspidata')
ott.taxon('Saxifraga').take(sax)
sax.rename('Saxifraga bicuspidata')
# JAR 2015-07-21 noticed, obviously wrong
ott.taxonThatContains('Ophiurina', 'Acrocnida brachiata').extant()
# straightening out an awful mess
ott.taxon('Saccharomycetes',
'Saccharomycotina').extant() # foo. don't know who sets this
ott.taxonThatContains('Rhynchonelloidea', 'Sphenarina').extant() # NCBI
# "Old" patch system
ott.edit('feed/ott/edits/')
# This is a randomly chosen bivalve to force Bivalvia to not be extinct
ott.taxon('Corculum cardissa', 'Bivalvia').extant()
# Similarly for roaches
ott.taxon('Periplaneta americana', 'Blattodea').extant()