def link_to_h2007(tax):
print '-- Putting families in Hibbett 2007 orders --'
# 2014-04-13 Romina #40, #60
for (order_name, family_names) in \
[('Neozygitales', ['Neozygitaceae']),
('Asterinales', ['Asterinaceae']),
('Savoryellales', ['Savoryella', 'Ascotaiwania', 'Ascothailandia']),
('Cladochytriales', ['Cladochytriaceae', 'Nowakowskiellaceae', 'Septochytriaceae', 'Endochytriaceae']),
('Jaapiales', ['Jaapiaceae']),
('Coniocybales', ['Coniocybaceae']),
('Hyaloraphidiales', ['Hyaloraphidiaceae']),
('Mytilinidiales', ['Mytilinidiaceae', 'Gloniaceae']),
]:
order = tax.maybeTaxon(order_name)
if order != None:
for family in family_names:
order.take(tax.taxon(family))
else:
print '*** Missing fungal order', foo[0]
# 2015-07-13 Romina
h2007_fam = 'http://figshare.com/articles/Fungal_Classification_2015/1465038'
some_claims = []
for (order, families) in \
[('Talbotiomycetales',['Talbotiomyces calosporus']),
('Moniliellales',['Moniliellaceae']),
('Malasseziales',['Malasseziaceae', 'Malassezia']),
('Trichotheliales',['Trichotheliaceae', 'Myeloconidiaceae']),
('Trichosporonales',['Sporobolomyces ruberrimus']),
('Holtermanniales',['Holtermanniella']),
('Lepidostromatales',['Lepidostromataceae']),
('Atheliales',['Atheliaceae']),
('Stereopsidales',['Stereopsidaceae']),
('Septobasidiales',['Septobasidiaceae']),
('Symbiotaphrinales',['Symbiotaphrina']),
('Caliciales',['Sphaerophoraceae']),
('Sarrameanales',['Sarrameanaceae']),
('Trapeliales',['Trapeliaceae']),
('Halosphaeriales',['Halosphaeriaceae']),
('Abrothallales',['Abrothallus']),
('Arctomiales',['Arctomiaceae']),
('Hymeneliales',['Hymeneliaceae']),
('Leprocaulales',['Leprocaulaceae']),
]:
for family in families:
some_claims.append(Has_child(order, family, h2007_fam))
make_claims(tax, some_claims)
# Loxosporales,synonym of Sarrameanales
make_claim(fungorum,
Whether_same('Sarrameanales', 'Loxosporales',
True, h2007_fam))
def link_to_h2007(tax):
print '-- Putting families in Hibbett 2007 orders --'
# 2014-04-13 Romina #40, #60
for (order_name, family_names) in \
[('Neozygitales', ['Neozygitaceae']),
('Asterinales', ['Asterinaceae']),
('Savoryellales', ['Savoryella', 'Ascotaiwania', 'Ascothailandia']),
('Cladochytriales', ['Cladochytriaceae', 'Nowakowskiellaceae', 'Septochytriaceae', 'Endochytriaceae']),
('Jaapiales', ['Jaapiaceae']),
('Coniocybales', ['Coniocybaceae']),
('Hyaloraphidiales', ['Hyaloraphidiaceae']),
('Mytilinidiales', ['Mytilinidiaceae', 'Gloniaceae']),
]:
order = tax.maybeTaxon(order_name)
if order != None:
for family in family_names:
order.take(tax.taxon(family))
else:
print '*** Missing fungal order', foo[0]
# 2015-07-13 Romina
h2007_fam = 'http://figshare.com/articles/Fungal_Classification_2015/1465038'
some_claims = []
for (order, families) in \
[('Talbotiomycetales',['Talbotiomyces calosporus']),
('Moniliellales',['Moniliellaceae']),
('Malasseziales',['Malasseziaceae', 'Malassezia']),
('Trichotheliales',['Trichotheliaceae', 'Myeloconidiaceae']),
('Trichosporonales',['Sporobolomyces ruberrimus']),
('Holtermanniales',['Holtermanniella']),
('Lepidostromatales',['Lepidostromataceae']),
('Atheliales',['Atheliaceae']),
('Stereopsidales',['Stereopsidaceae']),
('Septobasidiales',['Septobasidiaceae']),
('Symbiotaphrinales',['Symbiotaphrina']),
('Caliciales',['Sphaerophoraceae']),
('Sarrameanales',['Sarrameanaceae']),
('Trapeliales',['Trapeliaceae']),
('Halosphaeriales',['Halosphaeriaceae']),
('Abrothallales',['Abrothallus']),
('Arctomiales',['Arctomiaceae']),
('Hymeneliales',['Hymeneliaceae']),
('Leprocaulales',['Leprocaulaceae']),
]:
for family in families:
some_claims.append(Has_child(order, family, h2007_fam))
# Loxosporales,synonym of Sarrameanales
some_claims.append(
Whether_same('Sarrameanales', 'Loxosporales', True, h2007_fam))
make_claims(tax, some_claims)
def patch_gbif(gbif):
# - Touch-up -
# Rod Page blogged about this one
# http://iphylo.blogspot.com/2014/03/gbif-liverwort-taxonomy-broken.html
gbif.taxon('Jungermanniales','Marchantiophyta').absorb(gbif.taxon('Jungermanniales','Bryophyta'))
# Joseph 2013-07-23 https://github.com/OpenTreeOfLife/opentree/issues/62
# GBIF has two copies of Myospalax
gbif.taxon('6006429').absorb(gbif.taxon('2439119'))
# RR 2014-04-12 #47
gbif.taxon('Drake-brockmania').absorb(gbif.taxon('Drake-Brockmania'))
# RR #50 - this one is in NCBI, see above
gbif.taxon('Saxofridericia').absorb(gbif.taxon('4930834')) #Saxo-Fridericia
# RR #57 - the genus is in NCBI, see above
gbif.taxon('Solms-laubachia').absorb(gbif.taxon('4908941')) #Solms-Laubachia
gbif.taxon('Solms-laubachia pulcherrima').absorb(gbif.taxon('Solms-Laubachia pulcherrima'))
# RR #45
gbif.taxon('Cyrto-hypnum').absorb(gbif.taxon('4907605'))
# 2014-04-13 JAR noticed while grepping
claims = [
Whether_same('Chryso-Hypnum', 'Chryso-hypnum', True),
Whether_same('Drepano-Hypnum', 'Drepano-hypnum', True),
Whether_same('Complanato-Hypnum', 'Complanato-hypnum', True),
Whether_same('Leptorrhyncho-Hypnum', 'Leptorrhyncho-hypnum', True),
Whether_same('Trichoderma viride', 'Hypocrea rufa', True,
'https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86'), # Type
Whether_same('Hypocrea', With_ancestor('Trichoderma', 'Hypocrea rufa'), True,
'https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86'), # Type
# Doug Soltis 2015-02-17 https://github.com/OpenTreeOfLife/feedback/issues/59
# http://dx.doi.org/10.1016/0034-6667(95)00105-0
Whether_extant('Timothyia', False, 'https://github.com/OpenTreeOfLife/feedback/issues/59'),
]
make_claims(gbif, claims)
# See new versions above
# gbif.taxon('Chryso-hypnum').absorb(gbif.taxon('Chryso-Hypnum'))
# gbif.taxon('Complanato-Hypnum').rename('Complanato-hypnum')
# gbif.taxon('Leptorrhyncho-Hypnum').rename('Leptorrhyncho-hypnum')
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86
# Romina 2014-04-09
# GBIF has both Hypocrea and Trichoderma. And it has four Trichoderma synonyms...
# pick the one that contains bogo-type Hypocrea rufa
# See new versions above
# gbif.taxon('Trichoderma viride').rename('Hypocrea rufa') # Type
# gbif.taxon('Hypocrea').absorb(gbif.taxonThatContains('Trichoderma', 'Hypocrea rufa'))
# 2014-04-21 RR
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/45
for epithet in ['cylindraceum',
'lepidoziaceum',
'intermedium',
'espinosae',
'pseudoinvolvens',
'arzobispoae',
'sharpii',
'frontinoae',
'atlanticum',
'stevensii',
'brachythecium']:
claim = Whether_same('Cyrto-Hypnum ' + epithet, 'Cyrto-hypnum ' + epithet, True,
'https://github.com/OpenTreeOfLife/reference-taxonomy/issues/45')
claim.make_true(gbif)
# was gbif.taxon('Cyrto-hypnum ' + epithet).absorb(gbif.taxon('Cyrto-Hypnum ' + epithet))
# JAR 2014-04-23 Noticed while perusing silva/gbif conflicts
gbif.taxon('Ebriaceae').synonym('Ebriacea')
gbif.taxon('Acanthocystidae').absorb(gbif.taxon('Acanthocistidae'))
gbif.taxon('Dinophyta').synonym('Dinoflagellata')
# JAR 2014-06-29 stumbled on this while trying out new alignment
# methods and examining troublesome homonym Bullacta exarata.
# GBIF obviously puts it in the wrong place, see description at
# http://www.gbif.org/species/4599744 (it's a snail, not a shrimp).
bex = gbif.taxon('Bullacta exarata', 'Atyidae')
bec = gbif.taxon('Bullacta ecarata', 'Atyidae')
if bex != None and bec != None:
bex.absorb(bec)
bex.detach()
# Yan Wong 2014-12-16 https://github.com/OpenTreeOfLife/reference-taxonomy/issues/116
for name in ['Griphopithecus', 'Asiadapis',
'Lomorupithecus', 'Marcgodinotius', 'Muangthanhinius',
'Plesiopithecus', 'Suratius', 'Killikaike blakei', 'Rissoina bonneti',
# 'Mycosphaeroides' - gone
]:
claim = Whether_extant(name, False, 'https://github.com/OpenTreeOfLife/reference-taxonomy/issues/116')
claim.make_true(gbif)
# JAR 2014-07-18 - get rid of Helophorus duplication
# GBIF 3263442 = Helophorus Fabricius, 1775, from CoL
# in 6985 = Helophoridae Leach, 1815
# GBIF 6757656 = Helophorus Leach, from IRMNG homonym list
# in 7829 = Hydraenidae Mulsant, 1844
# ('Helophorus', 'Helophoridae') ('Helophorus', 'Hydraenidae')
gbif.taxon('3263442').absorb(gbif.taxon('6757656'))
# JAR 2015-06-27 there are two Myospalax myospalax
# The one in Spalacidae is the right one, Myospalacinae is the wrong one
# (according to NCBI)
# Probably should clean up the whole genus
# 2439121 = Myospalax myospalax (Laxmann, 1773) from CoL
gbif.taxon('2439121').absorb(gbif.taxon('6075534'))
# 4010070 pg_1378 Gelidiellaceae gbif:8998 -- ok, paraphyletic
# https://github.com/OpenTreeOfLife/feedback/issues/64
gbif.taxon('Plagiomene').extinct()
# https://github.com/OpenTreeOfLife/feedback/issues/65
gbif.taxon('Worlandia').extinct()
tip = gbif.taxon('6101461') # ('Tipuloidea', 'Hemiptera') gbif:6101461 - extinct
if tip != None:
tip.prune("about:blank#this-homonym-is-causing-too-much-trouble")
oph = gbif.taxon('4872240') # ('Ophiurina', 'Ophiurinidae') gbif:4872240 - extinct
if oph != None:
oph.prune("about:blank#this-homonym-is-causing-too-much-trouble")
# 2015-07-25 Extra Dipteras are confusing new division logic. Barren genus
gbif.taxon('3230674').prune(this_source)
# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/72
gbif.taxon('Myeladaphus').extinct()
# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/78
gbif.taxon('Oxyprinichthys').extinct()
# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/82
gbif.taxon('Tarsius thailandica').extinct()
return gbif
def patch_gbif(gbif):
# - Touch-up -
# Rod Page blogged about this one
# http://iphylo.blogspot.com/2014/03/gbif-liverwort-taxonomy-broken.html
gbif.taxon('Jungermanniales', 'Marchantiophyta').absorb(
gbif.taxon('Jungermanniales', 'Bryophyta'))
# Joseph 2013-07-23 https://github.com/OpenTreeOfLife/opentree/issues/62
# GBIF has two copies of Myospalax
gbif.taxon('6006429').absorb(gbif.taxon('2439119'))
# RR 2014-04-12 #47
gbif.taxon('Drake-brockmania').absorb(gbif.taxon('Drake-Brockmania'))
# RR #50 - this one is in NCBI, see above
gbif.taxon('Saxofridericia').absorb(
gbif.taxon('4930834')) #Saxo-Fridericia
# RR #57 - the genus is in NCBI, see above
gbif.taxon('Solms-laubachia').absorb(
gbif.taxon('4908941')) #Solms-Laubachia
gbif.taxon('Solms-laubachia pulcherrima').absorb(
gbif.taxon('Solms-Laubachia pulcherrima'))
# RR #45
gbif.taxon('Cyrto-hypnum').absorb(gbif.taxon('4907605'))
# 2014-04-13 JAR noticed while grepping
claims = [
Whether_same('Chryso-Hypnum', 'Chryso-hypnum', True),
Whether_same('Drepano-Hypnum', 'Drepano-hypnum', True),
Whether_same('Complanato-Hypnum', 'Complanato-hypnum', True),
Whether_same('Leptorrhyncho-Hypnum', 'Leptorrhyncho-hypnum', True),
Whether_same(
'Trichoderma viride', 'Hypocrea rufa', True,
'https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86'
), # Type
Whether_same(
'Hypocrea', With_ancestor('Trichoderma', 'Hypocrea rufa'), True,
'https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86'
), # Type
# Doug Soltis 2015-02-17 https://github.com/OpenTreeOfLife/feedback/issues/59
# http://dx.doi.org/10.1016/0034-6667(95)00105-0
Whether_extant('Timothyia', False,
'https://github.com/OpenTreeOfLife/feedback/issues/59'),
]
make_claims(gbif, claims)
# See new versions above
# gbif.taxon('Chryso-hypnum').absorb(gbif.taxon('Chryso-Hypnum'))
# gbif.taxon('Complanato-Hypnum').rename('Complanato-hypnum')
# gbif.taxon('Leptorrhyncho-Hypnum').rename('Leptorrhyncho-hypnum')
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86
# Romina 2014-04-09
# GBIF has both Hypocrea and Trichoderma. And it has four Trichoderma synonyms...
# pick the one that contains bogo-type Hypocrea rufa
# See new versions above
# gbif.taxon('Trichoderma viride').rename('Hypocrea rufa') # Type
# gbif.taxon('Hypocrea').absorb(gbif.taxonThatContains('Trichoderma', 'Hypocrea rufa'))
# 2014-04-21 RR
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/45
for epithet in [
'cylindraceum', 'lepidoziaceum', 'intermedium', 'espinosae',
'pseudoinvolvens', 'arzobispoae', 'sharpii', 'frontinoae',
'atlanticum', 'stevensii', 'brachythecium'
]:
claim = Whether_same(
'Cyrto-Hypnum ' + epithet, 'Cyrto-hypnum ' + epithet, True,
'https://github.com/OpenTreeOfLife/reference-taxonomy/issues/45')
claim.make_true(gbif)
# was gbif.taxon('Cyrto-hypnum ' + epithet).absorb(gbif.taxon('Cyrto-Hypnum ' + epithet))
# JAR 2014-04-23 Noticed while perusing silva/gbif conflicts
gbif.taxon('Ebriaceae').synonym('Ebriacea')
gbif.taxon('Acanthocystidae').absorb(gbif.taxon('Acanthocistidae'))
gbif.taxon('Dinophyta').synonym('Dinoflagellata')
# JAR 2014-06-29 stumbled on this while trying out new alignment
# methods and examining troublesome homonym Bullacta exarata.
# GBIF obviously puts it in the wrong place, see description at
# http://www.gbif.org/species/4599744 (it's a snail, not a shrimp).
bex = gbif.taxon('Bullacta exarata', 'Atyidae')
bec = gbif.taxon('Bullacta ecarata', 'Atyidae')
if bex != None and bec != None:
bex.absorb(bec)
bex.detach()
# Yan Wong 2014-12-16 https://github.com/OpenTreeOfLife/reference-taxonomy/issues/116
for name in [
'Griphopithecus',
'Asiadapis',
'Lomorupithecus',
'Marcgodinotius',
'Muangthanhinius',
'Plesiopithecus',
'Suratius',
'Killikaike blakei',
'Rissoina bonneti',
# 'Mycosphaeroides' - gone
]:
claim = Whether_extant(
name, False,
'https://github.com/OpenTreeOfLife/reference-taxonomy/issues/116')
claim.make_true(gbif)
# JAR 2014-07-18 - get rid of Helophorus duplication
# GBIF 3263442 = Helophorus Fabricius, 1775, from CoL
# in 6985 = Helophoridae Leach, 1815
# GBIF 6757656 = Helophorus Leach, from IRMNG homonym list
# in 7829 = Hydraenidae Mulsant, 1844
# ('Helophorus', 'Helophoridae') ('Helophorus', 'Hydraenidae')
gbif.taxon('3263442').absorb(gbif.taxon('6757656'))
# JAR 2015-06-27 there are two Myospalax myospalax
# The one in Spalacidae is the right one, Myospalacinae is the wrong one
# (according to NCBI)
# Probably should clean up the whole genus
# 2439121 = Myospalax myospalax (Laxmann, 1773) from CoL
gbif.taxon('2439121').absorb(gbif.taxon('6075534'))
# 4010070 pg_1378 Gelidiellaceae gbif:8998 -- ok, paraphyletic
# https://github.com/OpenTreeOfLife/feedback/issues/64
gbif.taxon('Plagiomene').extinct()
# https://github.com/OpenTreeOfLife/feedback/issues/65
gbif.taxon('Worlandia').extinct()
tip = gbif.taxon(
'6101461') # ('Tipuloidea', 'Hemiptera') gbif:6101461 - extinct
if tip != None:
tip.prune("about:blank#this-homonym-is-causing-too-much-trouble")
oph = gbif.taxon(
'4872240') # ('Ophiurina', 'Ophiurinidae') gbif:4872240 - extinct
if oph != None:
oph.prune("about:blank#this-homonym-is-causing-too-much-trouble")
# 2015-07-25 Extra Dipteras are confusing new division logic. Barren genus
gbif.taxon('3230674').prune(this_source)
# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/72
gbif.taxon('Myeladaphus').extinct()
# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/78
gbif.taxon('Oxyprinichthys').extinct()
# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/82
gbif.taxon('Tarsius thailandica').extinct()
return gbif
