silva = Taxonomy.getTaxonomy('tax/silva/', 'silva')

# Used in studies pg_2448,pg_2783,pg_2753, seen deprecated on 2015-07-20

silva.taxon('AF364847').rename('Pantoea ananatis LMG 20103') # ncbi:706191

silva.taxon('EF690403').rename('Pantoea ananatis B1-9') # ncbi:1048262

patch_silva(silva)

# Sample contamination

bad_name(silva, 'Trichoderma harzianum', 'life')

bad_name(silva, 'Sclerotinia homoeocarpa', 'life')

bad_name(silva, 'Puccinia triticina', 'life')

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/104

bad_name(silva, 'Caenorhabditis elegans', 'life')

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/100

bad_name(silva, 'Solanum lycopersicum', 'life')

# - Deal with parent/child homonyms in SILVA -

# Arbitrary choices here to eliminate ambiguities down the road when NCBI gets merged.

# (If the homonym is retained, then the merge algorithm will have no

# way to choose between them, and refuse to match either. It will

# then create a third homonym.)

# Note order dependence between the following two

silva.taxon('Intramacronucleata','Intramacronucleata').clobberName('Intramacronucleata inf.')

silva.taxon('Spirotrichea','Intramacronucleata inf.').clobberName('Spirotrichea inf.')

silva.taxon('Cyanobacteria','Bacteria').clobberName('Cyanobacteria sup.')

silva.taxon('Actinobacteria','Bacteria').clobberName('Actinobacteria sup.')

silva.taxon('Acidobacteria','Bacteria').clobberName('Acidobacteria sup.')

silva.taxon('Ochromonas','Ochromonadales').clobberName('Ochromonas sup.')

silva.taxon('Tetrasphaera','Tetrasphaera').clobberName('Tetrasphaera inf.')

# SILVA's placement of Rozella as a sibling of Fungi is contradicted

# by Hibbett 2007, which puts it under Fungi. Hibbett gets priority.

# We make the change to SILVA to prevent Nucletmycea from being

# labeled 'tattered'.

silva.taxon('Fungi').take(silva.taxon('Rozella'))

# 2014-04-12 Rick Ree #58 and #48 - make them match NCBI

silva.taxon('Arthrobacter Sp. PF2M5').rename('Arthrobacter sp. PF2M5')

silva.taxon('Halolamina sp. wsy15-h1').rename('Halolamina sp. WSY15-H1')

# RR #55 - this is a silva/ncbi homonym

silva.taxon('vesicomya').rename('Vesicomya')

# From Laura and Dail on 5 Feb 2014

# https://groups.google.com/forum/#!topic/opentreeoflife/a69fdC-N6pY

silva.taxon('Diatomea').rename('Bacillariophyta')

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/30

# https://github.com/OpenTreeOfLife/feedback/issues/5

for name in ['GAL08', 'GOUTA4', 'JL-ETNP-Z39', 'Kazan-3B-28',

'LD1-PA38', 'MVP-21', 'NPL-UPA2', 'OC31', 'RsaHF231',

'S2R-29', 'SBYG-2791', 'SM2F11', 'WCHB1-60', 'T58',

'LKM74', 'LEMD255', 'CV1-B1-93', 'H1-10', 'H26-1',

'M1-18D08', 'D4P07G08', 'DH147-EKD10', 'LG25-05',

'NAMAKO-1', 'RT5iin25', 'SA1-3C06', 'DH147-EKD23']:

silva.taxon(name).elide() #maybe just hide instead ?

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/79

Ml = silva.maybeTaxon('Melampsora lini')

if Ml != None: Ml.prune(this_source)

Ps = silva.maybeTaxon('Polyangium sorediatum')

if Ps != None: Ps.prune(this_source)

up = silva.maybeTaxon('unidentified plasmid')

if up != None: up.prune(this_source)

# https://github.com/OpenTreeOfLife/feedback/issues/45

# Not a legit name

# bad_name(silva, 'Choanoflagellida', 'Ichthyosporea')

# JAR noticed failed inclusion test - this is fixed in silva 117

silva.taxon('Bacteria').take(silva.maybeTaxon('Verrucomicrobia group'))

# EU930344 | D78004/#6 | Photorhabdus luminescens | samples | ncbi:1004165 |

# EU930342 | D78004/#6 | Photorhabdus luminescens | samples | ncbi:1004166 |

# 1004165 | 29488 | Photorhabdus luminescens subsp. caribbeanensis | subspecies |

# 1004166 | 29488 | Photorhabdus luminescens subsp. hainanensis | subspecies |

silva.taxon('EU930344').clobberName('Photorhabdus luminescens subsp. caribbeanensis')

silva.taxon('EU930342').clobberName('Photorhabdus luminescens subsp. hainanensis')

# 2015-10-12 JAR

# It is proving difficult to separate the three Ctenophora homonyms.

# Maybe it will help to add the phylum to our SILVA subset. The

# phylum is in the full SILVA and contains cluster AF293678, which

# has ref seq identified as Pleurobrachia pileus.

h2007 = Taxonomy.getNewick('feed/h2007/tree.tre', 'h2007')

# 2014-04-08 Misspelling

if h2007.maybeTaxon('Chaetothryriomycetidae') != None:

h2007.taxon('Chaetothryriomycetidae').rename('Chaetothyriomycetidae')

if h2007.maybeTaxon('Asteriniales') != None:

h2007.taxon('Asteriniales').rename('Asterinales')

else:

h2007.taxon('Asterinales').synonym('Asteriniales')

# h2007/if synonym https://github.com/OpenTreeOfLife/reference-taxonomy/issues/40

h2007.taxon('Urocystales').synonym('Urocystidales')

fung = Taxonomy.getTaxonomy('tax/fung/', 'if')

fung.analyzeMajorRankConflicts()

# 2014-04-14 Bad Fungi homonyms in new version of IF. 90156 is the good one.

# 90154 has no descendants

if fung.maybeTaxon('90154') != None:

print 'Removing Fungi 90154'

fung.taxon('90154').prune(this_source)

# 90155 is "Nom. inval." and has no descendants

if fung.maybeTaxon('90155') != None:

print 'Removing Fungi 90155'

fung.taxon('90155').prune(this_source)

fix_basal(fung)

# smush folds sibling taxa that have the same name.

# fung.smush()

if True:

patch_fung(fung)

else:

try:

patch_fung(fung)

except:

print '**** Exception in patch_fung'

fung.smush()

# analyzeMajorRankConflicts sets the "major_rank_conflict" flag when

# intermediate ranks are missing (e.g. a family that's a child of a

# class)

fung.analyzeMajorRankConflicts()

# JAR 2014-04-27 JAR found while investigating 'hidden' status of

# Thelohania butleri. Move out of Protozoa to prevent their being hidden

# --- this seems to have been fixed in the 2014-04 version of IF

# fung.taxon('Fungi').take(fung.taxon('Microsporidia'))

# *** Non-Fungi processing

# JAR 2014-05-13 Chlorophyte or fungus? This one is very confused.

# Pick it up from GBIF if at all

# Mycobank and EOL (via Mycobank) put in in Algae

# IF says it's a chlorophyte, not a fungus

# First Nature says it's a synonym for a fungus (Terana caerulea) 'Cobalt crust fungus'

# GBIF puts it in Basidiomycota (Fungi), synonym for Terana caerulea, in Phanerochaetaceae

# Study pg_391 puts it sister to Phlebiopsis gigantea, in Basidiomycota

# Study pg_1744 puts it sister to genus Phanerochaete, which is in Basidiomycota

# Study pg_1160 puts is close to Phanerochaete and Hyphodermella

# I'm thinking of putting it in Phanerochaetaceae. - GBIF does this for us.

fung.taxon('Byssus phosphorea').prune(this_source)

# IF Thraustochytriidae = SILVA Thraustochytriaceae ? (Stramenopiles)

# IF T. 90638 contains Sicyoidochytrium, Schizochytrium, Ulkenia, Thraustochytrium

# Parietichytrium, Elina, Botryochytrium, Althornia

# SILVA T. contains Ulkenia and a few others of these... I say yes.

thraust = fung.maybeTaxon('90377') # Seems to have gone away

if thraust != None:

thraust.synonym('Thraustochytriaceae')

thraust.synonym('Thraustochytriidae')

thraust.synonym('Thraustochytridae')

# IF Labyrinthulaceae = SILVA Labyrinthulomycetes ? NO.

# IF L. contains only Labyrinthomyxa, Labyrinthula

# SILVA L. contains a lot more than that.

# IF Hyphochytriaceae = SILVA Hyphochytriales ?

# SILVA Hyphochytriales = AB622284/#4 contains only

# Hypochitrium, Rhizidiomycetaceae

# There are two Bacillaria.

# 1. NCBI 3002, in Stramenopiles, contains Bacillaria paxillifer.

# No synonyms in NCBI.

# IF has Bacillaria as a synonym for Camillea (if:777).

# Bacillaria is not otherwise in IF.

# Cammillea in IF is in Stramenopiles.

# 2. NCBI 109369, in Pezizomycotina

# No synonyms in NCBI.

# NCBI 13677 = Camillea, a fish.

# There are two Polyangium, a bacterium (NCBI) and a flatworm (IF).

# smush folds sibling taxa that have the same name.

# (repeats - see load_fung() ???)

# fung.smush()

# *** Fungi processing

# JAR 2014-04-11 Missing in earlier IF, mistake in later IF -

# extraneous authority string. See Romina's issue #42

# This is a fungus.

cyph = fung.maybeTaxon('Cyphellopsis')

if cyph == None:

cyph = fung.maybeTaxon('Cyphellopsis Donk 1931')

if cyph != None:

cyph.rename('Cyphellopsis')

else:

cyph = fung.newTaxon('Cyphellopsis', 'genus', 'if:17439')

fung.taxon('Niaceae').take(cyph)

# Romina 2014-04-09

# IF has both Hypocrea and Trichoderma. Hypocrea is the right name.

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86

fung.taxon('Trichoderma viride').rename('Hypocrea rufa') # Type

fung.taxon('Hypocrea').absorb(fung.taxonThatContains('Trichoderma', 'Hypocrea rufa'))

# Romina https://github.com/OpenTreeOfLife/reference-taxonomy/issues/42

fung.taxon('Trichoderma deliquescens').rename('Hypocrea lutea')

fung.taxon('Asterinales').synonym('Asteriniales') #backward compatibility

# ** No taxon found with this name: Nowakowskiellaceae

# ** No taxon found with this name: Septochytriaceae

# ** No taxon found with this name: Jaapiaceae

# ** (null=if:81865 Rhizocarpaceae) is already a child of (null=h2007:212 Rhizocarpales)

# ** No taxon found with this name: Hyaloraphidiaceae

# Yan Wong https://github.com/OpenTreeOfLife/reference-taxonomy/issues/116

# fung.taxon('Mycosphaeroides').extinct() - gone

fung.taxon('Majasphaeridium').extinct()

fung.taxon('Urosporidium').prune(this_source) # parasitic protist, SILVA looks correct

fung.taxon('Bonamia').prune(this_source) # parasitic protist, SILVA looks correct

fung.taxon('Zonaria').prune(this_source)

fung.taxon('Ellobiopsis').prune(this_source)

# Our IF dump puts genus Saccharomycetes (21291) directly under Fungi

# (incertae sedis). The corresponding IF record on the site says

# "Position in classification: Fossil Fungi". Only two species, too

# easily confused with class Saccharamycetes (90791). Discovered while

# tracking down

# ** Ranks out of order: (if:21291 Saccharomycetes?) genus has child (if:90341 Saccharomycetidae?) subclass

# in GBIF.

# Neither SILVA nor h2007 has the class. GBIF used to have the genus,

# not sure if it still does.

cetes = fung.taxon('21291')

if cetes != None:

cetes.extinct()

cetes.prune("if:21291")

#cetes.rank = None

#tina = fung.taxon('Saccharomycetaceae', 'Fungi')

#if tina != None:

# tina.take(fung.taxon('Saccharomycetes', 'Fungi'))

#cetes.extant()

# JAR 2015-07-20 - largest unattached subtree was Microeccrina, which is dubious.

fung.taxon('Microeccrina').prune('http://www.nhm.ku.edu/~fungi/Monograph/Text/chapter12.htm')

# JAR 2015-07-20 - homonym, Nom. illegit.

fung.taxon('Acantharia').prune('http://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=8')

# JAR 2015-09-10 on perusing a long list of equivocal homonyms

# (weaklog.csv). Hibbett 2007 and NCBI put Microsporidia in Fungi.

fung.taxon('Fungi').take(fung.taxon('Microsporidia'))

# This is helpful if SAR is a division

# fung.taxon('SAR').take(fung.taxon('Oomycota'))

# 2015-09-15 Pezizomycotina has no parent pointer; without Fungi as a barrier,

# the placement of genus Onychophora is screwed up.

# Found while investigating https://github.com/OpenTreeOfLife/feedback/issues/88

fung.taxon('Ascomycota').take(fung.taxon('Pezizomycotina'))

# 2015-10-06 JAR noticed while debugging deprecated taxa list:

# This should cover Basidiomycota, Zygomycota, Glomeromycota, and Ascomycota

for taxon in fung:

if taxon.rank == 'phylum' and taxon.isRoot():

fung.taxon('Fungi').take(taxon)

# 2015-10-06 https://en.wikipedia.org/wiki/Taphrinomycotina

if fung.taxon('Taphrinomycotina').isRoot():

fung.taxon('Ascomycota').take(fung.taxon('Taphrinomycotina'))

if fung.taxon('Saccharomycotina').isRoot():

fung.taxon('Ascomycota').take(fung.taxon('Saccharomycotina'))

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))

ncbi = Taxonomy.getTaxonomy('tax/ncbi/', 'ncbi')

fix_SAR(ncbi)

ncbi.taxon('Viridiplantae').rename('Chloroplastida')

patch_ncbi(ncbi)

# analyzeOTUs sets flags on questionable taxa ("unclassified",

# hybrids, and so on) to allow the option of suppression downstream

ncbi.analyzeOTUs()

ncbi.analyzeContainers()

# New NCBI top level taxa introduced circa July 2014

for toplevel in ["Viroids", "other sequences", "unclassified sequences"]:

if ncbi.maybeTaxon(toplevel) != None:

ncbi.taxon(toplevel).prune(this_source)

# - Canonicalize division names (cf. skeleton) -

# JAR 2014-05-13 scrutinizing pin() and BarrierNodes. Wikipedia

# confirms these synonymies.

ncbi.taxon('Glaucocystophyceae').rename('Glaucophyta')

ncbi.taxon('Haptophyceae').rename('Haptophyta')

ncbi.taxon('Viruses').hide()

# - Touch-up -

# RR 2014-04-12 #49

ncbi.taxon('leotiomyceta').rename('Leotiomyceta')

# RR #53

ncbi.taxon('White-sloanea').synonym('White-Sloanea')

# RR #56

ncbi.taxon('sordariomyceta').rename('Sordariomyceta')

# RR #52

if ncbi.maybeTaxon('spinocalanus spinosus') != None:

ncbi.taxon('spinocalanus spinosus').rename('Spinocalanus spinosus')

if ncbi.maybeTaxon('spinocalanus angusticeps') != None:

ncbi.taxon('spinocalanus angusticeps').rename('Spinocalanus angusticeps')

# RR #59

ncbi.taxon('candidate division SR1').rename('Candidate division SR1')

ncbi.taxon('candidate division WS6').rename('Candidate division WS6')

ncbi.taxon('candidate division BRC1').rename('Candidate division BRC1')

ncbi.taxon('candidate division OP9').rename('Candidate division OP9')

ncbi.taxon('candidate division JS1').rename('Candidate division JS1')

# RR #51

ncbi.taxon('Dendro-hypnum').synonym('Dendro-Hypnum')

# RR #45

ncbi.taxon('Cyrto-hypnum').synonym('Cyrto-Hypnum')

# RR #54

ncbi.taxon('Sciuro-hypnum').synonym('Sciuro-Hypnum')

# RR 2014-04-12 #46

ncbi.taxon('Pechuel-loeschea').synonym('Pechuel-Loeschea')

# RR #50

ncbi.taxon('Saxofridericia').synonym('Saxo-Fridericia')

ncbi.taxon('Saxofridericia').synonym('Saxo-fridericia')

# RR #57

ncbi.taxon('Solms-laubachia').synonym('Solms-Laubachia')

# Romina 2014-04-09

# NCBI has both Hypocrea and Trichoderma.

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86

ncbi.taxon('Trichoderma viride').rename('Hypocrea rufa') # Type

ncbi.taxon('Hypocrea').absorb(ncbi.taxonThatContains('Trichoderma', 'Hypocrea rufa'))

# Mark Holder https://github.com/OpenTreeOfLife/reference-taxonomy/issues/120

ncbi.taxon('Cetartiodactyla').synonym('Artiodactyla')

# Cody Howard https://github.com/OpenTreeOfLife/feedback/issues/57

# http://dx.doi.org/10.1002/fedr.19971080106

ncbi.taxon('Massonieae').take(ncbi.taxon('Resnova'))

# From examining the deprecated OTU list. This one occurs in study pg_188

# Name got better, old name lost JAR 2015-06-27

# This could probably be automated, just by looking up the NCBI id

# in the right table.

for (oldname, ncbiid) in [

('Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505', '547043'),

('Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043', '566552'),

('Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775', '866789'),

('Borrelia sp. SV1', 498741), # Borrelia finlandensis

('Planchonella sp. Meyer 3013', 371649), #was 419398

('Planchonella sp. Takeuchi & al 17902', 419399),

('Sersalisia sp. Bartish and Ford 33', 346601), #was 346602

('Borrelia sp. SV1', 498741),

('Planchonella sp. Meyer 3013', 419398),

('Planchonella sp. Takeuchi & al 17902', 419399),

('Pycnandra sp. Munzinger 2618', 550765),

('Pycnandra sp. Munzinger 2615', 550764),

('Pycnandra sp. Munzinger 3135', 550768),

('Pycnandra sp. Lowry et al. 5786', 280721), #was 280735

('Osmolindsaea sp. SL02013b', 1393958),

('Osmolindsaea sp. SL-2013a', 1388881),

('Docosaccus sp. GW5429', 1503681), #was 582882

('Lellingeria sp. MAS-2010', 741642),

('Terpsichore sp. MAS-2010d', 741647),

('Terpsichore sp. MAS-2010c', 741646),

('Terpsichore sp. MAS-2010b', 741644),

# ('Narrabeena sp. 0CDN6739-K', 1342637), left no forwarding address

('Iochroma sp. Smith 337', 1545467), #was 362368

('Iochroma sp. Smith 370', 1545468), #was 362367

('cyanobacterium endosymbiont of Epithemia turgida isolate ETSB Lake Yunoko', 1228987),

('Pycnandra sp. McPherson and Munzinger 18106', 278656),

('Lellingeria sp. PHL-2010c', 861204),

('Lellingeria sp. PHL-2010d', 861206),

('Lellingeria sp. PHL-2010a', 861202),

('Pycnandra sp. Munzinger 2885', 550767),

('Pycnandra sp. Munzinger 2624', 550766),

('Caenorhabditis briggsae AF16', 6238), #was 473542

('Tachigali sp. Clarke 7212', 162921),

('Euretidae sp. HBFH 16-XI-02-1-001', 396898),

('Cedrela sp. 4 ANM-2010', 582833), #was 934059

('Schismatoglottis sp. SYW-2010f', 743908),

('Schismatoglottis sp. SYW-2010c', 743905),

('Pycnandra sp. Swenson 597', 282185),

('Planchonella sp. Meyer 3013', 73570),

('Pycnandra sp. Lowry et al. 5786', 9539),

('Docosaccus sp. GW5429', 7764),

('Narrabeena sp. 0CDN6739-K', 39542),

('Iochroma sp. Smith 337', 8960),

('Iochroma sp. Smith 370', 8953),

('Caenorhabditis briggsae AF16', 1949),

('Cedrela sp. 4 ANM-2010', 624),

]:

tax = ncbi.maybeTaxon(str(ncbiid))

if tax != None:

tax.synonym(oldname)

# Try to prevent confusion with GBIF genus Eucarya in Magnoliopsida

ncbi.taxon('Eukaryota').notCalled('Eucarya')

# JAR 2015-07-25 Prevent extinction of Myxogastria

ncbi.taxon('Myxogastria').notCalled('Myxomycetes')

# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/83

# https://dx.doi.org/10.1007/s10764-010-9443-1 paywalled

ncbi.taxon('Tarsius syrichta').rename('Carlito syrichta')

# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/84

ncbi.taxon('Tarsius bancanus').rename('Cephalopachus bancanus')

# Yan Wong 2015-10-10 http://www.iucnredlist.org/details/22732/0

uncia = ncbi.taxon('Uncia uncia')

uncia.rename('Panthera uncia')

ncbi.taxon('Panthera', 'Felidae').take(uncia)

# Marc Jones 2015-10-10 https://groups.google.com/d/msg/opentreeoflife/wCP7ervK8YE/DbbonQtkBQAJ

worms = Taxonomy.getTaxonomy('tax/worms/', 'worms')

worms.smush()

worms.taxon('Biota').rename('life')

worms.taxon('Animalia').synonym('Metazoa')

fix_basal(worms)

# 2015-02-17 According to WoRMS web site. Occurs in pg_1229

if worms.maybeTaxon('Scenedesmus communis') != None:

worms.taxon('Scenedesmus communis').synonym('Scenedesmus caudata')

# See NCBI

worms.taxon('Millericrinida').extant()

# Help to match up with IRMNG

worms.taxon('Ochrophyta').synonym('Heterokontophyta')

worms.smush() # Gracilimesus gorbunovi, pg_1783

gbif = Taxonomy.getTaxonomy('tax/gbif/', 'gbif')

gbif.smush()

# In GBIF, if a rank is skipped for some children but not others, that

# means the rank-skipped children are incertae sedis. Mark them so.

gbif.analyzeMajorRankConflicts()

fix_basal(gbif) # creates a Eukaryota node

gbif.taxon('Animalia').synonym('Metazoa')

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()

irmng = Taxonomy.getTaxonomy('tax/irmng/', 'irmng')

irmng.smush()

irmng.analyzeMajorRankConflicts()

fix_basal(irmng)

irmng.taxon('Animalia').synonym('Metazoa')

# JAR 2014-04-26 Flush all 'Unaccepted' taxa

irmng.taxon('Unaccepted', 'life').prune(this_source)

# Fixes

# Neopithecus (extinct) occurs in two places. Flush one, mark the other

irmng.taxon('1413316').prune(this_source) #Neopithecus in Mammalia

irmng.taxon('1413315').extinct() #Neopithecus in Primates (Pongidae)

# RR #50

# irmng.taxon('Saxo-Fridericia').rename('Saxofridericia')

# irmng.taxon('Saxofridericia').absorb(irmng.taxon('Saxo-fridericia'))

saxo = irmng.maybeTaxon('1063899')

if saxo != None:

saxo.absorb(irmng.taxon('1071613'))

# Romina 2014-04-09

# IRMNG has EIGHT different Trichodermas. (Four are synonyms of other things.)

# 1307461 = Trichoderma Persoon 1794, in Hypocreaceae

# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/86

irmng.taxon('Hypocrea').absorb(irmng.taxon('1307461'))

# JAR 2015-06-28

# The synonym Ochrothallus multipetalus -> Niemeyera multipetala

# is no good; it interferes with correct processing of Ochrothallus

# multipetalus. We could remove the synonym, but instead remove its

# target because no synonym-removal command is available.

irmng.taxon('Niemeyera multipetala').prune(this_source)

tip = irmng.taxon('Tipuloidea', 'Hemiptera') # irmng:1170022

if tip != None:

tip.prune("about:blank#this-homonym-is-causing-too-much-trouble")

oph = irmng.taxon('Ophiurina', 'Ophiurinidae') # irmng:1346026

if oph != None:

oph.prune("about:blank#this-homonym-is-causing-too-much-trouble")

# NCBI synonymizes Pelecypoda = Bivalvia

irmng.taxon('Bivalvia').absorb(irmng.taxon('Pelecypoda')) # bogus order

# hmm

irmng.taxon('Bivalvia').extant()

# This one was mapping to Blattodea, and making it extinct.

# Caused me a couple of hours of grief.

# My guess is it's because its unique child Sinogramma is in Blattodea in GBIF.

# Wikipedia says it's paraphyletic.

irmng.taxon('Blattoptera', 'Insecta').prune('https://en.wikipedia.org/wiki/Blattoptera')

# 2015-07-25 Found while trying to figure out why Theraphosidae was marked extinct.

# NCBI thinks that Theraphosidae and Aviculariidae are the same.

irmng.taxon('Aviculariidae').extant()

# 2015-07-25 Extra Dipteras are confusing new division logic. Barren genus

irmng.taxon('1323521').prune(this_source)

# 2015-09-10 This one is unclassified (Diptera) and is leading to confusion with two other Steinias.

irmng.taxon('1299622').prune(this_source)

# 2015-09-11 https://github.com/OpenTreeOfLife/feedback/issues/74

# Lymnea is a snail, not a shark

irmng.taxon('1317416').prune(this_source)

# 2015-10-12 JAR checked IRMNG online and this taxon (Ctenophora in Chelicerata) did not exist

if irmng.maybeTaxon('1279363') != None:

irmng.taxon('1279363').prune(this_source)

euk = tax.maybeTaxon('Eukaryota')

if euk == None:

euk = tax.newTaxon('Eukaryota', 'domain', 'ncbi:2759')

co = tax.maybeTaxon('cellular organisms')

if co != None: co.take(euk)

else:

li = tax.maybeTaxon('life')

if li != None: li.take(euk)

else:

print('* No parent "life" for Eukaryota, probably OK')

for name in ['Animalia', 'Fungi', 'Plantae']:

node = tax.maybeTaxon(name)

if node != None:

euk.take(node)

for name in ['Chromista', 'Protozoa', 'Protista']:

bad = tax.maybeTaxon(name)

if bad != None:

euk.take(bad)

bad.hide() # recursive

for child in bad.children:

child.incertaeSedis()

bad.elide()

sar = tax.maybeTaxon('SAR')

if sar == None:

euk = tax.taxon('Eukaryota')

s = tax.maybeTaxon('Stramenopiles')

if s == None:

s = tax.maybeTaxon('Heterokonta')

a = tax.maybeTaxon('Alveolata')

r = tax.maybeTaxon('Rhizaria')

if s != None or a != None or r != None:

sar = tax.newTaxon('SAR', None, 'silva:E17133/#2')

euk.take(sar)

if s != None: sar.take(s)

else: print '** No Stramenopiles'

if a != None: sar.take(a)

else: print '** No Alveolata'

if r != None: sar.take(r)

euk = tax.taxon('Eukaryota')

# 1. co-opt GBIF taxon for a slightly different purpose

plants = tax.maybeTaxon('Plantae')

if plants != None:

plants.rename('Chloroplastida')

# euk.take(plants) ???

if euk != None:

# JAR 2014-04-25 GBIF puts rhodophytes under Plantae, but it's not

# in Chloroplastida.

# Need to fix this before alignment because of division calculations.

# Plantae is a child of 'life' in GBIF, and Rhodophyta is one of many

# phyla below that. Move up to be a sibling of Plantae.

# This redefines GBIF Plantae, sort of, which is not nice.

# Discovered while looking at Bostrychia alignment problem.

# JAR 2014-05-13 similarly

# Glaucophyta - there's a GBIF/IRMNG false homonym, should be merged

# This needs to match the skeleton!

for name in ['Rhodophyta', 'Glaucophyta', 'Haptophyta', 'Fungi', 'Metazoa', 'Chloroplastida']:

# should check to see if this is an improvement in specificity?

rho = tax.maybeTaxon(name)

if rho != None: