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mdoering/clb-nub.yaml

Created August 22, 2023 08:00
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nub config 2023
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clb-nub.yaml
autoImport: true
validate: false
runAssertions: false
groupBasionyms: true
keepLonelyAutonyms: false
keepEmptyImplicitNames: false
blacklist:
- Calendrella cinerea ongumaensis # https://github.com/gbif/checklistbank/issues/47
- Tricholaema leucomelan namaqua # https://github.com/gbif/checklistbank/issues/46
- Hirundo D'Orbigny & Lafresnaye, 1838 # https://github.com/gbif/portal-feedback/issues/3250
- Unaccepted
- Incertae # https://github.com/gbif/portal-feedback/issues/1845
- Scientific # https://github.com/gbif/portal-feedback/issues/2726
- Scientific name
- Flowering plant
- Strawberry witches phytoplasma
- Grey lichens
- Lichens
- Lower plants (Lichens)
- Diptera larva
- Gen # https://github.com/gbif/checklistbank/issues/230
- Gen sp
- Gen spec
- Sedum rupestre Hacq. ex Nyman, 1879 # https://github.com/gbif/checklistbank/issues/233
- Polistes gen. Fuscopolistes Fuscopolistes # https://github.com/gbif/portal-feedback/issues/4750
- Polistes (Fuscopolistes) Fuscopolistes # https://github.com/gbif/portal-feedback/issues/4750
- Hyla QUOYI – HYLA PRASINA CASE # https://github.com/gbif/checklistbank/issues/273
- Phimenes de Saussure, 1855 # https://github.com/gbif/portal-feedback/issues/4749
- Strophorus burrelli Hoser, 2005 # https://github.com/gbif/portal-feedback/issues/4530
- Strophorus Fitzinger, 1843
sources:
- key: daacce49-b206-469b-8dc2-2257719f3afa # GBIF Backbone Patch
rank: KINGDOM
homonyms: true
unranked: true
- key: 7ea21580-4f06-469d-995b-3f713fdcc37c # GBIF Algae Classification
rank: PHYLUM
- key: 484039df-cd14-46d1-9a41-c406db8c7ced # Alucitoidea Hobern
rank: PHYLUM
- key: c815ecb1-b036-4617-b545-1bb65e0339cd # Pterophoroidea Hobern
rank: PHYLUM
- key: 7be186c4-5572-44e6-9f11-69ddbfd95078 # Hominidae
rank: PHYLUM
- key: a97f36e5-ded1-49cc-bdec-ac6170fc7b9c # Genome Taxonomy Database
rank: PHYLUM
OTU: true
nameTypeMapping:
HYBRID: OTU
BLACKLISTED: OTU
DOUBTFUL: OTU
NO_NAME: OTU
INFORMAL: OTU
- key: aa1bc573-f338-482d-b6aa-f371d57f20f5 # Genome Taxonomy Database supplement
rank: PHYLUM
OTU: true
nameTypeMapping:
HYBRID: OTU
BLACKLISTED: OTU
DOUBTFUL: OTU
NO_NAME: OTU
INFORMAL: OTU
- key: 7ddf754f-d193-4cc9-b351-99906754a03b # Catalogue of Life
rank: KINGDOM
homonyms: true
exclude:
- name: Bacteria # follow GTDB instead
rank: KINGDOM
- name: Archaea # follow GTDB instead
rank: KINGDOM
- key: 80dd9c94-241b-4d49-999f-c89de7648525 # World Spider Catalog
scope:
name: Arachnida
rank: CLASS
- key: f382f0ce-323a-4091-bb9f-add557f3a9a2 # World Checklist of Vascular Plants
scope:
name: Plantae
rank: KINGDOM
- key: 52a423d2-0486-4e77-bcee-6350d708d6ff # Prokaryotic Nomenclature Up-to-date
- key: e01b0cbb-a10a-420c-b5f3-a3b20cc266ad # ICTV Master Species List
- key: 47f16512-bf31-410f-B272-d151c996b2f6 # The Clements Checklist
scope:
name: Aves
rank: CLASS
- key: c696e5ee-9088-4d11-bdae-ab88daffab78 # IOC World Bird Names
scope:
name: Aves
rank: CLASS
- key: 47a779a6-a230-4edd-b787-19c3d2c80ab5 # Species Files ORG
- key: 994e75fa-b187-4b07-a30e-665f4acbe394 # Myriatrix
scope:
name: Arthropoda
rank: PHYLUM
exclude:
- name: Deleted taxa
rank: UNRANKED
- key: 763a8aa3-65de-443e-bd20-bbe958a1ef74 # New Zealand Marine Macroalgae
rank: FAMILY
- key: 2d59e5db-57ad-41ff-97d6-11f5fb264527 # World Register of Marine Species
- key: f43069fe-38c1-43e3-8293-37583dcf5547 # Danish Mycological Society - Checklist of Fungi
scope:
name: Fungi
rank: KINGDOM
- key: a43ec6d8-7b8a-4868-ad74-56b824c75698 # Fungi, flora and fauna of Madeira and Selvagens
- key: da38f103-4410-43d1-b716-ea6b1b92bbac # Catalogue of Afrotropical Bees
- key: ded724e7-3fde-49c5-bfa3-03b4045c4c5f # EDIT Cichorieae
- key: 56c83fd9-533b-4b77-a67a-cf521816866e # Catalogue of Tenebrionidae (Coleoptera) of North America
- key: 7a9bccd4-32fc-420e-a73b-352b92267571 # Checklist of Beetles (Coleoptera) of Canada and Alaska. Second Edition.
- key: e768b669-5f12-42b3-9bc7-ede76e4436fa # Carabodes cephalotes
- key: e402255a-aed1-4701-9b96-14368e1b5d6b # World Typhlocybinae database
- key: 96dfd141-7bca-4f82-9325-4420d24e0793 # Spinnengids
- key: 65c9103f-2fbf-414b-9b0b-e47ca96c5df2 # Afromoths
- key: bd25fbf7-278f-41d6-bc17-9f08f2632f70 # True Fruit Flies of the Afrotropical Region
- key: 1a540a73-a60d-4816-bff6-b1ac74b598c9 # DiversityTaxonNames Server
- key: 19491596-35ae-4a91-9a98-85cf505f1bd3 # IUCN redlist
- key: 672aca30-f1b5-43d3-8a2b-c1606125fa1b # Mammal Species of the World
scope:
name: Mammalia
rank: CLASS
- key: de8934f4-a136-481c-a87a-b0b202b80a31 # Dyntaxa - Svensk taxonomisk databas
exclude:
- name: Bursaphelenchus xylophilus # misapplied only!
rank: SPECIES
- key: aacd816d-662c-49d2-ad1a-97e66e2a2908 # Flora of Brazil
- key: 4dd32523-a3a3-43b7-84df-4cda02f15cf7 # Dutch Species Register
- key: a6c6cead-b5ce-4a4e-8cf5-1542ba708dec # Artsnavnebasen
- key: bae5856f-da10-4333-90a0-5a2135361b30 # Leipzig catalogue of vascular plants
scope:
name: Plantae
rank: KINGDOM
exclude:
- name: Paradiophyllochloa cordovensis # https://github.com/gbif/portal-feedback/issues/4835
rank: SPECIES
- name: Paradiophyllochloa missiona
rank: SPECIES
- name: Paradiophyllochloa ovulifera
rank: SPECIES
- name: Paradiophyllochloa penicillata
rank: SPECIES
- key: 3f8a1297-3259-4700-91fc-acc4170b27ce # Database of Vascular Plants of Canada (VASCAN)
scope:
name: Plantae
rank: KINGDOM
- key: 1ffe055f-adda-461e-823a-d98e53d1e8de # Annotated checklist of endemic species from the Western Balkans
- key: 4b3e4a71-704a-485c-917c-20a89944ea37 # Danish national list
exclude:
- name: Fungi
rank: KINGDOM
- key: dbaa27eb-29e7-4cbb-8eab-3f689cfce116 # UK Species Inventory
- key: d9a4eedb-e985-4456-ad46-3df8472e00e8 # Plant List with literature
scope:
name: Plantae
rank: KINGDOM
- key: 9ca92552-f23a-41a8-a140-01abaa31c931 # ITIS
- key: 0e61f8fe-7d25-4f81-ada7-d970bbb2c6d6 # TAXREF
- key: 66dd0960-2d7d-46ee-a491-87b9adcfe7b1 # GRIN Taxonomy
scope:
name: Plantae
rank: KINGDOM
- key: 1ec61203-14fa-4fbd-8ee5-a4a80257b45a # The National Checklist of Taiwan
- key: e1c9e885-9d8c-45b5-9f7d-b710ac2b303b # Endemic species in Taiwan
- key: 1ffe055f-adda-461e-823a-d98e53d1e8de # Annotated checklist of endemic species from the Western Balkans
- key: 90d9e8a6-0ce1-472d-b682-3451095dbc5a # Fauna Europaea
- key: c301eb23-63d4-48dd-addf-b2a9c9c260fd # Asiloid Flies. New taxa of Diptera Apioceridae, Asilidae, and Mydidae
- key: 8d431c96-9e2f-4249-8b0a-d875e3273908 # Catalogue of the type specimens of Cosmopterigidae
- key: b267ac9b-6516-458e-bea7-7643842187f7 # Catalogue of the type specimens of Polycestinae
- key: 5c7bf05c-2890-48e8-9b65-a6060cb75d6d # Catalogue of the type specimens of Bufonidae and Megophryidae
- key: e2116003-7282-4547-bf24-dabe0a0d76ee # Systema Dipterorum
scope:
name: Diptera
rank: ORDER
- key: 046bbc50-cae2-47ff-aa43-729fbf53f7c5 # International Plant Names Index
scope:
name: Plantae
rank: KINGDOM
- key: 80b4b440-eaca-4860-aadf-d0dfdd3e856e # Official Lists and Indexes of Names in Zoology
scope:
name: Animalia
rank: KINGDOM
- key: c8227bb4-4143-443f-8cb2-51f9576aff14 # ZooBank
rank: GENUS
scope:
name: Animalia
rank: KINGDOM
- key: 61a5f178-b5fb-4484-b6d8-9b129739e59d # UNITE - Unified system for the DNA based fungal species linked to the classification
OTU: true
exclude:
- name: Alveolata
rank: KINGDOM
- name: Amoebozoa
rank: KINGDOM
- name: Apusozoa
rank: KINGDOM
- name: Choanoflagellozoa
rank: KINGDOM
- name: Cryptista
rank: KINGDOM
- name: Euglenozoa
rank: KINGDOM
- name: Eukaryota kgd Incertae sedis
rank: KINGDOM
- name: Filasteriae
rank: KINGDOM
- name: Fornicata
rank: KINGDOM
- name: Glaucocystoplantae
rank: KINGDOM
- name: Haptista
rank: KINGDOM
- name: Heterolobosa
rank: KINGDOM
- name: Ichthyosporia
rank: KINGDOM
- name: Metazoa
rank: KINGDOM
- name: Nucleariae
rank: KINGDOM
- name: Parabasalia
rank: KINGDOM
- name: Picozoa
rank: KINGDOM
- name: Planomonada
rank: KINGDOM
- name: Protista
rank: KINGDOM
- key: 4cec8fef-f129-4966-89b7-4f8439aba058 # iBOL/BOLD
OTU: true
exclude:
- name: Curculionidae
rank: GENUS
- key: f65a5234-a8f5-4c03-baa6-029fb56ac55b # Cortinariaceae from Index Fungorum API
scope:
name: Fungi
rank: KINGDOM
- key: bf3db7c9-5e5d-4fd0-bd5b-94539eaf9598 # Index Fungorum
scope:
name: Fungi
rank: KINGDOM
- key: 0ed9e0d4-af21-4f49-9f49-11e75d690b93 # Backbone Nomenclator
- key: 0938172b-2086-439c-a1dd-c21cb0109ed5 # IRMNG
- key: 5c0b1470-8884-4914-ae76-70a7c81d6d08 # Catálogo de Plantas y Líquenes de Colombia
- key: 6c9c4b08-4cec-4160-a708-7f16060d7db0 # Lista de referencia de especies de aves de Colombia - 2020
scope:
name: Aves
rank: CLASS
- key: 973da290-27d9-48cc-9e29-3186dafdb506 # Lista de especies de vertebrados registrados en jurisdicción del Departamento del Huila
- key: 00e791be-36ae-40ee-8165-0b2cb0b8c84f # Famous species
rank: GENUS
- key: 7ce8aef0-9e92-11dc-8738-b8a03c50a862 # Plazi ORG
rank: GENUS
synonyms: false
- key: fcab086c-35a9-4080-90f9-7a644afbe81c # Russian Earthworms, pt1
scope:
name: Clitellata
rank: CLASS
- key: 4aace3c6-f108-439a-82af-b4615404a236 # Russian Earthworms, pt2
scope:
name: Clitellata
rank: CLASS
- key: c33ce2f2-c3cc-43a5-a380-fe4526d63650 # Paleobiology Database
- key: 6e4c3b6f-0126-4c5f-bd63-fe6ffd3b29fa # Family Classification Patch
# excluded datasets from publishers like Plazi
datasetExclusions:
- c35887df-f50e-4c13-8b29-5f23d0e1df75 # Hyla Quoyi-Hyla Prasina Case
# epithets keyed by family
basionymExclusions:
Chrysomelidae:
- nigripennis # https://github.com/gbif/checklistbank/issues/179
Orchidaceae:
- extinctoria # https://github.com/gbif/portal-feedback/issues/4170
Cicadellidae:
- guttulata # https://github.com/CatalogueOfLife/testing/issues/135
Nymphalidae:
- mylitta # https://github.com/gbif/portal-feedback/issues/4332
# Wrong homonyms above species rank that should be excluded from the backbone, regardless of which source they came from.
# List of canonical names with its direct parent to identifiy the version to be removed.
# All other names with the same canonical name, but different parent, are kept.
homonymExclusions:
# order
Diplomonadida:
- Eopharyngea
Piroplasmida:
- Miozoa
Trichomonadida:
- Trichomonadea
# families
Glossoscolecidae:
- Crassiclitellata
# genera
Abisara:
- Riodinidae
Actinosphaera:
- Watznaueriaceae
Aethia:
- Lonchocephalidae
Alesa:
- Riodinidae
Anama:
- Cerambycidae
Ancyluris:
- Riodinidae
Aniculus:
- Paguridea
Anteros:
- Riodinidae
Apodemia:
- Riodinidae
Argyrogrammana:
- Riodinidae
Aricoris:
- Riodinidae
Arpadites:
- Trachyceratidae
Audre:
- Riodinidae
Axiagasta:
- Geometridae
Babesia:
- Aegyptianella
Baeotis:
- Riodinidae
Barbicornis:
- Riodinidae
Barroisiceras:
- Muniericeratidae
Bartramia:
- Bryopsida
Cadosinopsis:
- Thoracosphaeraceae
Calephelis:
- Riodinidae
Calydna:
- Riodinidae
Caria:
- Riodinidae
Carterus:
- Curculionidae
Cerceris:
- Masaridae
Chaetophora:
- Chaetophoraceae
Chalodeta:
- Riodinidae
Chamaelimnas:
- Riodinidae
Charis:
- Riodinidae
Chorinea:
- Riodinidae
Cicada:
- Animalia
- Cicadellidae
Clionites:
- Sandlingitidae
Cnemidophorus:
- Curculionidae
Coccinella:
- Hydrophilidae
- Mollusca
Colaciticus:
- Riodinidae
Cremna:
- Riodinidae
Curculionites:
- Coleoptera
Cyrtia:
- Syringothyrididae
Dardanus:
- Paguridae
Dicallaneura:
- Riodinidae
Discias:
- Bresiliidae
Dodona:
- Riodinidae
Ducellieria:
- Ducellieriaceae
Dysmathia:
- Riodinidae
Ematurgina:
- Riodinidae
Emesis:
- Riodinidae
Endemosarca:
- Endemosarcaceae
Esthemopsis:
- Riodinidae
Eurybia:
- Riodinidae
Euselasia:
- Riodinidae
Heliodiscus:
- Bacillariophyceae
Hermathena:
- Riodinidae
Heteronyx:
- Curculionidae
Hiatella:
- Lyonsiidae
Hirundo:
- Annelida
Hyphilaria:
- Riodinidae
Ichneumon:
- Eulophidae
Imelda:
- Riodinidae
Ithomeis:
- Riodinidae
Ithomiola:
- Riodinidae
Ixodes:
- Aves
Jerdonia:
- Aves # https://github.com/gbif/portal-feedback/issues/2724
Komiella:
- Rugosochonetidae
Lasaia:
- Riodinidae
Lemonias:
- Riodinidae
Lepricornis:
- Riodinidae
Leucochimona:
- Riodinidae
Ligniera:
- Plasmodiophoraceae
Lyropteryx:
- Riodinidae
Lytoceras:
- Tetragonitidae
Melanis:
- Riodinidae
Membranosorus:
- Plasmodiophoraceae
Menander:
- Riodinidae
Mesene:
- Riodinidae
Mesenopsis:
- Riodinidae
Mesosemia:
- Riodinidae
Metacharis:
- Riodinidae
Milvus:
- Falconidae
Monethe:
- Riodinidae
Musca:
- Tachinidae
Napaea:
- Riodinidae
Necyria:
- Riodinidae
Nymphidium:
- Riodinidae
Octomyxa:
- Plasmodiophoraceae
Octotoma:
- Dryophthoridae
Oligomerus:
- Ptinidae
Omma:
- Cupedidae
Pachythone:
- Riodinidae
Panara:
- Riodinidae
Pandemos:
- Riodinidae
Paracrangon:
- Hippolytidae
Parahoplites:
- Deshayesitidae
Paralaxita:
- Riodinidae
Pelecanus:
- Dinosauria
Phaenochitonia:
- Riodinidae
Planaria:
- Nemertea
Plasmodiophora:
- Plasmodiophoraceae
Platyrhynchus:
- Attelabidae
Pleuridium:
- Archidiaceae
Polycaena:
- Riodinidae
Polymyxa:
- Plasmodiophoraceae
Praetaxila:
- Riodinidae
Productus:
- Aulostegidae
Productus:
- Linoproductidae
Productus:
- Productellidae
Psorergates:
- Cheyletidae
Pterographium:
- Riodinidae
Raphidiophrys:
- Raphidiophryidae
Rodinia:
- Riodinidae
Roeberella:
- Riodinidae
Semomesia:
- Riodinidae
Setabis:
- Riodinidae
Siseme:
- Riodinidae
Sorodiscus:
- Plasmodiophoraceae
Sphex:
- Pompilidae
Sphex:
- Vespidae
Spirifer:
- Paeckelmanellidae
Spiriferina:
- Paraspiriferinidae
Spiriferina:
- Spiriferellidae
Sporomyxa:
- Plasmodiophoraceae
Stichelia:
- Riodinidae
Symmachia:
- Riodinidae
Syrmatia:
- Riodinidae
Taxila:
- Riodinidae
Teratophthalma:
- Riodinidae
Tetramyxa:
- Plasmodiophoraceae
Tettigonia:
- Cicadidae
Thalassomyces:
- Ellobiopsidae
Themone:
- Riodinidae
Theope:
- Riodinidae
Vrilletta:
- Curculionidae
Woronina:
- Plasmodiophoraceae
Xenandra:
- Riodinidae
Zelotaea:
- Riodinidae
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