messaging: host: mq.gbif.org virtualHost: /users/mdoering username: clb password: clb neo: neoRepository: /tmp/col/neo mappedMemory: 2048 neoSources: neoRepository: /tmp/col/neo mappedMemory: 256 sourceLoaderThreads: 3 clb: serverName: backbonebuild-vh.gbif.org databaseName: clb user: clb password: "%BBJu2MgstXJ" maximumPoolSize: 8 minimumIdle: 2 idleTimeout: 60000 connectionTimeout: 2000 parserTimeout: 20000 registry: wsUrl: http://api.gbif.org/v1 autoImport: true validate: false runAssertions: false groupBasionyms: true keepLonelyAutonyms: false keepEmptyImplicitNames: false reportDir: /home/crap/logs 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