From c54b53e12c5914bc9ad68a39315c0ee2e565adc6 Mon Sep 17 00:00:00 2001 From: DOH-LMT2303 Date: Fri, 8 Nov 2024 01:21:45 +0000 Subject: [PATCH 1/8] Add mapping file host to host genus and host type --- .../defaults/host_hostgenus_hosttype_map.tsv | 284 ++++++++++++++++++ 1 file changed, 284 insertions(+) create mode 100644 ingest/defaults/host_hostgenus_hosttype_map.tsv diff --git a/ingest/defaults/host_hostgenus_hosttype_map.tsv b/ingest/defaults/host_hostgenus_hosttype_map.tsv new file mode 100644 index 0000000..a1d6b5e --- /dev/null +++ b/ingest/defaults/host_hostgenus_hosttype_map.tsv @@ -0,0 +1,284 @@ +"Host" "Host_Genus" "Host_Type" +"Homo sapiens" "Homo" "Human" +"Culex pipiens" "Culex" "Mosquito" +"Culex annulirostris" "Culex" "Mosquito" +"Culex perexiguus" "Culex" "Mosquito" +"Ochlerotatus communis" "Ochlerotatus" "Mosquito" +"Anopheles maculipennis" "Anopheles" "Mosquito" +"Culex quinquefasciatus" "Culex" "Mosquito" +"Anopheles atroparvus" "Anopheles" "Mosquito" +"Culex modestus" "Culex" "Mosquito" +"Culex tarsalis" "Culex" "Mosquito" +"Culex restuans" "Culex" "Mosquito" +"Culiseta melanura" "Culiseta" "Mosquito" +"Aedes cinereus" "Aedes" "Mosquito" +"Culex" "Culex" "Mosquito" +"Culex erraticus" "Culex" "Mosquito" +"Culex salinarius" "Culex" "Mosquito" +"Coquillettidia perturbans" "Coquillettidia" "Mosquito" +"Psorophora ferox" "Psorophora" "Mosquito" +"Culiseta morsitans" "Culiseta" "Mosquito" +"Ochlerotatus canadensis" "Ochlerotatus" "Mosquito" +"Culex tritaeniorhynchus" "Culex" "Mosquito" +"Culex vishnui" "Culex" "Mosquito" +"Culex neavei" "Culex" "Mosquito" +"Culex poicilipes" "Culex" "Mosquito" +"Culex bitaeniorhynchus" "Culex" "Mosquito" +"Culex perfuscus" "Culex" "Mosquito" +"Culex antennatus" "Culex" "Mosquito" +"Aedes vexans" "Aedes" "Mosquito" +"Culex pseudovishnui" "Culex" "Mosquito" +"Culex gelidus" "Culex" "Mosquito" +"Coquillettidia" "Coquillettidia" "Mosquito" +"Aedes dalzieli" "Aedes" "Mosquito" +"Mansonia uniformis" "Mansonia" "Mosquito" +"Anopheles stephensi" "Anopheles" "Mosquito" +"Culex sitiens" "Culex" "Mosquito" +"Culiseta longiareolata" "Culiseta" "Mosquito" +"Culex pipiens sensu lato" "Culex" "Mosquito" +"Culex theileri" "Culex" "Mosquito" +"Culex univittatus" "Culex" "Mosquito" +"Culicidae" "Culicidae" "Mosquito" +"Aedes albopictus" "Aedes" "Mosquito" +"Anopheles hyrcanus" "Anopheles" "Mosquito" +"Coquillettidia richiardii" "Coquillettidia" "Mosquito" +"Anopheles plumbeus" "Anopheles" "Mosquito" +"Culex pipiens complex" "Culex" "Mosquito" +"Psorophora" "Psorophora" "Mosquito" +"Culex stigmatosoma" "Culex" "Mosquito" +"Culex erythrothorax" "Culex" "Mosquito" +"Culex nigripalpus" "Culex" "Mosquito" +"Culex pipiens pipiens" "Culex" "Mosquito" +"Culex whitmorei" "Culex" "Mosquito" +"Anopheles bancroftii" "Anopheles" "Mosquito" +"Culex squamosus" "Culex" "Mosquito" +"Anopheles farauti" "Anopheles" "Mosquito" +"Culex pullus" "Culex" "Mosquito" +"Culiseta" "Culiseta" "Mosquito" +"Aedes sp." "Aedes" "Mosquito" +"Anopheles sp." "Anopheles" "Mosquito" +"Anopheles pauliani" "Anopheles" "Mosquito" +"Anopheles coustani" "Anopheles" "Mosquito" +"Aedeomyia madagascarica" "Aedeomyia" "Mosquito" +"Ochlerotatus dorsalis" "Ochlerotatus" "Mosquito" +"Ochlerotatus trivittatus" "Ochlerotatus" "Mosquito" +"Culiseta inornata" "Culiseta" "Mosquito" +"Ochlerotatus flavescens" "Ochlerotatus" "Mosquito" +"Ochlerotatus spencerii" "Ochlerotatus" "Mosquito" +"Uranotaenia unguiculata" "Uranotaenia" "Mosquito" +"Ochlerotatus caspius" "Ochlerotatus" "Mosquito" +"Ochlerotatus sollicitans" "Ochlerotatus" "Mosquito" +"Ochlerotatus triseriatus" "Ochlerotatus" "Mosquito" +"Ochlerotatus cantator" "Ochlerotatus" "Mosquito" +"Ochlerotatus sticticus" "Ochlerotatus" "Mosquito" +"Aedes rossicus" "Aedes" "Mosquito" +"Uranotaenia" "Uranotaenia" "Mosquito" +"Culex interrogator" "Culex" "Mosquito" +"Anopheles messeae" "Anopheles" "Mosquito" +"Pica pica" "Pica" "Bird" +"Corvus cornix" "Corvus" "Bird" +"Accipiter gentilis" "Accipiter" "Bird" +"Cuculus canorus" "Cuculus" "Bird" +"Falco peregrinus" "Falco" "Bird" +"Corvus" "Corvus" "Bird" +"Corvus brachyrhynchos" "Corvus" "Bird" +"Aphelocoma californica" "Aphelocoma" "Bird" +"Aphelocoma" "Aphelocoma" "Bird" +"Accipiter cooperii" "Accipiter" "Bird" +"Cyanocitta cristata" "Cyanocitta" "Bird" +"Corvus corax" "Corvus" "Bird" +"Corvus frugilegus" "Corvus" "Bird" +"Corvus corone" "Corvus" "Bird" +"Accipiter" "Accipiter" "Bird" +"Falco tinnunculus" "Falco" "Bird" +"Accipiter striatus" "Accipiter" "Bird" +"Pica nuttalli" "Pica" "Bird" +"Falco sparverius" "Falco" "Bird" +"Pica hudsonia" "Pica" "Bird" +"Accipiter nisus" "Accipiter" "Bird" +"Falco" "Falco" "Bird" +"Corvus ossifragus" "Corvus" "Bird" +"Falco columbarius" "Falco" "Bird" +"Falco punctatus" "Falco" "Bird" +"Equus caballus" "Equus" "Horse" +"Equus caballus x Equus asinus" "Equus" "Horse" +"Hyalomma marginatum" "Hyalomma" "Tick" +"Hyalomma scupense" "Hyalomma" "Tick" +"Dermacentor marginatus" "Dermacentor" "Tick" +"Rhipicephalus guilhoni" "Rhipicephalus" "Tick" +"Hyalomma" "Hyalomma" "Tick" +"Hyalomma marginatum marginatum" "Hyalomma" "Tick" +"Rhipicephalus pulchellus" "Rhipicephalus" "Tick" +"Hyalomma plumbeum plumbeum" "Hyalomma" "Tick" +"Camelus bactrianus" "Camelus" "Other" +"Rallus aquaticus" "Rallus" "Other" +"Garrulus glandarius" "Garrulus" "Other" +"Crocodylus niloticus" "Crocodylus" "Other" +"Anatidae" "Anatidae" "Other" +"Corvidae" "Corvidae" "Other" +"Strigidae" "Strigidae" "Other" +"Columbidae" "Columbidae" "Other" +"Turdus philomelos" "Turdus" "Other" +"Sturnus vulgaris" "Sturnus" "Other" +"Turdus migratorius" "Turdus" "Other" +"Haliaeetus leucocephalus" "Haliaeetus" "Other" +"Mimus polyglottos" "Mimus" "Other" +"Haemorhous mexicanus" "Haemorhous" "Other" +"Phasianinae" "Phasianinae" "Other" +"Phoenicopterus roseus" "Phoenicopterus" "Other" +"Euphagus cyanocephalus" "Euphagus" "Other" +"Passeridae" "Passeridae" "Other" +"Passer domesticus" "Passer" "Other" +"Galliformes" "Galliformes" "Other" +"Tyto alba" "Tyto" "Other" +"Buteo swainsoni" "Buteo" "Other" +"Hirundo rustica" "Hirundo" "Other" +"Accipitridae" "Accipitridae" "Other" +"Sylvia atricapilla" "Sylvia" "Other" +"Strix nebulosa" "Strix" "Other" +"Athene noctua" "Athene" "Other" +"Phalacrocorax carbo" "Phalacrocorax" "Other" +"Aegypius monachus" "Aegypius" "Other" +"Pandion haliaetus" "Pandion" "Other" +"Asio otus" "Asio" "Other" +"Gallus gallus" "Gallus" "Other" +"Coloeus monedula" "Coloeus" "Other" +"Podiceps cristatus" "Podiceps" "Other" +"Trichoglossus moluccanus" "Trichoglossus" "Other" +"Phoenicopterus chilensis" "Phoenicopterus" "Other" +"Parus major" "Parus" "Other" +"Phoenicopterus sp." "Phoenicopterus" "Other" +"Pyrrhocorax graculus" "Pyrrhocorax" "Other" +"Buteo" "Buteo" "Other" +"Bubo scandiacus" "Bubo" "Other" +"Serinus canaria" "Serinus" "Other" +"Passer sp." "Passer" "Other" +"Phoenicopterus ruber" "Phoenicopterus" "Other" +"Cyanistes caeruleus" "Cyanistes" "Other" +"Lathamus discolor" "Lathamus" "Other" +"Mergus squamatus" "Mergus" "Other" +"Bombycilla garrulus" "Bombycilla" "Other" +"Phylloscopus collybita" "Phylloscopus" "Other" +"Vicugna pacos" "Vicugna" "Other" +"Mastomys erythroleucus" "Mastomys" "Other" +"Canis lupus familiaris" "Canis" "Other" +"Equus" "Equus" "Other" +"Panthera leo" "Panthera" "Other" +"Larus michahellis" "Larus" "Other" +"Turdus merula" "Turdus" "Other" +"Columba palumbus" "Columba" "Other" +"Egretta garzetta" "Egretta" "Other" +"Streptopelia decaocto" "Streptopelia" "Other" +"Equus asinus" "Equus" "Other" +"Apus apus" "Apus" "Other" +"Hirundinidae" "Hirundinidae" "Other" +"Curruca conspicillata" "Curruca" "Other" +"Strix aluco" "Strix" "Other" +"Aves" "Aves" "Other" +"Anser" "Anser" "Other" +"Larus crassirostris" "Larus" "Other" +"Strix nebulosa lapponica" "Strix" "Other" +"Chiroptera" "Chiroptera" "Other" +"Buteo buteo" "Buteo" "Other" +"Pluvialis apricaria" "Pluvialis" "Other" +"Phoenicoparrus andinus" "Phoenicoparrus" "Other" +"Trichoglossus haematodus" "Trichoglossus" "Other" +"Spheniscus humboldti" "Spheniscus" "Other" +"Equus ferus" "Equus" "Other" +"Prunella modularis" "Prunella" "Other" +"Acrocephalus dumetorum" "Acrocephalus" "Other" +"Crocodylus porosus" "Crocodylus" "Other" +"Giraffa giraffa" "Giraffa" "Other" +"Ovis aries" "Ovis" "Other" +"Syncerus caffer" "Syncerus" "Other" +"Alopochen aegyptiaca" "Alopochen" "Other" +"Cygnus olor" "Cygnus" "Other" +"Spinus tristis" "Spinus" "Other" +"Poecile atricapillus" "Poecile" "Other" +"Buteo lineatus" "Buteo" "Other" +"Baeolophus inornatus" "Baeolophus" "Other" +"Pheucticus melanocephalus" "Pheucticus" "Other" +"Calypte costae" "Calypte" "Other" +"Zenaida macroura" "Zenaida" "Other" +"Parulidae" "Parulidae" "Other" +"Bubo virginianus" "Bubo" "Other" +"Buteo jamaicensis" "Buteo" "Other" +"Baeolophus bicolor" "Baeolophus" "Other" +"Bos taurus" "Bos" "Other" +"Clanga pomarina" "Clanga" "Other" +"Quelea quelea" "Quelea" "Other" +"Streptopelia capicola" "Streptopelia" "Other" +"Oena capensis" "Oena" "Other" +"Oriolus flavocinctus" "Oriolus" "Other" +"Larus delawarensis" "Larus" "Other" +"Colaptes auratus" "Colaptes" "Other" +"Quiscalus quiscula" "Quiscalus" "Other" +"Cardinalis cardinalis" "Cardinalis" "Other" +"Sciurus carolinensis" "Sciurus" "Other" +"Columba livia" "Columba" "Other" +"Camelus dromedarius" "Camelus" "Other" +"Nestor notabilis" "Nestor" "Other" +"Pelecanus erythrorhynchos" "Pelecanus" "Other" +"Phalacrocorax auritus" "Phalacrocorax" "Other" +"Sternula antillarum" "Sternula" "Other" +"Branta canadensis" "Branta" "Other" +"Anas platyrhynchos" "Anas" "Other" +"Pelecanus" "Pelecanus" "Other" +"Loriini" "Loriini" "Other" +"Sternula" "Sternula" "Other" +"Quiscalus major" "Quiscalus" "Other" +"Gymnogyps californianus" "Gymnogyps" "Other" +"Asio flammeus" "Asio" "Other" +"Coragyps atratus" "Coragyps" "Other" +"Pelecanus occidentalis" "Pelecanus" "Other" +"Cygnus buccinator" "Cygnus" "Other" +"Charadrius melodus" "Charadrius" "Other" +"Ictinia mississippiensis" "Ictinia" "Other" +"Buteo regalis" "Buteo" "Other" +"Calidris alba" "Calidris" "Other" +"Sturnidae" "Sturnidae" "Other" +"Mimus" "Mimus" "Other" +"Larus smithsonianus" "Larus" "Other" +"Actitis macularius" "Actitis" "Other" +"Chroicocephalus ridibundus" "Chroicocephalus" "Other" +"Hylocichla mustelina" "Hylocichla" "Other" +"Toxostoma rufum" "Toxostoma" "Other" +"Poecile carolinensis" "Poecile" "Other" +"Meleagris gallopavo" "Meleagris" "Other" +"Ixodoidea" "Ixodoidea" "Other" +"Rodentia" "Rodentia" "Other" +"Lanius ludovicianus" "Lanius" "Other" +"Sciuridae" "Sciuridae" "Other" +"Mus musculus" "Mus" "Other" +"Aegithalos caudatus" "Aegithalos" "Other" +"Phasianus colchicus" "Phasianus" "Other" +"Haliaeetus albicilla" "Haliaeetus" "Other" +"Crocodylus moreletii" "Crocodylus" "Other" +"Alectorobius capensis" "Alectorobius" "Other" +"Orcinus orca" "Orcinus" "Other" +"Laridae" "Laridae" "Other" +"Mesocricetus auratus" "Mesocricetus" "Other" +"Sciurus niger" "Sciurus" "Other" +"Aquila chrysaetos" "Aquila" "Other" +"Rousettus leschenaultii" "Rousettus" "Other" +"Pelophylax ridibundus" "Pelophylax" "Other" +"Agelaius phoeniceus" "Agelaius" "Other" +"Aquila fasciata" "Aquila" "Other" +"Aquila adalberti" "Aquila" "Other" +"Coracopsis vasa" "Coracopsis" "Other" +"Cardinalis" "Cardinalis" "Other" +"Fulica" "Fulica" "Other" +"Quiscalus" "Quiscalus" "Other" +"Phalacrocoracidae" "Phalacrocoracidae" "Other" +"Butorides virescens" "Butorides" "Other" +"Ardeidae" "Ardeidae" "Other" +"Dumetella" "Dumetella" "Other" +"Cricetinae" "Cricetinae" "Other" +"Bubulcus ibis" "Bubulcus" "Other" +"Spatula querquedula" "Spatula" "Other" +"Bonasa umbellus" "Bonasa" "Other" +"Ciconiidae" "Ciconiidae" "Other" +"Ichthyaetus leucophthalmus" "Ichthyaetus" "Other" +"Molothrus ater" "Molothrus" "Other" +"Mephitis mephitis" "Mephitis" "Other" +"Platycercus" "Platycercus" "Other" From 94ed8f3e62f645cbf75a2279bb05a05e89d85aa1 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 13 Nov 2024 13:41:15 -0800 Subject: [PATCH 2/8] Ingest: apply mapping to add host genus and host type fields --- ingest/defaults/config.yaml | 2 + .../defaults/host_hostgenus_hosttype_map.tsv | 2 +- ingest/rules/curate.smk | 7 +++ ingest/scripts/transform-new-fields | 50 +++++++++++++++++++ 4 files changed, 60 insertions(+), 1 deletion(-) create mode 100755 ingest/scripts/transform-new-fields diff --git a/ingest/defaults/config.yaml b/ingest/defaults/config.yaml index bfadc56..8d491f3 100644 --- a/ingest/defaults/config.yaml +++ b/ingest/defaults/config.yaml @@ -112,6 +112,8 @@ curate: 'location', 'state', 'host', + 'host_genus', + 'host_type', 'is_lab_host', #'date_submitted', #'sra_accession', diff --git a/ingest/defaults/host_hostgenus_hosttype_map.tsv b/ingest/defaults/host_hostgenus_hosttype_map.tsv index a1d6b5e..f1edcb2 100644 --- a/ingest/defaults/host_hostgenus_hosttype_map.tsv +++ b/ingest/defaults/host_hostgenus_hosttype_map.tsv @@ -1,4 +1,4 @@ -"Host" "Host_Genus" "Host_Type" +"host" "host_genus" "host_type" "Homo sapiens" "Homo" "Human" "Culex pipiens" "Culex" "Mosquito" "Culex annulirostris" "Culex" "Mosquito" diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk index 77dc91a..da5b549 100644 --- a/ingest/rules/curate.smk +++ b/ingest/rules/curate.smk @@ -46,6 +46,7 @@ rule curate: sequences_ndjson="data/genbank.ndjson", all_geolocation_rules="data/all-geolocation-rules.tsv", annotations=config["curate"]["annotations"], + manual_mapping="defaults/host_hostgenus_hosttype_map.tsv", output: metadata="data/raw_metadata_curated.tsv", sequences="results/sequences.fasta", @@ -98,6 +99,12 @@ rule curate: | ./scripts/post_process_metadata.py \ | ./scripts/add-field-names \ --metadata-columns {params.metadata_columns} \ + | ./scripts/transform-new-fields \ + --map-tsv {input.manual_mapping} \ + --map-id host \ + --metadata-id host \ + --map-fields host_genus host_type \ + --pass-through true \ | augur curate apply-record-annotations \ --annotations {input.annotations} \ --id-field {params.annotations_id} \ diff --git a/ingest/scripts/transform-new-fields b/ingest/scripts/transform-new-fields new file mode 100755 index 0000000..a846990 --- /dev/null +++ b/ingest/scripts/transform-new-fields @@ -0,0 +1,50 @@ +#! /usr/bin/env python3 + +import argparse +import json +import csv +from sys import stdin, stdout + +def parse_args(): + parser = argparse.ArgumentParser( + description="Transform JSON data by applying a TSV mapping and adding new columns." + ) + parser.add_argument("--map-tsv", required=True, + help="Path to the TSV mapping file.") + parser.add_argument("--map-id", required=True, + help="Column name in the map TSV to use as the mapping key.") + parser.add_argument("--metadata-id", required=True, + help="Column name in the metadata JSON to use as the mapping key.") + parser.add_argument("--map-fields", nargs="+", required=True, + help="Columns to add from the mapping file.") + parser.add_argument("--pass-through", default=False, + help="If set, pass through the original value when no mapping is found.") + return parser.parse_args() + +def load_mapping(map_tsv, map_id, map_fields): + mapping = {} + with open(map_tsv, 'r', encoding='utf-8') as f: + reader = csv.DictReader(f, delimiter='\t') + for row in reader: + key = row[map_id] + mapping[key] = {col: row[col] for col in map_fields} + return mapping + +def main(): + args = parse_args() + mapping = load_mapping(args.map_tsv, args.map_id, args.map_fields) + + for line in stdin: + record = json.loads(line) + key = record.get(args.metadata_id, '') + + if key in mapping: + record.update(mapping[key]) + elif args.pass_through: + for col in args.map_fields: + record[col] = record.get(args.metadata_id, '') + + stdout.write(json.dumps(record) + '\n') + +if __name__ == "__main__": + main() From 14638211c7865c5125b070a95f140c238580cecd Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 13 Nov 2024 14:03:30 -0800 Subject: [PATCH 3/8] Phylogenetic: add host genus and type coloring to trees --- phylogenetic/defaults/auspice_config.json | 6 +++++- phylogenetic/defaults/auspice_config_global.json | 8 ++++++-- 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/phylogenetic/defaults/auspice_config.json b/phylogenetic/defaults/auspice_config.json index 44da9c1..a352ec5 100644 --- a/phylogenetic/defaults/auspice_config.json +++ b/phylogenetic/defaults/auspice_config.json @@ -10,7 +10,9 @@ {"key": "lineage", "title": "Pathoplexus lineage", "type": "categorical"}, {"key": "clade_membership", "title": "Clade", "type": "categorical"}, {"key": "author", "title": "Authors", "type": "categorical"}, - {"key": "host", "title": "Host Species", "type": "categorical"} + {"key": "host", "title": "Host Species", "type": "categorical"}, + {"key": "host_genus", "title": "Host Genus", "type": "categorical"}, + {"key": "host_type", "title": "Host Type", "type": "categorical"} ], "geo_resolutions": [ "state", @@ -29,6 +31,8 @@ "author", "clade_membership", "host", + "host_genus", + "host_type", "lineage" ], "display_defaults": { diff --git a/phylogenetic/defaults/auspice_config_global.json b/phylogenetic/defaults/auspice_config_global.json index 37ce140..26ab194 100644 --- a/phylogenetic/defaults/auspice_config_global.json +++ b/phylogenetic/defaults/auspice_config_global.json @@ -8,7 +8,9 @@ {"key": "lineage", "title": "Pathoplexus lineage", "type": "categorical"}, {"key": "clade_membership", "title": "Clade", "type": "categorical"}, {"key": "author", "title": "Authors", "type": "categorical"}, - {"key": "host", "title": "Host Species", "type": "categorical"} + {"key": "host", "title": "Host Species", "type": "categorical"}, + {"key": "host_genus", "title": "Host Genus", "type": "categorical"}, + {"key": "host_type", "title": "Host Type", "type": "categorical"} ], "geo_resolutions": [ "region", @@ -23,7 +25,9 @@ "region", "country", "author", - "host" + "host", + "host_genus", + "host_type" ], "display_defaults": { "color_by": "region", From 70842954383ca229879ec7720cbaabee95fa7713 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 13 Nov 2024 16:16:45 -0800 Subject: [PATCH 4/8] Apply some sorting, add japonicus --- .../defaults/host_hostgenus_hosttype_map.tsv | 483 +++++++++--------- 1 file changed, 242 insertions(+), 241 deletions(-) diff --git a/ingest/defaults/host_hostgenus_hosttype_map.tsv b/ingest/defaults/host_hostgenus_hosttype_map.tsv index f1edcb2..47cf4ff 100644 --- a/ingest/defaults/host_hostgenus_hosttype_map.tsv +++ b/ingest/defaults/host_hostgenus_hosttype_map.tsv @@ -1,284 +1,285 @@ "host" "host_genus" "host_type" "Homo sapiens" "Homo" "Human" -"Culex pipiens" "Culex" "Mosquito" -"Culex annulirostris" "Culex" "Mosquito" -"Culex perexiguus" "Culex" "Mosquito" -"Ochlerotatus communis" "Ochlerotatus" "Mosquito" -"Anopheles maculipennis" "Anopheles" "Mosquito" -"Culex quinquefasciatus" "Culex" "Mosquito" -"Anopheles atroparvus" "Anopheles" "Mosquito" -"Culex modestus" "Culex" "Mosquito" -"Culex tarsalis" "Culex" "Mosquito" -"Culex restuans" "Culex" "Mosquito" -"Culiseta melanura" "Culiseta" "Mosquito" +"Aedeomyia madagascarica" "Aedeomyia" "Mosquito" +"Aedes albopictus" "Aedes" "Mosquito" "Aedes cinereus" "Aedes" "Mosquito" -"Culex" "Culex" "Mosquito" -"Culex erraticus" "Culex" "Mosquito" -"Culex salinarius" "Culex" "Mosquito" +"Aedes dalzieli" "Aedes" "Mosquito" +"Aedes japonicus" "Aedes" "Mosquito" +"Aedes rossicus" "Aedes" "Mosquito" +"Aedes sp." "Aedes" "Mosquito" +"Aedes vexans" "Aedes" "Mosquito" +"Anopheles atroparvus" "Anopheles" "Mosquito" +"Anopheles bancroftii" "Anopheles" "Mosquito" +"Anopheles coustani" "Anopheles" "Mosquito" +"Anopheles farauti" "Anopheles" "Mosquito" +"Anopheles hyrcanus" "Anopheles" "Mosquito" +"Anopheles maculipennis" "Anopheles" "Mosquito" +"Anopheles messeae" "Anopheles" "Mosquito" +"Anopheles pauliani" "Anopheles" "Mosquito" +"Anopheles plumbeus" "Anopheles" "Mosquito" +"Anopheles sp." "Anopheles" "Mosquito" +"Anopheles stephensi" "Anopheles" "Mosquito" "Coquillettidia perturbans" "Coquillettidia" "Mosquito" -"Psorophora ferox" "Psorophora" "Mosquito" -"Culiseta morsitans" "Culiseta" "Mosquito" -"Ochlerotatus canadensis" "Ochlerotatus" "Mosquito" -"Culex tritaeniorhynchus" "Culex" "Mosquito" -"Culex vishnui" "Culex" "Mosquito" -"Culex neavei" "Culex" "Mosquito" -"Culex poicilipes" "Culex" "Mosquito" +"Coquillettidia richiardii" "Coquillettidia" "Mosquito" +"Coquillettidia" "Coquillettidia" "Mosquito" +"Culex annulirostris" "Culex" "Mosquito" +"Culex antennatus" "Culex" "Mosquito" "Culex bitaeniorhynchus" "Culex" "Mosquito" +"Culex erraticus" "Culex" "Mosquito" +"Culex erythrothorax" "Culex" "Mosquito" +"Culex gelidus" "Culex" "Mosquito" +"Culex interrogator" "Culex" "Mosquito" +"Culex modestus" "Culex" "Mosquito" +"Culex neavei" "Culex" "Mosquito" +"Culex nigripalpus" "Culex" "Mosquito" +"Culex perexiguus" "Culex" "Mosquito" "Culex perfuscus" "Culex" "Mosquito" -"Culex antennatus" "Culex" "Mosquito" -"Aedes vexans" "Aedes" "Mosquito" +"Culex pipiens complex" "Culex" "Mosquito" +"Culex pipiens pipiens" "Culex" "Mosquito" +"Culex pipiens sensu lato" "Culex" "Mosquito" +"Culex pipiens" "Culex" "Mosquito" +"Culex poicilipes" "Culex" "Mosquito" "Culex pseudovishnui" "Culex" "Mosquito" -"Culex gelidus" "Culex" "Mosquito" -"Coquillettidia" "Coquillettidia" "Mosquito" -"Aedes dalzieli" "Aedes" "Mosquito" -"Mansonia uniformis" "Mansonia" "Mosquito" -"Anopheles stephensi" "Anopheles" "Mosquito" +"Culex pullus" "Culex" "Mosquito" +"Culex quinquefasciatus" "Culex" "Mosquito" +"Culex restuans" "Culex" "Mosquito" +"Culex salinarius" "Culex" "Mosquito" "Culex sitiens" "Culex" "Mosquito" -"Culiseta longiareolata" "Culiseta" "Mosquito" -"Culex pipiens sensu lato" "Culex" "Mosquito" +"Culex squamosus" "Culex" "Mosquito" +"Culex stigmatosoma" "Culex" "Mosquito" +"Culex tarsalis" "Culex" "Mosquito" "Culex theileri" "Culex" "Mosquito" +"Culex tritaeniorhynchus" "Culex" "Mosquito" "Culex univittatus" "Culex" "Mosquito" -"Culicidae" "Culicidae" "Mosquito" -"Aedes albopictus" "Aedes" "Mosquito" -"Anopheles hyrcanus" "Anopheles" "Mosquito" -"Coquillettidia richiardii" "Coquillettidia" "Mosquito" -"Anopheles plumbeus" "Anopheles" "Mosquito" -"Culex pipiens complex" "Culex" "Mosquito" -"Psorophora" "Psorophora" "Mosquito" -"Culex stigmatosoma" "Culex" "Mosquito" -"Culex erythrothorax" "Culex" "Mosquito" -"Culex nigripalpus" "Culex" "Mosquito" -"Culex pipiens pipiens" "Culex" "Mosquito" +"Culex vishnui" "Culex" "Mosquito" "Culex whitmorei" "Culex" "Mosquito" -"Anopheles bancroftii" "Anopheles" "Mosquito" -"Culex squamosus" "Culex" "Mosquito" -"Anopheles farauti" "Anopheles" "Mosquito" -"Culex pullus" "Culex" "Mosquito" +"Culex" "Culex" "Mosquito" +"Culicidae" "Culicidae" "Mosquito" +"Culiseta inornata" "Culiseta" "Mosquito" +"Culiseta longiareolata" "Culiseta" "Mosquito" +"Culiseta melanura" "Culiseta" "Mosquito" +"Culiseta morsitans" "Culiseta" "Mosquito" "Culiseta" "Culiseta" "Mosquito" -"Aedes sp." "Aedes" "Mosquito" -"Anopheles sp." "Anopheles" "Mosquito" -"Anopheles pauliani" "Anopheles" "Mosquito" -"Anopheles coustani" "Anopheles" "Mosquito" -"Aedeomyia madagascarica" "Aedeomyia" "Mosquito" +"Mansonia uniformis" "Mansonia" "Mosquito" +"Ochlerotatus canadensis" "Ochlerotatus" "Mosquito" +"Ochlerotatus cantator" "Ochlerotatus" "Mosquito" +"Ochlerotatus caspius" "Ochlerotatus" "Mosquito" +"Ochlerotatus communis" "Ochlerotatus" "Mosquito" "Ochlerotatus dorsalis" "Ochlerotatus" "Mosquito" -"Ochlerotatus trivittatus" "Ochlerotatus" "Mosquito" -"Culiseta inornata" "Culiseta" "Mosquito" "Ochlerotatus flavescens" "Ochlerotatus" "Mosquito" -"Ochlerotatus spencerii" "Ochlerotatus" "Mosquito" -"Uranotaenia unguiculata" "Uranotaenia" "Mosquito" -"Ochlerotatus caspius" "Ochlerotatus" "Mosquito" "Ochlerotatus sollicitans" "Ochlerotatus" "Mosquito" -"Ochlerotatus triseriatus" "Ochlerotatus" "Mosquito" -"Ochlerotatus cantator" "Ochlerotatus" "Mosquito" +"Ochlerotatus spencerii" "Ochlerotatus" "Mosquito" "Ochlerotatus sticticus" "Ochlerotatus" "Mosquito" -"Aedes rossicus" "Aedes" "Mosquito" +"Ochlerotatus triseriatus" "Ochlerotatus" "Mosquito" +"Ochlerotatus trivittatus" "Ochlerotatus" "Mosquito" +"Psorophora ferox" "Psorophora" "Mosquito" +"Psorophora" "Psorophora" "Mosquito" +"Uranotaenia unguiculata" "Uranotaenia" "Mosquito" "Uranotaenia" "Uranotaenia" "Mosquito" -"Culex interrogator" "Culex" "Mosquito" -"Anopheles messeae" "Anopheles" "Mosquito" -"Pica pica" "Pica" "Bird" -"Corvus cornix" "Corvus" "Bird" +"Dermacentor marginatus" "Dermacentor" "Tick" +"Hyalomma marginatum marginatum" "Hyalomma" "Tick" +"Hyalomma marginatum" "Hyalomma" "Tick" +"Hyalomma plumbeum plumbeum" "Hyalomma" "Tick" +"Hyalomma scupense" "Hyalomma" "Tick" +"Hyalomma" "Hyalomma" "Tick" +"Rhipicephalus guilhoni" "Rhipicephalus" "Tick" +"Rhipicephalus pulchellus" "Rhipicephalus" "Tick" +"Alectorobius capensis" "Alectorobius" "Tick" +"Accipiter cooperii" "Accipiter" "Bird" "Accipiter gentilis" "Accipiter" "Bird" -"Cuculus canorus" "Cuculus" "Bird" -"Falco peregrinus" "Falco" "Bird" -"Corvus" "Corvus" "Bird" -"Corvus brachyrhynchos" "Corvus" "Bird" +"Accipiter nisus" "Accipiter" "Bird" +"Accipiter striatus" "Accipiter" "Bird" +"Accipiter" "Accipiter" "Bird" "Aphelocoma californica" "Aphelocoma" "Bird" "Aphelocoma" "Aphelocoma" "Bird" -"Accipiter cooperii" "Accipiter" "Bird" -"Cyanocitta cristata" "Cyanocitta" "Bird" +"Corvus brachyrhynchos" "Corvus" "Bird" "Corvus corax" "Corvus" "Bird" -"Corvus frugilegus" "Corvus" "Bird" +"Corvus cornix" "Corvus" "Bird" "Corvus corone" "Corvus" "Bird" -"Accipiter" "Accipiter" "Bird" -"Falco tinnunculus" "Falco" "Bird" -"Accipiter striatus" "Accipiter" "Bird" -"Pica nuttalli" "Pica" "Bird" -"Falco sparverius" "Falco" "Bird" -"Pica hudsonia" "Pica" "Bird" -"Accipiter nisus" "Accipiter" "Bird" -"Falco" "Falco" "Bird" +"Corvus frugilegus" "Corvus" "Bird" "Corvus ossifragus" "Corvus" "Bird" +"Corvus" "Corvus" "Bird" +"Cuculus canorus" "Cuculus" "Bird" +"Cyanocitta cristata" "Cyanocitta" "Bird" "Falco columbarius" "Falco" "Bird" +"Falco peregrinus" "Falco" "Bird" "Falco punctatus" "Falco" "Bird" -"Equus caballus" "Equus" "Horse" +"Falco sparverius" "Falco" "Bird" +"Falco tinnunculus" "Falco" "Bird" +"Falco" "Falco" "Bird" +"Pica hudsonia" "Pica" "Bird" +"Pica nuttalli" "Pica" "Bird" +"Pica pica" "Pica" "Bird" +"Accipitridae" "Accipitridae" "Bird" +"Acrocephalus dumetorum" "Acrocephalus" "Bird" +"Actitis macularius" "Actitis" "Bird" +"Aegithalos caudatus" "Aegithalos" "Bird" +"Aegypius monachus" "Aegypius" "Bird" +"Agelaius phoeniceus" "Agelaius" "Bird" +"Alopochen aegyptiaca" "Alopochen" "Bird" +"Anas platyrhynchos" "Anas" "Bird" +"Anatidae" "Anatidae" "Bird" +"Anser" "Anser" "Bird" +"Apus apus" "Apus" "Bird" +"Aquila adalberti" "Aquila" "Bird" +"Aquila chrysaetos" "Aquila" "Bird" +"Aquila fasciata" "Aquila" "Bird" +"Ardeidae" "Ardeidae" "Bird" +"Asio flammeus" "Asio" "Bird" +"Asio otus" "Asio" "Bird" +"Athene noctua" "Athene" "Bird" +"Aves" "Aves" "Bird" +"Baeolophus bicolor" "Baeolophus" "Bird" +"Baeolophus inornatus" "Baeolophus" "Bird" +"Bombycilla garrulus" "Bombycilla" "Bird" +"Bonasa umbellus" "Bonasa" "Bird" +"Branta canadensis" "Branta" "Bird" +"Bubo scandiacus" "Bubo" "Bird" +"Bubo virginianus" "Bubo" "Bird" +"Bubulcus ibis" "Bubulcus" "Bird" +"Buteo buteo" "Buteo" "Bird" +"Buteo jamaicensis" "Buteo" "Bird" +"Buteo lineatus" "Buteo" "Bird" +"Buteo regalis" "Buteo" "Bird" +"Buteo swainsoni" "Buteo" "Bird" +"Buteo" "Buteo" "Bird" +"Cardinalis cardinalis" "Cardinalis" "Bird" +"Cardinalis" "Cardinalis" "Bird" +"Corvidae" "Corvidae" "Bird" +"Strigidae" "Strigidae" "Bird" +"Strix aluco" "Strix" "Bird" +"Strix nebulosa lapponica" "Strix" "Bird" +"Strix nebulosa" "Strix" "Bird" +"Sturnidae" "Sturnidae" "Bird" +"Sturnus vulgaris" "Sturnus" "Bird" +"Sylvia atricapilla" "Sylvia" "Bird" +"Toxostoma rufum" "Toxostoma" "Bird" +"Trichoglossus haematodus" "Trichoglossus" "Bird" +"Trichoglossus moluccanus" "Trichoglossus" "Bird" +"Turdus merula" "Turdus" "Bird" +"Turdus migratorius" "Turdus" "Bird" +"Turdus philomelos" "Turdus" "Bird" +"Tyto alba" "Tyto" "Bird" +"Zenaida macroura" "Zenaida" "Bird" +"Gallus gallus" "Gallus" "Bird" +"Pheucticus melanocephalus" "Pheucticus" "Bird" +"Phoenicoparrus andinus" "Phoenicoparrus" "Bird" +"Phoenicopterus chilensis" "Phoenicopterus" "Bird" +"Phoenicopterus roseus" "Phoenicopterus" "Bird" +"Phoenicopterus ruber" "Phoenicopterus" "Bird" +"Phoenicopterus sp." "Phoenicopterus" "Bird" "Equus caballus x Equus asinus" "Equus" "Horse" -"Hyalomma marginatum" "Hyalomma" "Tick" -"Hyalomma scupense" "Hyalomma" "Tick" -"Dermacentor marginatus" "Dermacentor" "Tick" -"Rhipicephalus guilhoni" "Rhipicephalus" "Tick" -"Hyalomma" "Hyalomma" "Tick" -"Hyalomma marginatum marginatum" "Hyalomma" "Tick" -"Rhipicephalus pulchellus" "Rhipicephalus" "Tick" -"Hyalomma plumbeum plumbeum" "Hyalomma" "Tick" +"Equus caballus" "Equus" "Horse" +"Equus asinus" "Equus" "Horse" +"Equus ferus" "Equus" "Horse" +"Equus" "Equus" "Horse" +"Bos taurus" "Bos" "Other" +"Butorides virescens" "Butorides" "Other" +"Calidris alba" "Calidris" "Other" +"Calypte costae" "Calypte" "Other" "Camelus bactrianus" "Camelus" "Other" -"Rallus aquaticus" "Rallus" "Other" -"Garrulus glandarius" "Garrulus" "Other" -"Crocodylus niloticus" "Crocodylus" "Other" -"Anatidae" "Anatidae" "Other" -"Corvidae" "Corvidae" "Other" -"Strigidae" "Strigidae" "Other" +"Camelus dromedarius" "Camelus" "Other" +"Canis lupus familiaris" "Canis" "Other" +"Charadrius melodus" "Charadrius" "Other" +"Chiroptera" "Chiroptera" "Other" +"Chroicocephalus ridibundus" "Chroicocephalus" "Other" +"Ciconiidae" "Ciconiidae" "Other" +"Clanga pomarina" "Clanga" "Other" +"Colaptes auratus" "Colaptes" "Other" +"Coloeus monedula" "Coloeus" "Other" +"Columba livia" "Columba" "Other" +"Columba palumbus" "Columba" "Other" "Columbidae" "Columbidae" "Other" -"Turdus philomelos" "Turdus" "Other" -"Sturnus vulgaris" "Sturnus" "Other" -"Turdus migratorius" "Turdus" "Other" -"Haliaeetus leucocephalus" "Haliaeetus" "Other" -"Mimus polyglottos" "Mimus" "Other" -"Haemorhous mexicanus" "Haemorhous" "Other" -"Phasianinae" "Phasianinae" "Other" -"Phoenicopterus roseus" "Phoenicopterus" "Other" +"Coracopsis vasa" "Coracopsis" "Other" +"Coragyps atratus" "Coragyps" "Other" +"Cricetinae" "Cricetinae" "Other" +"Crocodylus moreletii" "Crocodylus" "Other" +"Crocodylus niloticus" "Crocodylus" "Other" +"Crocodylus porosus" "Crocodylus" "Other" +"Curruca conspicillata" "Curruca" "Other" +"Cyanistes caeruleus" "Cyanistes" "Other" +"Cygnus buccinator" "Cygnus" "Other" +"Cygnus olor" "Cygnus" "Other" +"Dumetella" "Dumetella" "Other" +"Egretta garzetta" "Egretta" "Other" "Euphagus cyanocephalus" "Euphagus" "Other" -"Passeridae" "Passeridae" "Other" -"Passer domesticus" "Passer" "Other" +"Fulica" "Fulica" "Other" "Galliformes" "Galliformes" "Other" -"Tyto alba" "Tyto" "Other" -"Buteo swainsoni" "Buteo" "Other" +"Garrulus glandarius" "Garrulus" "Other" +"Giraffa giraffa" "Giraffa" "Other" +"Gymnogyps californianus" "Gymnogyps" "Other" +"Haemorhous mexicanus" "Haemorhous" "Other" +"Haliaeetus albicilla" "Haliaeetus" "Other" +"Haliaeetus leucocephalus" "Haliaeetus" "Other" +"Hirundinidae" "Hirundinidae" "Other" "Hirundo rustica" "Hirundo" "Other" -"Accipitridae" "Accipitridae" "Other" -"Sylvia atricapilla" "Sylvia" "Other" -"Strix nebulosa" "Strix" "Other" -"Athene noctua" "Athene" "Other" -"Phalacrocorax carbo" "Phalacrocorax" "Other" -"Aegypius monachus" "Aegypius" "Other" +"Hylocichla mustelina" "Hylocichla" "Other" +"Ichthyaetus leucophthalmus" "Ichthyaetus" "Other" +"Ictinia mississippiensis" "Ictinia" "Other" +"Ixodoidea" "Ixodoidea" "Other" +"Lanius ludovicianus" "Lanius" "Other" +"Laridae" "Laridae" "Other" +"Larus crassirostris" "Larus" "Other" +"Larus delawarensis" "Larus" "Other" +"Larus michahellis" "Larus" "Other" +"Larus smithsonianus" "Larus" "Other" +"Lathamus discolor" "Lathamus" "Other" +"Loriini" "Loriini" "Other" +"Mastomys erythroleucus" "Mastomys" "Other" +"Meleagris gallopavo" "Meleagris" "Other" +"Mephitis mephitis" "Mephitis" "Other" +"Mergus squamatus" "Mergus" "Other" +"Mesocricetus auratus" "Mesocricetus" "Other" +"Mimus polyglottos" "Mimus" "Other" +"Mimus" "Mimus" "Other" +"Molothrus ater" "Molothrus" "Other" +"Mus musculus" "Mus" "Other" +"Nestor notabilis" "Nestor" "Other" +"Oena capensis" "Oena" "Other" +"Orcinus orca" "Orcinus" "Other" +"Oriolus flavocinctus" "Oriolus" "Other" +"Ovis aries" "Ovis" "Other" "Pandion haliaetus" "Pandion" "Other" -"Asio otus" "Asio" "Other" -"Gallus gallus" "Gallus" "Other" -"Coloeus monedula" "Coloeus" "Other" -"Podiceps cristatus" "Podiceps" "Other" -"Trichoglossus moluccanus" "Trichoglossus" "Other" -"Phoenicopterus chilensis" "Phoenicopterus" "Other" +"Panthera leo" "Panthera" "Other" +"Parulidae" "Parulidae" "Other" "Parus major" "Parus" "Other" -"Phoenicopterus sp." "Phoenicopterus" "Other" -"Pyrrhocorax graculus" "Pyrrhocorax" "Other" -"Buteo" "Buteo" "Other" -"Bubo scandiacus" "Bubo" "Other" -"Serinus canaria" "Serinus" "Other" +"Passer domesticus" "Passer" "Other" "Passer sp." "Passer" "Other" -"Phoenicopterus ruber" "Phoenicopterus" "Other" -"Cyanistes caeruleus" "Cyanistes" "Other" -"Lathamus discolor" "Lathamus" "Other" -"Mergus squamatus" "Mergus" "Other" -"Bombycilla garrulus" "Bombycilla" "Other" +"Passeridae" "Passeridae" "Other" +"Pelecanus erythrorhynchos" "Pelecanus" "Other" +"Pelecanus occidentalis" "Pelecanus" "Other" +"Pelecanus" "Pelecanus" "Other" +"Pelophylax ridibundus" "Pelophylax" "Other" +"Phalacrocoracidae" "Phalacrocoracidae" "Other" +"Phalacrocorax auritus" "Phalacrocorax" "Other" +"Phalacrocorax carbo" "Phalacrocorax" "Other" +"Phasianinae" "Phasianinae" "Other" +"Phasianus colchicus" "Phasianus" "Other" "Phylloscopus collybita" "Phylloscopus" "Other" -"Vicugna pacos" "Vicugna" "Other" -"Mastomys erythroleucus" "Mastomys" "Other" -"Canis lupus familiaris" "Canis" "Other" -"Equus" "Equus" "Other" -"Panthera leo" "Panthera" "Other" -"Larus michahellis" "Larus" "Other" -"Turdus merula" "Turdus" "Other" -"Columba palumbus" "Columba" "Other" -"Egretta garzetta" "Egretta" "Other" -"Streptopelia decaocto" "Streptopelia" "Other" -"Equus asinus" "Equus" "Other" -"Apus apus" "Apus" "Other" -"Hirundinidae" "Hirundinidae" "Other" -"Curruca conspicillata" "Curruca" "Other" -"Strix aluco" "Strix" "Other" -"Aves" "Aves" "Other" -"Anser" "Anser" "Other" -"Larus crassirostris" "Larus" "Other" -"Strix nebulosa lapponica" "Strix" "Other" -"Chiroptera" "Chiroptera" "Other" -"Buteo buteo" "Buteo" "Other" +"Platycercus" "Platycercus" "Other" "Pluvialis apricaria" "Pluvialis" "Other" -"Phoenicoparrus andinus" "Phoenicoparrus" "Other" -"Trichoglossus haematodus" "Trichoglossus" "Other" -"Spheniscus humboldti" "Spheniscus" "Other" -"Equus ferus" "Equus" "Other" -"Prunella modularis" "Prunella" "Other" -"Acrocephalus dumetorum" "Acrocephalus" "Other" -"Crocodylus porosus" "Crocodylus" "Other" -"Giraffa giraffa" "Giraffa" "Other" -"Ovis aries" "Ovis" "Other" -"Syncerus caffer" "Syncerus" "Other" -"Alopochen aegyptiaca" "Alopochen" "Other" -"Cygnus olor" "Cygnus" "Other" -"Spinus tristis" "Spinus" "Other" +"Podiceps cristatus" "Podiceps" "Other" "Poecile atricapillus" "Poecile" "Other" -"Buteo lineatus" "Buteo" "Other" -"Baeolophus inornatus" "Baeolophus" "Other" -"Pheucticus melanocephalus" "Pheucticus" "Other" -"Calypte costae" "Calypte" "Other" -"Zenaida macroura" "Zenaida" "Other" -"Parulidae" "Parulidae" "Other" -"Bubo virginianus" "Bubo" "Other" -"Buteo jamaicensis" "Buteo" "Other" -"Baeolophus bicolor" "Baeolophus" "Other" -"Bos taurus" "Bos" "Other" -"Clanga pomarina" "Clanga" "Other" +"Poecile carolinensis" "Poecile" "Other" +"Prunella modularis" "Prunella" "Other" +"Pyrrhocorax graculus" "Pyrrhocorax" "Other" "Quelea quelea" "Quelea" "Other" -"Streptopelia capicola" "Streptopelia" "Other" -"Oena capensis" "Oena" "Other" -"Oriolus flavocinctus" "Oriolus" "Other" -"Larus delawarensis" "Larus" "Other" -"Colaptes auratus" "Colaptes" "Other" -"Quiscalus quiscula" "Quiscalus" "Other" -"Cardinalis cardinalis" "Cardinalis" "Other" -"Sciurus carolinensis" "Sciurus" "Other" -"Columba livia" "Columba" "Other" -"Camelus dromedarius" "Camelus" "Other" -"Nestor notabilis" "Nestor" "Other" -"Pelecanus erythrorhynchos" "Pelecanus" "Other" -"Phalacrocorax auritus" "Phalacrocorax" "Other" -"Sternula antillarum" "Sternula" "Other" -"Branta canadensis" "Branta" "Other" -"Anas platyrhynchos" "Anas" "Other" -"Pelecanus" "Pelecanus" "Other" -"Loriini" "Loriini" "Other" -"Sternula" "Sternula" "Other" "Quiscalus major" "Quiscalus" "Other" -"Gymnogyps californianus" "Gymnogyps" "Other" -"Asio flammeus" "Asio" "Other" -"Coragyps atratus" "Coragyps" "Other" -"Pelecanus occidentalis" "Pelecanus" "Other" -"Cygnus buccinator" "Cygnus" "Other" -"Charadrius melodus" "Charadrius" "Other" -"Ictinia mississippiensis" "Ictinia" "Other" -"Buteo regalis" "Buteo" "Other" -"Calidris alba" "Calidris" "Other" -"Sturnidae" "Sturnidae" "Other" -"Mimus" "Mimus" "Other" -"Larus smithsonianus" "Larus" "Other" -"Actitis macularius" "Actitis" "Other" -"Chroicocephalus ridibundus" "Chroicocephalus" "Other" -"Hylocichla mustelina" "Hylocichla" "Other" -"Toxostoma rufum" "Toxostoma" "Other" -"Poecile carolinensis" "Poecile" "Other" -"Meleagris gallopavo" "Meleagris" "Other" -"Ixodoidea" "Ixodoidea" "Other" +"Quiscalus quiscula" "Quiscalus" "Other" +"Quiscalus" "Quiscalus" "Other" +"Rallus aquaticus" "Rallus" "Other" "Rodentia" "Rodentia" "Other" -"Lanius ludovicianus" "Lanius" "Other" +"Rousettus leschenaultii" "Rousettus" "Other" "Sciuridae" "Sciuridae" "Other" -"Mus musculus" "Mus" "Other" -"Aegithalos caudatus" "Aegithalos" "Other" -"Phasianus colchicus" "Phasianus" "Other" -"Haliaeetus albicilla" "Haliaeetus" "Other" -"Crocodylus moreletii" "Crocodylus" "Other" -"Alectorobius capensis" "Alectorobius" "Other" -"Orcinus orca" "Orcinus" "Other" -"Laridae" "Laridae" "Other" -"Mesocricetus auratus" "Mesocricetus" "Other" +"Sciurus carolinensis" "Sciurus" "Other" "Sciurus niger" "Sciurus" "Other" -"Aquila chrysaetos" "Aquila" "Other" -"Rousettus leschenaultii" "Rousettus" "Other" -"Pelophylax ridibundus" "Pelophylax" "Other" -"Agelaius phoeniceus" "Agelaius" "Other" -"Aquila fasciata" "Aquila" "Other" -"Aquila adalberti" "Aquila" "Other" -"Coracopsis vasa" "Coracopsis" "Other" -"Cardinalis" "Cardinalis" "Other" -"Fulica" "Fulica" "Other" -"Quiscalus" "Quiscalus" "Other" -"Phalacrocoracidae" "Phalacrocoracidae" "Other" -"Butorides virescens" "Butorides" "Other" -"Ardeidae" "Ardeidae" "Other" -"Dumetella" "Dumetella" "Other" -"Cricetinae" "Cricetinae" "Other" -"Bubulcus ibis" "Bubulcus" "Other" +"Serinus canaria" "Serinus" "Other" "Spatula querquedula" "Spatula" "Other" -"Bonasa umbellus" "Bonasa" "Other" -"Ciconiidae" "Ciconiidae" "Other" -"Ichthyaetus leucophthalmus" "Ichthyaetus" "Other" -"Molothrus ater" "Molothrus" "Other" -"Mephitis mephitis" "Mephitis" "Other" -"Platycercus" "Platycercus" "Other" +"Spheniscus humboldti" "Spheniscus" "Other" +"Spinus tristis" "Spinus" "Other" +"Sternula antillarum" "Sternula" "Other" +"Sternula" "Sternula" "Other" +"Streptopelia capicola" "Streptopelia" "Other" +"Streptopelia decaocto" "Streptopelia" "Other" +"Syncerus caffer" "Syncerus" "Other" +"Vicugna pacos" "Vicugna" "Other" From 70fbe18db0ace56c533b4578e834d0ac9a6c31f7 Mon Sep 17 00:00:00 2001 From: DOH-LMT2303 Date: Fri, 15 Nov 2024 17:42:44 +0000 Subject: [PATCH 5/8] Further classifying birds and ticks from host_type other --- .../defaults/host_hostgenus_hosttype_map.tsv | 569 +++++++++--------- 1 file changed, 284 insertions(+), 285 deletions(-) diff --git a/ingest/defaults/host_hostgenus_hosttype_map.tsv b/ingest/defaults/host_hostgenus_hosttype_map.tsv index 47cf4ff..096edb2 100644 --- a/ingest/defaults/host_hostgenus_hosttype_map.tsv +++ b/ingest/defaults/host_hostgenus_hosttype_map.tsv @@ -1,285 +1,284 @@ -"host" "host_genus" "host_type" -"Homo sapiens" "Homo" "Human" -"Aedeomyia madagascarica" "Aedeomyia" "Mosquito" -"Aedes albopictus" "Aedes" "Mosquito" -"Aedes cinereus" "Aedes" "Mosquito" -"Aedes dalzieli" "Aedes" "Mosquito" -"Aedes japonicus" "Aedes" "Mosquito" -"Aedes rossicus" "Aedes" "Mosquito" -"Aedes sp." "Aedes" "Mosquito" -"Aedes vexans" "Aedes" "Mosquito" -"Anopheles atroparvus" "Anopheles" "Mosquito" -"Anopheles bancroftii" "Anopheles" "Mosquito" -"Anopheles coustani" "Anopheles" "Mosquito" -"Anopheles farauti" "Anopheles" "Mosquito" -"Anopheles hyrcanus" "Anopheles" "Mosquito" -"Anopheles maculipennis" "Anopheles" "Mosquito" -"Anopheles messeae" "Anopheles" "Mosquito" -"Anopheles pauliani" "Anopheles" "Mosquito" -"Anopheles plumbeus" "Anopheles" "Mosquito" -"Anopheles sp." "Anopheles" "Mosquito" -"Anopheles stephensi" "Anopheles" "Mosquito" -"Coquillettidia perturbans" "Coquillettidia" "Mosquito" -"Coquillettidia richiardii" "Coquillettidia" "Mosquito" -"Coquillettidia" "Coquillettidia" "Mosquito" -"Culex annulirostris" "Culex" "Mosquito" -"Culex antennatus" "Culex" "Mosquito" -"Culex bitaeniorhynchus" "Culex" "Mosquito" -"Culex erraticus" "Culex" "Mosquito" -"Culex erythrothorax" "Culex" "Mosquito" -"Culex gelidus" "Culex" "Mosquito" -"Culex interrogator" "Culex" "Mosquito" -"Culex modestus" "Culex" "Mosquito" -"Culex neavei" "Culex" "Mosquito" -"Culex nigripalpus" "Culex" "Mosquito" -"Culex perexiguus" "Culex" "Mosquito" -"Culex perfuscus" "Culex" "Mosquito" -"Culex pipiens complex" "Culex" "Mosquito" -"Culex pipiens pipiens" "Culex" "Mosquito" -"Culex pipiens sensu lato" "Culex" "Mosquito" -"Culex pipiens" "Culex" "Mosquito" -"Culex poicilipes" "Culex" "Mosquito" -"Culex pseudovishnui" "Culex" "Mosquito" -"Culex pullus" "Culex" "Mosquito" -"Culex quinquefasciatus" "Culex" "Mosquito" -"Culex restuans" "Culex" "Mosquito" -"Culex salinarius" "Culex" "Mosquito" -"Culex sitiens" "Culex" "Mosquito" -"Culex squamosus" "Culex" "Mosquito" -"Culex stigmatosoma" "Culex" "Mosquito" -"Culex tarsalis" "Culex" "Mosquito" -"Culex theileri" "Culex" "Mosquito" -"Culex tritaeniorhynchus" "Culex" "Mosquito" -"Culex univittatus" "Culex" "Mosquito" -"Culex vishnui" "Culex" "Mosquito" -"Culex whitmorei" "Culex" "Mosquito" -"Culex" "Culex" "Mosquito" -"Culicidae" "Culicidae" "Mosquito" -"Culiseta inornata" "Culiseta" "Mosquito" -"Culiseta longiareolata" "Culiseta" "Mosquito" -"Culiseta melanura" "Culiseta" "Mosquito" -"Culiseta morsitans" "Culiseta" "Mosquito" -"Culiseta" "Culiseta" "Mosquito" -"Mansonia uniformis" "Mansonia" "Mosquito" -"Ochlerotatus canadensis" "Ochlerotatus" "Mosquito" -"Ochlerotatus cantator" "Ochlerotatus" "Mosquito" -"Ochlerotatus caspius" "Ochlerotatus" "Mosquito" -"Ochlerotatus communis" "Ochlerotatus" "Mosquito" -"Ochlerotatus dorsalis" "Ochlerotatus" "Mosquito" -"Ochlerotatus flavescens" "Ochlerotatus" "Mosquito" -"Ochlerotatus sollicitans" "Ochlerotatus" "Mosquito" -"Ochlerotatus spencerii" "Ochlerotatus" "Mosquito" -"Ochlerotatus sticticus" "Ochlerotatus" "Mosquito" -"Ochlerotatus triseriatus" "Ochlerotatus" "Mosquito" -"Ochlerotatus trivittatus" "Ochlerotatus" "Mosquito" -"Psorophora ferox" "Psorophora" "Mosquito" -"Psorophora" "Psorophora" "Mosquito" -"Uranotaenia unguiculata" "Uranotaenia" "Mosquito" -"Uranotaenia" "Uranotaenia" "Mosquito" -"Dermacentor marginatus" "Dermacentor" "Tick" -"Hyalomma marginatum marginatum" "Hyalomma" "Tick" -"Hyalomma marginatum" "Hyalomma" "Tick" -"Hyalomma plumbeum plumbeum" "Hyalomma" "Tick" -"Hyalomma scupense" "Hyalomma" "Tick" -"Hyalomma" "Hyalomma" "Tick" -"Rhipicephalus guilhoni" "Rhipicephalus" "Tick" -"Rhipicephalus pulchellus" "Rhipicephalus" "Tick" -"Alectorobius capensis" "Alectorobius" "Tick" -"Accipiter cooperii" "Accipiter" "Bird" -"Accipiter gentilis" "Accipiter" "Bird" -"Accipiter nisus" "Accipiter" "Bird" -"Accipiter striatus" "Accipiter" "Bird" -"Accipiter" "Accipiter" "Bird" -"Aphelocoma californica" "Aphelocoma" "Bird" -"Aphelocoma" "Aphelocoma" "Bird" -"Corvus brachyrhynchos" "Corvus" "Bird" -"Corvus corax" "Corvus" "Bird" -"Corvus cornix" "Corvus" "Bird" -"Corvus corone" "Corvus" "Bird" -"Corvus frugilegus" "Corvus" "Bird" -"Corvus ossifragus" "Corvus" "Bird" -"Corvus" "Corvus" "Bird" -"Cuculus canorus" "Cuculus" "Bird" -"Cyanocitta cristata" "Cyanocitta" "Bird" -"Falco columbarius" "Falco" "Bird" -"Falco peregrinus" "Falco" "Bird" -"Falco punctatus" "Falco" "Bird" -"Falco sparverius" "Falco" "Bird" -"Falco tinnunculus" "Falco" "Bird" -"Falco" "Falco" "Bird" -"Pica hudsonia" "Pica" "Bird" -"Pica nuttalli" "Pica" "Bird" -"Pica pica" "Pica" "Bird" -"Accipitridae" "Accipitridae" "Bird" -"Acrocephalus dumetorum" "Acrocephalus" "Bird" -"Actitis macularius" "Actitis" "Bird" -"Aegithalos caudatus" "Aegithalos" "Bird" -"Aegypius monachus" "Aegypius" "Bird" -"Agelaius phoeniceus" "Agelaius" "Bird" -"Alopochen aegyptiaca" "Alopochen" "Bird" -"Anas platyrhynchos" "Anas" "Bird" -"Anatidae" "Anatidae" "Bird" -"Anser" "Anser" "Bird" -"Apus apus" "Apus" "Bird" -"Aquila adalberti" "Aquila" "Bird" -"Aquila chrysaetos" "Aquila" "Bird" -"Aquila fasciata" "Aquila" "Bird" -"Ardeidae" "Ardeidae" "Bird" -"Asio flammeus" "Asio" "Bird" -"Asio otus" "Asio" "Bird" -"Athene noctua" "Athene" "Bird" -"Aves" "Aves" "Bird" -"Baeolophus bicolor" "Baeolophus" "Bird" -"Baeolophus inornatus" "Baeolophus" "Bird" -"Bombycilla garrulus" "Bombycilla" "Bird" -"Bonasa umbellus" "Bonasa" "Bird" -"Branta canadensis" "Branta" "Bird" -"Bubo scandiacus" "Bubo" "Bird" -"Bubo virginianus" "Bubo" "Bird" -"Bubulcus ibis" "Bubulcus" "Bird" -"Buteo buteo" "Buteo" "Bird" -"Buteo jamaicensis" "Buteo" "Bird" -"Buteo lineatus" "Buteo" "Bird" -"Buteo regalis" "Buteo" "Bird" -"Buteo swainsoni" "Buteo" "Bird" -"Buteo" "Buteo" "Bird" -"Cardinalis cardinalis" "Cardinalis" "Bird" -"Cardinalis" "Cardinalis" "Bird" -"Corvidae" "Corvidae" "Bird" -"Strigidae" "Strigidae" "Bird" -"Strix aluco" "Strix" "Bird" -"Strix nebulosa lapponica" "Strix" "Bird" -"Strix nebulosa" "Strix" "Bird" -"Sturnidae" "Sturnidae" "Bird" -"Sturnus vulgaris" "Sturnus" "Bird" -"Sylvia atricapilla" "Sylvia" "Bird" -"Toxostoma rufum" "Toxostoma" "Bird" -"Trichoglossus haematodus" "Trichoglossus" "Bird" -"Trichoglossus moluccanus" "Trichoglossus" "Bird" -"Turdus merula" "Turdus" "Bird" -"Turdus migratorius" "Turdus" "Bird" -"Turdus philomelos" "Turdus" "Bird" -"Tyto alba" "Tyto" "Bird" -"Zenaida macroura" "Zenaida" "Bird" -"Gallus gallus" "Gallus" "Bird" -"Pheucticus melanocephalus" "Pheucticus" "Bird" -"Phoenicoparrus andinus" "Phoenicoparrus" "Bird" -"Phoenicopterus chilensis" "Phoenicopterus" "Bird" -"Phoenicopterus roseus" "Phoenicopterus" "Bird" -"Phoenicopterus ruber" "Phoenicopterus" "Bird" -"Phoenicopterus sp." "Phoenicopterus" "Bird" -"Equus caballus x Equus asinus" "Equus" "Horse" -"Equus caballus" "Equus" "Horse" -"Equus asinus" "Equus" "Horse" -"Equus ferus" "Equus" "Horse" -"Equus" "Equus" "Horse" -"Bos taurus" "Bos" "Other" -"Butorides virescens" "Butorides" "Other" -"Calidris alba" "Calidris" "Other" -"Calypte costae" "Calypte" "Other" -"Camelus bactrianus" "Camelus" "Other" -"Camelus dromedarius" "Camelus" "Other" -"Canis lupus familiaris" "Canis" "Other" -"Charadrius melodus" "Charadrius" "Other" -"Chiroptera" "Chiroptera" "Other" -"Chroicocephalus ridibundus" "Chroicocephalus" "Other" -"Ciconiidae" "Ciconiidae" "Other" -"Clanga pomarina" "Clanga" "Other" -"Colaptes auratus" "Colaptes" "Other" -"Coloeus monedula" "Coloeus" "Other" -"Columba livia" "Columba" "Other" -"Columba palumbus" "Columba" "Other" -"Columbidae" "Columbidae" "Other" -"Coracopsis vasa" "Coracopsis" "Other" -"Coragyps atratus" "Coragyps" "Other" -"Cricetinae" "Cricetinae" "Other" -"Crocodylus moreletii" "Crocodylus" "Other" -"Crocodylus niloticus" "Crocodylus" "Other" -"Crocodylus porosus" "Crocodylus" "Other" -"Curruca conspicillata" "Curruca" "Other" -"Cyanistes caeruleus" "Cyanistes" "Other" -"Cygnus buccinator" "Cygnus" "Other" -"Cygnus olor" "Cygnus" "Other" -"Dumetella" "Dumetella" "Other" -"Egretta garzetta" "Egretta" "Other" -"Euphagus cyanocephalus" "Euphagus" "Other" -"Fulica" "Fulica" "Other" -"Galliformes" "Galliformes" "Other" -"Garrulus glandarius" "Garrulus" "Other" -"Giraffa giraffa" "Giraffa" "Other" -"Gymnogyps californianus" "Gymnogyps" "Other" -"Haemorhous mexicanus" "Haemorhous" "Other" -"Haliaeetus albicilla" "Haliaeetus" "Other" -"Haliaeetus leucocephalus" "Haliaeetus" "Other" -"Hirundinidae" "Hirundinidae" "Other" -"Hirundo rustica" "Hirundo" "Other" -"Hylocichla mustelina" "Hylocichla" "Other" -"Ichthyaetus leucophthalmus" "Ichthyaetus" "Other" -"Ictinia mississippiensis" "Ictinia" "Other" -"Ixodoidea" "Ixodoidea" "Other" -"Lanius ludovicianus" "Lanius" "Other" -"Laridae" "Laridae" "Other" -"Larus crassirostris" "Larus" "Other" -"Larus delawarensis" "Larus" "Other" -"Larus michahellis" "Larus" "Other" -"Larus smithsonianus" "Larus" "Other" -"Lathamus discolor" "Lathamus" "Other" -"Loriini" "Loriini" "Other" -"Mastomys erythroleucus" "Mastomys" "Other" -"Meleagris gallopavo" "Meleagris" "Other" -"Mephitis mephitis" "Mephitis" "Other" -"Mergus squamatus" "Mergus" "Other" -"Mesocricetus auratus" "Mesocricetus" "Other" -"Mimus polyglottos" "Mimus" "Other" -"Mimus" "Mimus" "Other" -"Molothrus ater" "Molothrus" "Other" -"Mus musculus" "Mus" "Other" -"Nestor notabilis" "Nestor" "Other" -"Oena capensis" "Oena" "Other" -"Orcinus orca" "Orcinus" "Other" -"Oriolus flavocinctus" "Oriolus" "Other" -"Ovis aries" "Ovis" "Other" -"Pandion haliaetus" "Pandion" "Other" -"Panthera leo" "Panthera" "Other" -"Parulidae" "Parulidae" "Other" -"Parus major" "Parus" "Other" -"Passer domesticus" "Passer" "Other" -"Passer sp." "Passer" "Other" -"Passeridae" "Passeridae" "Other" -"Pelecanus erythrorhynchos" "Pelecanus" "Other" -"Pelecanus occidentalis" "Pelecanus" "Other" -"Pelecanus" "Pelecanus" "Other" -"Pelophylax ridibundus" "Pelophylax" "Other" -"Phalacrocoracidae" "Phalacrocoracidae" "Other" -"Phalacrocorax auritus" "Phalacrocorax" "Other" -"Phalacrocorax carbo" "Phalacrocorax" "Other" -"Phasianinae" "Phasianinae" "Other" -"Phasianus colchicus" "Phasianus" "Other" -"Phylloscopus collybita" "Phylloscopus" "Other" -"Platycercus" "Platycercus" "Other" -"Pluvialis apricaria" "Pluvialis" "Other" -"Podiceps cristatus" "Podiceps" "Other" -"Poecile atricapillus" "Poecile" "Other" -"Poecile carolinensis" "Poecile" "Other" -"Prunella modularis" "Prunella" "Other" -"Pyrrhocorax graculus" "Pyrrhocorax" "Other" -"Quelea quelea" "Quelea" "Other" -"Quiscalus major" "Quiscalus" "Other" -"Quiscalus quiscula" "Quiscalus" "Other" -"Quiscalus" "Quiscalus" "Other" -"Rallus aquaticus" "Rallus" "Other" -"Rodentia" "Rodentia" "Other" -"Rousettus leschenaultii" "Rousettus" "Other" -"Sciuridae" "Sciuridae" "Other" -"Sciurus carolinensis" "Sciurus" "Other" -"Sciurus niger" "Sciurus" "Other" -"Serinus canaria" "Serinus" "Other" -"Spatula querquedula" "Spatula" "Other" -"Spheniscus humboldti" "Spheniscus" "Other" -"Spinus tristis" "Spinus" "Other" -"Sternula antillarum" "Sternula" "Other" -"Sternula" "Sternula" "Other" -"Streptopelia capicola" "Streptopelia" "Other" -"Streptopelia decaocto" "Streptopelia" "Other" -"Syncerus caffer" "Syncerus" "Other" -"Vicugna pacos" "Vicugna" "Other" +host host_genus host_type +Homo sapiens Homo Human +Aedeomyia madagascarica Aedeomyia Mosquito +Aedes albopictus Aedes Mosquito +Aedes cinereus Aedes Mosquito +Aedes dalzieli Aedes Mosquito +Aedes rossicus Aedes Mosquito +Aedes sp. Aedes Mosquito +Aedes vexans Aedes Mosquito +Anopheles atroparvus Anopheles Mosquito +Anopheles bancroftii Anopheles Mosquito +Anopheles coustani Anopheles Mosquito +Anopheles farauti Anopheles Mosquito +Anopheles hyrcanus Anopheles Mosquito +Anopheles maculipennis Anopheles Mosquito +Anopheles messeae Anopheles Mosquito +Anopheles pauliani Anopheles Mosquito +Anopheles plumbeus Anopheles Mosquito +Anopheles sp. Anopheles Mosquito +Anopheles stephensi Anopheles Mosquito +Coquillettidia Coquillettidia Mosquito +Coquillettidia perturbans Coquillettidia Mosquito +Coquillettidia richiardii Coquillettidia Mosquito +Culex Culex Mosquito +Culex annulirostris Culex Mosquito +Culex antennatus Culex Mosquito +Culex bitaeniorhynchus Culex Mosquito +Culex erraticus Culex Mosquito +Culex erythrothorax Culex Mosquito +Culex gelidus Culex Mosquito +Culex interrogator Culex Mosquito +Culex modestus Culex Mosquito +Culex neavei Culex Mosquito +Culex nigripalpus Culex Mosquito +Culex perexiguus Culex Mosquito +Culex perfuscus Culex Mosquito +Culex pipiens Culex Mosquito +Culex pipiens complex Culex Mosquito +Culex pipiens pipiens Culex Mosquito +Culex pipiens sensu lato Culex Mosquito +Culex poicilipes Culex Mosquito +Culex pseudovishnui Culex Mosquito +Culex pullus Culex Mosquito +Culex quinquefasciatus Culex Mosquito +Culex restuans Culex Mosquito +Culex salinarius Culex Mosquito +Culex sitiens Culex Mosquito +Culex squamosus Culex Mosquito +Culex stigmatosoma Culex Mosquito +Culex tarsalis Culex Mosquito +Culex theileri Culex Mosquito +Culex tritaeniorhynchus Culex Mosquito +Culex univittatus Culex Mosquito +Culex vishnui Culex Mosquito +Culex whitmorei Culex Mosquito +Culicidae Culicidae Mosquito +Culiseta Culiseta Mosquito +Culiseta inornata Culiseta Mosquito +Culiseta longiareolata Culiseta Mosquito +Culiseta melanura Culiseta Mosquito +Culiseta morsitans Culiseta Mosquito +Mansonia uniformis Mansonia Mosquito +Ochlerotatus canadensis Ochlerotatus Mosquito +Ochlerotatus cantator Ochlerotatus Mosquito +Ochlerotatus caspius Ochlerotatus Mosquito +Ochlerotatus communis Ochlerotatus Mosquito +Ochlerotatus dorsalis Ochlerotatus Mosquito +Ochlerotatus flavescens Ochlerotatus Mosquito +Ochlerotatus sollicitans Ochlerotatus Mosquito +Ochlerotatus spencerii Ochlerotatus Mosquito +Ochlerotatus sticticus Ochlerotatus Mosquito +Ochlerotatus triseriatus Ochlerotatus Mosquito +Ochlerotatus trivittatus Ochlerotatus Mosquito +Psorophora Psorophora Mosquito +Psorophora ferox Psorophora Mosquito +Uranotaenia Uranotaenia Mosquito +Uranotaenia unguiculata Uranotaenia Mosquito +Accipiter Accipiter Bird +Accipiter cooperii Accipiter Bird +Accipiter gentilis Accipiter Bird +Accipiter nisus Accipiter Bird +Accipiter striatus Accipiter Bird +Accipitridae Accipitridae Bird +Acrocephalus dumetorum Acrocephalus Bird +Actitis macularius Actitis Bird +Aegithalos caudatus Aegithalos Bird +Aegypius monachus Aegypius Bird +Agelaius phoeniceus Agelaius Bird +Alopochen aegyptiaca Alopochen Bird +Anas platyrhynchos Anas Bird +Anatidae Anatidae Bird +Anser Anser Bird +Aphelocoma Aphelocoma Bird +Aphelocoma californica Aphelocoma Bird +Apus apus Apus Bird +Aquila adalberti Aquila Bird +Aquila chrysaetos Aquila Bird +Aquila fasciata Aquila Bird +Ardeidae Ardeidae Bird +Asio flammeus Asio Bird +Asio otus Asio Bird +Athene noctua Athene Bird +Aves Aves Bird +Baeolophus bicolor Baeolophus Bird +Baeolophus inornatus Baeolophus Bird +Bombycilla garrulus Bombycilla Bird +Bonasa umbellus Bonasa Bird +Branta canadensis Branta Bird +Bubo scandiacus Bubo Bird +Bubo virginianus Bubo Bird +Bubulcus ibis Bubulcus Bird +Buteo Buteo Bird +Buteo buteo Buteo Bird +Buteo jamaicensis Buteo Bird +Buteo lineatus Buteo Bird +Buteo regalis Buteo Bird +Buteo swainsoni Buteo Bird +Butorides virescens Butorides Bird +Calidris alba Calidris Bird +Calypte costae Calypte Bird +Cardinalis Cardinalis Bird +Cardinalis cardinalis Cardinalis Bird +Charadrius melodus Charadrius Bird +Chroicocephalus ridibundus Chroicocephalus Bird +Ciconiidae Ciconiidae Bird +Clanga pomarina Clanga Bird +Colaptes auratus Colaptes Bird +Coloeus monedula Coloeus Bird +Columba livia Columba Bird +Columba palumbus Columba Bird +Columbidae Columbidae Bird +Coracopsis vasa Coracopsis Bird +Coragyps atratus Coragyps Bird +Corvidae Corvidae Bird +Corvus Corvus Bird +Corvus brachyrhynchos Corvus Bird +Corvus corax Corvus Bird +Corvus cornix Corvus Bird +Corvus corone Corvus Bird +Corvus frugilegus Corvus Bird +Corvus ossifragus Corvus Bird +Cuculus canorus Cuculus Bird +Curruca conspicillata Curruca Bird +Cyanistes caeruleus Cyanistes Bird +Cyanocitta cristata Cyanocitta Bird +Cygnus buccinator Cygnus Bird +Cygnus olor Cygnus Bird +Dumetella Dumetella Bird +Egretta garzetta Egretta Bird +Euphagus cyanocephalus Euphagus Bird +Falco Falco Bird +Falco columbarius Falco Bird +Falco peregrinus Falco Bird +Falco punctatus Falco Bird +Falco sparverius Falco Bird +Falco tinnunculus Falco Bird +Fulica Fulica Bird +Galliformes Galliformes Bird +Gallus gallus Gallus Bird +Garrulus glandarius Garrulus Bird +Gymnogyps californianus Gymnogyps Bird +Haemorhous mexicanus Haemorhous Bird +Haliaeetus albicilla Haliaeetus Bird +Haliaeetus leucocephalus Haliaeetus Bird +Hirundinidae Hirundinidae Bird +Hirundo rustica Hirundo Bird +Hylocichla mustelina Hylocichla Bird +Ichthyaetus leucophthalmus Ichthyaetus Bird +Ictinia mississippiensis Ictinia Bird +Lanius ludovicianus Lanius Bird +Larus crassirostris Larus Bird +Larus delawarensis Larus Bird +Larus michahellis Larus Bird +Larus smithsonianus Larus Bird +Lathamus discolor Lathamus Bird +Loriini Loriini Bird +Meleagris gallopavo Meleagris Bird +Mergus squamatus Mergus Bird +Mimus Mimus Bird +Mimus polyglottos Mimus Bird +Molothrus ater Molothrus Bird +Nestor notabilis Nestor Bird +Oena capensis Oena Bird +Oriolus flavocinctus Oriolus Bird +Pandion haliaetus Pandion Bird +Parulidae Parulidae Bird +Parus major Parus Bird +Passer domesticus Passer Bird +Passer sp. Passer Bird +Passeridae Passeridae Bird +Pelecanus Pelecanus Bird +Pelecanus erythrorhynchos Pelecanus Bird +Pelecanus occidentalis Pelecanus Bird +Phalacrocoracidae Phalacrocoracidae Bird +Phalacrocorax auritus Phalacrocorax Bird +Phalacrocorax carbo Phalacrocorax Bird +Phasianinae Phasianinae Bird +Phasianus colchicus Phasianus Bird +Pheucticus melanocephalus Pheucticus Bird +Phoenicoparrus andinus Phoenicoparrus Bird +Phoenicopterus chilensis Phoenicopterus Bird +Phoenicopterus roseus Phoenicopterus Bird +Phoenicopterus ruber Phoenicopterus Bird +Phoenicopterus sp. Phoenicopterus Bird +Phylloscopus collybita Phylloscopus Bird +Pica hudsonia Pica Bird +Pica nuttalli Pica Bird +Pica pica Pica Bird +Pluvialis apricaria Pluvialis Bird +Podiceps cristatus Podiceps Bird +Poecile atricapillus Poecile Bird +Poecile carolinensis Poecile Bird +Prunella modularis Prunella Bird +Pyrrhocorax graculus Pyrrhocorax Bird +Quelea quelea Quelea Bird +Quiscalus Quiscalus Bird +Quiscalus major Quiscalus Bird +Quiscalus quiscula Quiscalus Bird +Rallus aquaticus Rallus Bird +Serinus canaria Serinus Bird +Spatula querquedula Spatula Bird +Spheniscus humboldti Spheniscus Bird +Spinus tristis Spinus Bird +Sternula Sternula Bird +Sternula antillarum Sternula Bird +Streptopelia capicola Streptopelia Bird +Streptopelia decaocto Streptopelia Bird +Strigidae Strigidae Bird +Strix aluco Strix Bird +Strix nebulosa Strix Bird +Strix nebulosa lapponica Strix Bird +Sturnidae Sturnidae Bird +Sturnus vulgaris Sturnus Bird +Sylvia atricapilla Sylvia Bird +Toxostoma rufum Toxostoma Bird +Trichoglossus haematodus Trichoglossus Bird +Trichoglossus moluccanus Trichoglossus Bird +Turdus merula Turdus Bird +Turdus migratorius Turdus Bird +Turdus philomelos Turdus Bird +Tyto alba Tyto Bird +Zenaida macroura Zenaida Bird +Equus caballus Equus Horse +Equus caballus x Equus asinus Equus Horse +Alectorobius capensis Alectorobius Tick +Dermacentor marginatus Dermacentor Tick +Hyalomma Hyalomma Tick +Hyalomma marginatum Hyalomma Tick +Hyalomma marginatum marginatum Hyalomma Tick +Hyalomma plumbeum plumbeum Hyalomma Tick +Hyalomma scupense Hyalomma Tick +Ixodoidea Ixodoidea Tick +Rhipicephalus guilhoni Rhipicephalus Tick +Rhipicephalus pulchellus Rhipicephalus Tick +Bos taurus Bos Other +Camelus bactrianus Camelus Other +Camelus dromedarius Camelus Other +Canis lupus familiaris Canis Other +Chiroptera Chiroptera Other +Cricetinae Cricetinae Other +Crocodylus moreletii Crocodylus Other +Crocodylus niloticus Crocodylus Other +Crocodylus porosus Crocodylus Other +Equus Equus Other +Equus asinus Equus Other +Equus ferus Equus Other +Giraffa giraffa Giraffa Other +Laridae Laridae Other +Mastomys erythroleucus Mastomys Other +Mephitis mephitis Mephitis Other +Mesocricetus auratus Mesocricetus Other +Mus musculus Mus Other +Orcinus orca Orcinus Other +Ovis aries Ovis Other +Panthera leo Panthera Other +Pelophylax ridibundus Pelophylax Other +Platycercus Platycercus Other +Rodentia Rodentia Other +Rousettus leschenaultii Rousettus Other +Sciuridae Sciuridae Other +Sciurus carolinensis Sciurus Other +Sciurus niger Sciurus Other +Syncerus caffer Syncerus Other +Vicugna pacos Vicugna Other From d46f0e53de437eeef21fb9b4b473723beb266619 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Sat, 16 Nov 2024 00:46:44 -0800 Subject: [PATCH 6/8] Add data provenence statements to the auspice view --- phylogenetic/defaults/auspice_config.json | 6 ++++++ phylogenetic/defaults/auspice_config_global.json | 6 ++++++ phylogenetic/defaults/description.md | 5 +++++ 3 files changed, 17 insertions(+) diff --git a/phylogenetic/defaults/auspice_config.json b/phylogenetic/defaults/auspice_config.json index a352ec5..3913356 100644 --- a/phylogenetic/defaults/auspice_config.json +++ b/phylogenetic/defaults/auspice_config.json @@ -1,5 +1,11 @@ { "title": "Washington Focused West Nile Virus Build", + "data_provenance": [ + { + "name": "GenBank", + "url": "https://www.ncbi.nlm.nih.gov/genbank/" + } + ], "colorings": [ {"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Sampling Date", "type": "continuous"}, diff --git a/phylogenetic/defaults/auspice_config_global.json b/phylogenetic/defaults/auspice_config_global.json index 26ab194..b7b598b 100644 --- a/phylogenetic/defaults/auspice_config_global.json +++ b/phylogenetic/defaults/auspice_config_global.json @@ -1,5 +1,11 @@ { "title": "Global West Nile Virus Build", + "data_provenance": [ + { + "name": "GenBank", + "url": "https://www.ncbi.nlm.nih.gov/genbank/" + } + ], "colorings": [ {"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Sampling Date", "type": "continuous"}, diff --git a/phylogenetic/defaults/description.md b/phylogenetic/defaults/description.md index 60e5e46..38354ea 100644 --- a/phylogenetic/defaults/description.md +++ b/phylogenetic/defaults/description.md @@ -1,3 +1,8 @@ We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain. Special thanks to individuals at the [Northwest Pathogen Genomics Center of Excellence](https://github.com/NW-PaGe) and [Grubaugh lab](https://grubaughlab.com/) for comments, code and suggestions. + +We curate sequence data and metadata from NCBI as starting point for our analyses. For global lineage designations, we query [pathoplexus](https://pathoplexus.org/) for lineage assignments and exclusively work with NCBI-sourced records at this time. Curated sequences and metadata are available as flat files at: + +* [data.nextstrain.org/files/workflows/WNV/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/WNV/sequences.fasta.zst) +* [data.nextstrain.org/files/workflows/WNV/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/WNV/metadata.tsv.zst) From 506502794781ff6a3aebbd63c3948f4cabb01e40 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Sat, 16 Nov 2024 02:14:01 -0800 Subject: [PATCH 7/8] Add Aedes japonicus --- ingest/defaults/host_hostgenus_hosttype_map.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/ingest/defaults/host_hostgenus_hosttype_map.tsv b/ingest/defaults/host_hostgenus_hosttype_map.tsv index 096edb2..c8c5a9d 100644 --- a/ingest/defaults/host_hostgenus_hosttype_map.tsv +++ b/ingest/defaults/host_hostgenus_hosttype_map.tsv @@ -4,6 +4,7 @@ Aedeomyia madagascarica Aedeomyia Mosquito Aedes albopictus Aedes Mosquito Aedes cinereus Aedes Mosquito Aedes dalzieli Aedes Mosquito +Aedes japonicus Aedes Mosquito Aedes rossicus Aedes Mosquito Aedes sp. Aedes Mosquito Aedes vexans Aedes Mosquito From 9c96add6d5554715d3cd851596a10e1bf0235303 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Sat, 16 Nov 2024 18:19:03 -0800 Subject: [PATCH 8/8] Add Ochlerotatus taeniorhynchus --- ingest/defaults/host_hostgenus_hosttype_map.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/ingest/defaults/host_hostgenus_hosttype_map.tsv b/ingest/defaults/host_hostgenus_hosttype_map.tsv index c8c5a9d..fdffcf7 100644 --- a/ingest/defaults/host_hostgenus_hosttype_map.tsv +++ b/ingest/defaults/host_hostgenus_hosttype_map.tsv @@ -70,6 +70,7 @@ Ochlerotatus flavescens Ochlerotatus Mosquito Ochlerotatus sollicitans Ochlerotatus Mosquito Ochlerotatus spencerii Ochlerotatus Mosquito Ochlerotatus sticticus Ochlerotatus Mosquito +Ochlerotatus taeniorhynchus Ochlerotatus Mosquito Ochlerotatus triseriatus Ochlerotatus Mosquito Ochlerotatus trivittatus Ochlerotatus Mosquito Psorophora Psorophora Mosquito