From 322c408b5dbbb914347a8ef5ce4172bcf68c4ea7 Mon Sep 17 00:00:00 2001 From: OntoBot Date: Tue, 21 Apr 2020 14:44:06 -0400 Subject: [PATCH] Update NCBITaxon import. --- src/ontology/imports/ncbitaxon_import.obo | 163 ++++---- src/ontology/imports/ncbitaxon_import.owl | 429 +++++++++++----------- 2 files changed, 317 insertions(+), 275 deletions(-) diff --git a/src/ontology/imports/ncbitaxon_import.obo b/src/ontology/imports/ncbitaxon_import.obo index 0aad4ca06d..cc22b12494 100644 --- a/src/ontology/imports/ncbitaxon_import.obo +++ b/src/ontology/imports/ncbitaxon_import.obo @@ -34,13 +34,14 @@ relationship: RO:0002162 NCBITaxon:1117 ! in taxon Cyanobacteria [Term] id: NCBITaxon:117565 -name: Hyperotreti +name: Myxini synonym: "Agnatha" RELATED [] synonym: "fish" EXACT [] synonym: "fishes" EXACT [] +synonym: "Hyperotreti" RELATED [] is_a: NCBITaxon:1476529 ! Cyclostomata disjoint_from: NCBITaxon:117569 ! Hyperoartia -relationship: RO:0002162 NCBITaxon:117565 ! in taxon Hyperotreti +relationship: RO:0002162 NCBITaxon:117565 ! in taxon Myxini [Term] id: NCBITaxon:117569 @@ -77,8 +78,15 @@ relationship: RO:0002162 NCBITaxon:119089 ! in taxon Chromadorea id: NCBITaxon:1206794 name: Ecdysozoa is_a: NCBITaxon:33317 ! Protostomia +disjoint_from: NCBITaxon:2697495 ! Spiralia relationship: RO:0002162 NCBITaxon:1206794 ! in taxon Ecdysozoa +[Term] +id: NCBITaxon:1206795 +name: Lophotrochozoa +is_a: NCBITaxon:2697495 ! Spiralia +relationship: RO:0002162 NCBITaxon:1206795 ! in taxon Lophotrochozoa + [Term] id: NCBITaxon:1292243 name: Continenticola @@ -158,9 +166,7 @@ relationship: RO:0002162 NCBITaxon:1437180 ! in taxon Acrogymnospermae [Term] id: NCBITaxon:1445966 name: Gnetidae -is_a: NCBITaxon:1437180 ! Acrogymnospermae -disjoint_from: NCBITaxon:3312 ! Coniferophyta -disjoint_from: NCBITaxon:58022 ! Gnetophyta +is_a: NCBITaxon:3372 ! Gnetopsida relationship: RO:0002162 NCBITaxon:1445966 ! in taxon Gnetidae [Term] @@ -260,7 +266,7 @@ relationship: RO:0002162 NCBITaxon:2058185 ! in taxon Dictyosteliaceae [Term] id: NCBITaxon:2058949 name: Dictyosteliales -is_a: NCBITaxon:33083 ! Dictyostelids +is_a: NCBITaxon:33083 ! Dictyostelia relationship: RO:0002162 NCBITaxon:2058949 ! in taxon Dictyosteliales [Term] @@ -324,16 +330,63 @@ relationship: RO:0002162 NCBITaxon:2605435 ! in taxon Evosea id: NCBITaxon:2611341 name: Metamonada is_a: NCBITaxon:2759 ! Eukaryota -disjoint_from: NCBITaxon:3027 ! Cryptophyta +disjoint_from: NCBITaxon:2611352 ! Discoba +disjoint_from: NCBITaxon:2698737 ! Sar +disjoint_from: NCBITaxon:3027 ! Cryptophyceae disjoint_from: NCBITaxon:33090 ! Viridiplantae disjoint_from: NCBITaxon:33154 ! Opisthokonta -disjoint_from: NCBITaxon:33630 ! Alveolata -disjoint_from: NCBITaxon:33634 ! Stramenopiles -disjoint_from: NCBITaxon:33682 ! Euglenozoa disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae disjoint_from: NCBITaxon:554915 ! Amoebozoa relationship: RO:0002162 NCBITaxon:2611341 ! in taxon Metamonada +[Term] +id: NCBITaxon:2611352 +name: Discoba +is_a: NCBITaxon:2759 ! Eukaryota +disjoint_from: NCBITaxon:2698737 ! Sar +disjoint_from: NCBITaxon:3027 ! Cryptophyceae +disjoint_from: NCBITaxon:33090 ! Viridiplantae +disjoint_from: NCBITaxon:33154 ! Opisthokonta +disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae +disjoint_from: NCBITaxon:554915 ! Amoebozoa +relationship: RO:0002162 NCBITaxon:2611352 ! in taxon Discoba + +[Term] +id: NCBITaxon:2684882 +name: Zygnematophycidae +is_a: NCBITaxon:131209 ! Zygnemophyceae +relationship: RO:0002162 NCBITaxon:2684882 ! in taxon Zygnematophycidae + +[Term] +id: NCBITaxon:2697495 +name: Spiralia +is_a: NCBITaxon:33317 ! Protostomia +relationship: RO:0002162 NCBITaxon:2697495 ! in taxon Spiralia + +[Term] +id: NCBITaxon:2698737 +name: Sar +synonym: "SAR supergroup" RELATED [] +is_a: NCBITaxon:2759 ! Eukaryota +disjoint_from: NCBITaxon:3027 ! Cryptophyceae +disjoint_from: NCBITaxon:33090 ! Viridiplantae +disjoint_from: NCBITaxon:33154 ! Opisthokonta +disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae +disjoint_from: NCBITaxon:554915 ! Amoebozoa +relationship: RO:0002162 NCBITaxon:2698737 ! in taxon Sar + +[Term] +id: NCBITaxon:2704647 +name: Metakinetoplastina +is_a: NCBITaxon:5653 ! Kinetoplastea +relationship: RO:0002162 NCBITaxon:2704647 ! in taxon Metakinetoplastina + +[Term] +id: NCBITaxon:2704949 +name: Trypanosomatida +is_a: NCBITaxon:2704647 ! Metakinetoplastina +relationship: RO:0002162 NCBITaxon:2704949 ! in taxon Trypanosomatida + [Term] id: NCBITaxon:2759 name: Eukaryota @@ -386,23 +439,20 @@ relationship: RO:0002162 NCBITaxon:2864 ! in taxon Dinophyceae [Term] id: NCBITaxon:3027 -name: Cryptophyta +name: Cryptophyceae synonym: "algae" RELATED [] synonym: "Chromophyta" RELATED [] synonym: "Cryptomonadida" RELATED [] synonym: "cryptomonads" EXACT [] synonym: "cryptomonads" RELATED [] -synonym: "Cryptophyceae" RELATED [] +synonym: "Cryptophyta" RELATED [] synonym: "cryptophytes" RELATED [] is_a: NCBITaxon:2759 ! Eukaryota disjoint_from: NCBITaxon:33090 ! Viridiplantae disjoint_from: NCBITaxon:33154 ! Opisthokonta -disjoint_from: NCBITaxon:33630 ! Alveolata -disjoint_from: NCBITaxon:33634 ! Stramenopiles -disjoint_from: NCBITaxon:33682 ! Euglenozoa disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae disjoint_from: NCBITaxon:554915 ! Amoebozoa -relationship: RO:0002162 NCBITaxon:3027 ! in taxon Cryptophyta +relationship: RO:0002162 NCBITaxon:3027 ! in taxon Cryptophyceae [Term] id: NCBITaxon:314146 @@ -428,7 +478,7 @@ relationship: RO:0002162 NCBITaxon:314295 ! in taxon Hominoidea [Term] id: NCBITaxon:3176 name: Zygnematales -is_a: NCBITaxon:131209 ! Zygnemophyceae +is_a: NCBITaxon:2684882 ! Zygnematophycidae relationship: RO:0002162 NCBITaxon:3176 ! in taxon Zygnematales [Term] @@ -479,14 +529,14 @@ relationship: RO:0002162 NCBITaxon:32561 ! in taxon Sauria [Term] id: NCBITaxon:33083 -name: Dictyostelids +name: Dictyostelia synonym: "cellular slime molds" RELATED [] -synonym: "Dictyostelia" RELATED [] synonym: "dictyostelid cellular slime molds" EXACT [] synonym: "Dictyostelida" RELATED [] +synonym: "Dictyostelids" RELATED [] synonym: "Dictyosteliida" RELATED [] is_a: NCBITaxon:142796 ! Eumycetozoa -relationship: RO:0002162 NCBITaxon:33083 ! in taxon Dictyostelids +relationship: RO:0002162 NCBITaxon:33083 ! in taxon Dictyostelia [Term] id: NCBITaxon:33090 @@ -499,9 +549,6 @@ synonym: "green plants" EXACT [] synonym: "green plants" RELATED [] is_a: NCBITaxon:2759 ! Eukaryota disjoint_from: NCBITaxon:33154 ! Opisthokonta -disjoint_from: NCBITaxon:33630 ! Alveolata -disjoint_from: NCBITaxon:33634 ! Stramenopiles -disjoint_from: NCBITaxon:33682 ! Euglenozoa disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae disjoint_from: NCBITaxon:554915 ! Amoebozoa relationship: RO:0002162 NCBITaxon:33090 ! in taxon Viridiplantae @@ -511,6 +558,7 @@ id: NCBITaxon:3312 name: Coniferophyta synonym: "conifers" RELATED [] is_a: NCBITaxon:1437180 ! Acrogymnospermae +disjoint_from: NCBITaxon:3372 ! Gnetopsida disjoint_from: NCBITaxon:58022 ! Gnetophyta relationship: RO:0002162 NCBITaxon:3312 ! in taxon Coniferophyta @@ -520,9 +568,6 @@ name: Opisthokonta synonym: "Fungi/Metazoa group" RELATED [] synonym: "opisthokonts" RELATED [] is_a: NCBITaxon:2759 ! Eukaryota -disjoint_from: NCBITaxon:33630 ! Alveolata -disjoint_from: NCBITaxon:33634 ! Stramenopiles -disjoint_from: NCBITaxon:33682 ! Euglenozoa disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae disjoint_from: NCBITaxon:554915 ! Amoebozoa relationship: RO:0002162 NCBITaxon:33154 ! in taxon Opisthokonta @@ -550,7 +595,6 @@ id: NCBITaxon:33317 name: Protostomia is_a: NCBITaxon:33213 ! Bilateria disjoint_from: NCBITaxon:33511 ! Deuterostomia -disjoint_from: NCBITaxon:6157 ! Platyhelminthes relationship: RO:0002162 NCBITaxon:33317 ! in taxon Protostomia [Term] @@ -571,18 +615,14 @@ id: NCBITaxon:33511 name: Deuterostomia synonym: "deuterostomes" EXACT [] is_a: NCBITaxon:33213 ! Bilateria -disjoint_from: NCBITaxon:6157 ! Platyhelminthes relationship: RO:0002162 NCBITaxon:33511 ! in taxon Deuterostomia [Term] id: NCBITaxon:33630 name: Alveolata synonym: "alveolates" EXACT [] -is_a: NCBITaxon:2759 ! Eukaryota +is_a: NCBITaxon:2698737 ! Sar disjoint_from: NCBITaxon:33634 ! Stramenopiles -disjoint_from: NCBITaxon:33682 ! Euglenozoa -disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae -disjoint_from: NCBITaxon:554915 ! Amoebozoa relationship: RO:0002162 NCBITaxon:33630 ! in taxon Alveolata [Term] @@ -592,21 +632,25 @@ synonym: "Chromophyta" RELATED [] synonym: "Heterokonta" RELATED [] synonym: "heterokonts" EXACT [] synonym: "Straminipila" RELATED [] -is_a: NCBITaxon:2759 ! Eukaryota -disjoint_from: NCBITaxon:33682 ! Euglenozoa -disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae -disjoint_from: NCBITaxon:554915 ! Amoebozoa +is_a: NCBITaxon:2698737 ! Sar relationship: RO:0002162 NCBITaxon:33634 ! in taxon Stramenopiles [Term] id: NCBITaxon:33682 name: Euglenozoa synonym: "Euglenozoans" RELATED [] -is_a: NCBITaxon:2759 ! Eukaryota -disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae -disjoint_from: NCBITaxon:554915 ! Amoebozoa +is_a: NCBITaxon:2611352 ! Discoba relationship: RO:0002162 NCBITaxon:33682 ! in taxon Euglenozoa +[Term] +id: NCBITaxon:3372 +name: Gnetopsida +synonym: "Chlamydospermopsida" RELATED [] +synonym: "Gneticae" RELATED [] +is_a: NCBITaxon:1437180 ! Acrogymnospermae +disjoint_from: NCBITaxon:58022 ! Gnetophyta +relationship: RO:0002162 NCBITaxon:3372 ! in taxon Gnetopsida + [Term] id: NCBITaxon:3378 name: Gnetales @@ -739,8 +783,8 @@ relationship: RO:0002162 NCBITaxon:451866 ! in taxon Taphrinomycotina [Term] id: NCBITaxon:4751 name: Fungi -synonym: "fungi" EXACT [] synonym: "fungi" RELATED [] +synonym: "Mycota" RELATED [] is_a: NCBITaxon:33154 ! Opisthokonta relationship: RO:0002162 NCBITaxon:4751 ! in taxon Fungi @@ -752,12 +796,12 @@ relationship: RO:0002162 NCBITaxon:47570 ! in taxon Schizotrypanum [Term] id: NCBITaxon:4762 -name: Oomycetes +name: Oomycota +synonym: "Oomycetes" RELATED [] synonym: "oomycetes" RELATED [] -synonym: "Oomycota" RELATED [] synonym: "Peronosporomycetes" RELATED [] is_a: NCBITaxon:33634 ! Stramenopiles -relationship: RO:0002162 NCBITaxon:4762 ! in taxon Oomycetes +relationship: RO:0002162 NCBITaxon:4762 ! in taxon Oomycota [Term] id: NCBITaxon:4890 @@ -808,7 +852,6 @@ id: NCBITaxon:4896 name: Schizosaccharomyces pombe synonym: "fission yeast" EXACT [] synonym: "Schizosaccharomyces malidevorans" RELATED [] -synonym: "Schizosaccharomyces pombeP" RELATED [] is_a: NCBITaxon:4895 ! Schizosaccharomyces relationship: RO:0002162 NCBITaxon:4896 ! in taxon Schizosaccharomyces pombe @@ -825,15 +868,12 @@ name: Saccharomyces cerevisiae synonym: "baker's yeast" EXACT [] synonym: "brewer's yeast" EXACT [] synonym: "Candida robusta" RELATED [] +synonym: "Mycoderma cerevisiae" RELATED [] synonym: "S. cerevisiae" EXACT [] -synonym: "Saccaromyces cerevisiae" RELATED [] -synonym: "Saccharomyce cerevisiae" RELATED [] synonym: "Saccharomyces capensis" RELATED [] synonym: "Saccharomyces italicus" RELATED [] synonym: "Saccharomyces oviformis" RELATED [] synonym: "Saccharomyces uvarum var. melibiosus" RELATED [] -synonym: "Saccharomyes cerevisiae" RELATED [] -synonym: "Sccharomyces cerevisiae" RELATED [] is_a: NCBITaxon:4930 ! Saccharomyces relationship: RO:0002162 NCBITaxon:4932 ! in taxon Saccharomyces cerevisiae @@ -849,7 +889,6 @@ name: Yarrowia lipolytica synonym: "Candida lipolytica" RELATED [] synonym: "Endomycopsis lipolytica" RELATED [] synonym: "Mycotorula lipolytica" RELATED [] -synonym: "Yallowia lipolitica" RELATED [] is_a: NCBITaxon:4951 ! Yarrowia relationship: RO:0002162 NCBITaxon:4952 ! in taxon Yarrowia lipolytica @@ -880,18 +919,18 @@ relationship: RO:0002162 NCBITaxon:55885 ! in taxon Peloderinae [Term] id: NCBITaxon:5653 -name: Kinetoplastida -synonym: "Kinetoplastea" RELATED [] +name: Kinetoplastea +synonym: "Kinetoplastida" RELATED [] synonym: "kinetoplastids" RELATED [] synonym: "kinetoplasts" EXACT [] synonym: "Protomonadida" RELATED [] is_a: NCBITaxon:33682 ! Euglenozoa -relationship: RO:0002162 NCBITaxon:5653 ! in taxon Kinetoplastida +relationship: RO:0002162 NCBITaxon:5653 ! in taxon Kinetoplastea [Term] id: NCBITaxon:5654 name: Trypanosomatidae -is_a: NCBITaxon:5653 ! Kinetoplastida +is_a: NCBITaxon:2704949 ! Trypanosomatida relationship: RO:0002162 NCBITaxon:5654 ! in taxon Trypanosomatidae [Term] @@ -1004,7 +1043,7 @@ name: Platyhelminthes synonym: "flatworm" EXACT [] synonym: "flatworms" EXACT [] synonym: "flatworms" RELATED [] -is_a: NCBITaxon:33213 ! Bilateria +is_a: NCBITaxon:1206795 ! Lophotrochozoa relationship: RO:0002162 NCBITaxon:6157 ! in taxon Platyhelminthes [Term] @@ -1141,7 +1180,6 @@ relationship: RO:0002162 NCBITaxon:7745 ! in taxon Petromyzontiformes id: NCBITaxon:7746 name: Petromyzontidae synonym: "lampreys" EXACT [] -synonym: "Petromyzonidae" RELATED [] is_a: NCBITaxon:7745 ! Petromyzontiformes relationship: RO:0002162 NCBITaxon:7746 ! in taxon Petromyzontidae @@ -1150,7 +1188,7 @@ id: NCBITaxon:7761 name: Myxiniformes synonym: "hagfishes" RELATED [] synonym: "Myxinoidea" RELATED [] -is_a: NCBITaxon:117565 ! Hyperotreti +is_a: NCBITaxon:117565 ! Myxini relationship: RO:0002162 NCBITaxon:7761 ! in taxon Myxiniformes [Term] @@ -1279,20 +1317,7 @@ relationship: RO:0002162 NCBITaxon:9605 ! in taxon Homo [Term] id: NCBITaxon:9606 name: Homo sapiens -synonym: "Home sapiens" RELATED [] -synonym: "Homo sampiens" RELATED [] -synonym: "Homo sapeins" RELATED [] -synonym: "Homo sapian" RELATED [] -synonym: "Homo sapians" RELATED [] -synonym: "Homo sapien" RELATED [] -synonym: "Homo sapience" RELATED [] -synonym: "Homo sapiense" RELATED [] -synonym: "Homo sapients" RELATED [] -synonym: "Homo sapines" RELATED [] -synonym: "Homo spaiens" RELATED [] -synonym: "Homo spiens" RELATED [] synonym: "human" EXACT [] -synonym: "Humo sapiens" RELATED [] synonym: "man" EXACT [] is_a: NCBITaxon:9605 ! Homo relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens diff --git a/src/ontology/imports/ncbitaxon_import.owl b/src/ontology/imports/ncbitaxon_import.owl index 06a4c571d9..7e31aad86a 100644 --- a/src/ontology/imports/ncbitaxon_import.owl +++ b/src/ontology/imports/ncbitaxon_import.owl @@ -221,7 +221,8 @@ fish fishes Agnatha - Hyperotreti + Hyperotreti + Myxini @@ -303,11 +304,27 @@ + Ecdysozoa + + + + + + + + + + + Lophotrochozoa + + + + @@ -477,15 +494,13 @@ - + - - Gnetidae @@ -847,12 +862,11 @@ + + - - - Metamonada @@ -860,6 +874,108 @@ + + + + + + + + + + + + + + + + + Discoba + + + + + + + + + + + + + + + Zygnematophycidae + + + + + + + + + + + + + + + Spiralia + + + + + + + + + + + + + + + + + + + + SAR supergroup + Sar + + + + + + + + + + + + + + + Metakinetoplastina + + + + + + + + + + + + + + + Trypanosomatida + + + + @@ -958,19 +1074,16 @@ - - - cryptomonads Chromophyta Cryptomonadida - Cryptophyceae + Cryptophyta algae cryptomonads cryptophytes - Cryptophyta + Cryptophyceae @@ -1026,7 +1139,7 @@ - + @@ -1149,11 +1262,11 @@ dictyostelid cellular slime molds - Dictyostelia Dictyostelida + Dictyostelids Dictyosteliida cellular slime molds - Dictyostelids + Dictyostelia @@ -1169,9 +1282,6 @@ - - - Chlorophyta/Embryophyta group @@ -1195,6 +1305,7 @@ + conifers Coniferophyta @@ -1212,9 +1323,6 @@ - - - Fungi/Metazoa group @@ -1271,7 +1379,6 @@ - Protostomia @@ -1318,7 +1425,6 @@ - deuterostomes Deuterostomia @@ -1328,7 +1434,7 @@ - + @@ -1336,9 +1442,6 @@ - - - alveolates Alveolata @@ -1348,16 +1451,13 @@ - + - - - heterokonts Chromophyta Heterokonta @@ -1370,21 +1470,37 @@ - + - - Euglenozoans Euglenozoa + + + + + + + + + + + + Chlamydospermopsida + Gneticae + Gnetopsida + + + + @@ -1686,7 +1802,7 @@ - fungi + Mycota fungi Fungi @@ -1718,10 +1834,10 @@ - Oomycota + Oomycetes Peronosporomycetes oomycetes - Oomycetes + Oomycota @@ -1836,7 +1952,6 @@ fission yeast Schizosaccharomyces malidevorans - Schizosaccharomyces pombeP Schizosaccharomyces pombe @@ -1872,14 +1987,11 @@ baker's yeast brewer's yeast Candida robusta - Saccaromyces cerevisiae - Saccharomyce cerevisiae + Mycoderma cerevisiae Saccharomyces capensis Saccharomyces italicus Saccharomyces oviformis Saccharomyces uvarum var. melibiosus - Saccharomyes cerevisiae - Sccharomyces cerevisiae Saccharomyces cerevisiae @@ -1913,7 +2025,6 @@ Candida lipolytica Endomycopsis lipolytica Mycotorula lipolytica - Yallowia lipolitica Yarrowia lipolytica @@ -1991,10 +2102,10 @@ kinetoplasts - Kinetoplastea + Kinetoplastida Protomonadida kinetoplastids - Kinetoplastida + Kinetoplastea @@ -2002,7 +2113,7 @@ - + @@ -2247,7 +2358,7 @@ - + @@ -2556,7 +2667,6 @@ lampreys - Petromyzonidae Petromyzontidae @@ -2858,19 +2968,6 @@ human man - Home sapiens - Homo sampiens - Homo sapeins - Homo sapian - Homo sapians - Homo sapien - Homo sapience - Homo sapiense - Homo sapients - Homo sapines - Homo spaiens - Homo spiens - Humo sapiens Homo sapiens @@ -2906,41 +3003,31 @@ - + - + - - - - - - - - - - - + - + - + - + @@ -3010,17 +3097,7 @@ - - - - - - - - - - - + @@ -3030,7 +3107,7 @@ - + @@ -3040,7 +3117,7 @@ - + @@ -3050,7 +3127,7 @@ - + @@ -3060,7 +3137,7 @@ - + @@ -3086,47 +3163,27 @@ - - - - - - - - - - - - - - - - - - - - - + - + - + - + - + @@ -3136,7 +3193,7 @@ - + @@ -3146,37 +3203,7 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -3186,7 +3213,7 @@ - + @@ -3196,47 +3223,37 @@ - - - - - - - - - - - + - + - + - + - + - + - + @@ -3246,7 +3263,7 @@ - + @@ -3256,137 +3273,137 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -3396,7 +3413,7 @@ - + @@ -3406,51 +3423,51 @@ - + - + - + - + - + - + - + - + - + - +