diff --git a/package-lock.json b/package-lock.json index 89d21ce0..78469d23 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,15 +1,15 @@ { "name": "@phyloref/phyx", - "version": "1.1.1", + "version": "1.2.0", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@phyloref/phyx", - "version": "1.1.1", + "version": "1.2.0", "license": "MIT", "dependencies": { - "jsonld": "^5.0.0", + "jsonld": "^8.3.3", "lodash": "^4.17.20", "moment": "^2.27.0", "newick-js": "^1.2.1", @@ -137,16 +137,26 @@ "dev": true }, "node_modules/@digitalbazaar/http-client": { - "version": "1.2.0", - "resolved": "https://registry.npmjs.org/@digitalbazaar/http-client/-/http-client-1.2.0.tgz", - "integrity": "sha512-W9KQQ5pUJcaR0I4c2HPJC0a7kRbZApIorZgPnEDwMBgj16iQzutGLrCXYaZOmxqVLVNqqlQ4aUJh+HBQZy4W6Q==", + "version": "3.4.1", + "resolved": "https://registry.npmjs.org/@digitalbazaar/http-client/-/http-client-3.4.1.tgz", + "integrity": "sha512-Ahk1N+s7urkgj7WvvUND5f8GiWEPfUw0D41hdElaqLgu8wZScI8gdI0q+qWw5N1d35x7GCRH2uk9mi+Uzo9M3g==", + "license": "BSD-3-Clause", "dependencies": { - "esm": "^3.2.22", - "ky": "^0.25.1", - "ky-universal": "^0.8.2" + "ky": "^0.33.3", + "ky-universal": "^0.11.0", + "undici": "^5.21.2" }, "engines": { - "node": ">=10.0.0" + "node": ">=14.0" + } + }, + "node_modules/@fastify/busboy": { + "version": "2.1.1", + "resolved": "https://registry.npmjs.org/@fastify/busboy/-/busboy-2.1.1.tgz", + "integrity": "sha512-vBZP4NlzfOlerQTnba4aqZoMhE/a9HY7HRqoOPaETQcSQuWEIyZMHGfVu6w9wGtGK5fED5qRs2DteVCjOH60sA==", + "license": "MIT", + "engines": { + "node": ">=14" } }, "node_modules/@nodelib/fs.scandir": { @@ -262,6 +272,7 @@ "version": "3.0.0", "resolved": "https://registry.npmjs.org/abort-controller/-/abort-controller-3.0.0.tgz", "integrity": "sha512-h8lQ8tacZYnR3vNQTgibj+tODHI5/+l06Au2Pcriv/Gmet0eaj4TwWH41sO9wnHDiQsEj19q0drzdWdeAHtweg==", + "license": "MIT", "dependencies": { "event-target-shim": "^5.0.0" }, @@ -1111,11 +1122,12 @@ } }, "node_modules/data-uri-to-buffer": { - "version": "3.0.1", - "resolved": "https://registry.npmjs.org/data-uri-to-buffer/-/data-uri-to-buffer-3.0.1.tgz", - "integrity": "sha512-WboRycPNsVw3B3TL559F7kuBUM4d8CgMEvk6xEJlOp7OBPjt6G7z8WMWlD2rOFZLk6OYfFIUGsCOWzcQH9K2og==", + "version": "4.0.1", + "resolved": "https://registry.npmjs.org/data-uri-to-buffer/-/data-uri-to-buffer-4.0.1.tgz", + "integrity": "sha512-0R9ikRb668HB7QDxT1vkpuUBtqc53YyAwMwGeUFKRojY/NWKvdZ+9UYtRfGmhqNbRkTSVpMbmyhXipFFv2cb/A==", + "license": "MIT", "engines": { - "node": ">= 6" + "node": ">= 12" } }, "node_modules/data-view-buffer": { @@ -2345,14 +2357,6 @@ "node": ">=4" } }, - "node_modules/esm": { - "version": "3.2.25", - "resolved": "https://registry.npmjs.org/esm/-/esm-3.2.25.tgz", - "integrity": "sha512-U1suiZ2oDVWv4zPO56S0NcR5QriEahGtdN2OR6FiOG4WJvcjBVFB0qI4+eKoWFH483PKGuLuu6V8Z4T5g63UVA==", - "engines": { - "node": ">=6" - } - }, "node_modules/espree": { "version": "5.0.1", "resolved": "https://registry.npmjs.org/espree/-/espree-5.0.1.tgz", @@ -2444,6 +2448,7 @@ "version": "5.0.1", "resolved": "https://registry.npmjs.org/event-target-shim/-/event-target-shim-5.0.1.tgz", "integrity": "sha512-i/2XbnSz/uxRCU6+NdVJgKWDTM427+MqYbkQzD321DuCQJUqOuJKIA0IM2+W2xtYHdKOmZ4dR6fExsd4SXL+WQ==", + "license": "MIT", "engines": { "node": ">=6" } @@ -2523,16 +2528,26 @@ } }, "node_modules/fetch-blob": { - "version": "2.1.2", - "resolved": "https://registry.npmjs.org/fetch-blob/-/fetch-blob-2.1.2.tgz", - "integrity": "sha512-YKqtUDwqLyfyMnmbw8XD6Q8j9i/HggKtPEI+pZ1+8bvheBu78biSmNaXWusx1TauGqtUUGx/cBb1mKdq2rLYow==", - "engines": { - "node": "^10.17.0 || >=12.3.0" - }, - "peerDependenciesMeta": { - "domexception": { - "optional": true + "version": "3.2.0", + "resolved": "https://registry.npmjs.org/fetch-blob/-/fetch-blob-3.2.0.tgz", + "integrity": "sha512-7yAQpD2UMJzLi1Dqv7qFYnPbaPx7ZfFK6PiIxQ4PfkGPyNyl2Ugx+a/umUonmKqjhM4DnfbMvdX6otXq83soQQ==", + "funding": [ + { + "type": "github", + "url": "https://github.com/sponsors/jimmywarting" + }, + { + "type": "paypal", + "url": "https://paypal.me/jimmywarting" } + ], + "license": "MIT", + "dependencies": { + "node-domexception": "^1.0.0", + "web-streams-polyfill": "^3.0.3" + }, + "engines": { + "node": "^12.20 || >= 14.13" } }, "node_modules/figures": { @@ -2656,6 +2671,18 @@ "node": ">= 0.12" } }, + "node_modules/formdata-polyfill": { + "version": "4.0.10", + "resolved": "https://registry.npmjs.org/formdata-polyfill/-/formdata-polyfill-4.0.10.tgz", + "integrity": "sha512-buewHzMvYL29jdeQTVILecSaZKnt/RJWjoZCF5OW60Z67/GmSLBkOFM7qh1PI3zFNtJbaZL5eQu1vLfazOwj4g==", + "license": "MIT", + "dependencies": { + "fetch-blob": "^3.1.2" + }, + "engines": { + "node": ">=12.20.0" + } + }, "node_modules/fs-extra": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-5.0.0.tgz", @@ -3975,17 +4002,18 @@ } }, "node_modules/jsonld": { - "version": "5.2.0", - "resolved": "https://registry.npmjs.org/jsonld/-/jsonld-5.2.0.tgz", - "integrity": "sha512-JymgT6Xzk5CHEmHuEyvoTNviEPxv6ihLWSPu1gFdtjSAyM6cFqNrv02yS/SIur3BBIkCf0HjizRc24d8/FfQKw==", + "version": "8.3.3", + "resolved": "https://registry.npmjs.org/jsonld/-/jsonld-8.3.3.tgz", + "integrity": "sha512-9YcilrF+dLfg9NTEof/mJLMtbdX1RJ8dbWtJgE00cMOIohb1lIyJl710vFiTaiHTl6ZYODJuBd32xFvUhmv3kg==", + "license": "BSD-3-Clause", "dependencies": { - "@digitalbazaar/http-client": "^1.1.0", + "@digitalbazaar/http-client": "^3.4.1", "canonicalize": "^1.0.1", "lru-cache": "^6.0.0", - "rdf-canonize": "^3.0.0" + "rdf-canonize": "^3.4.0" }, "engines": { - "node": ">=12" + "node": ">=14" } }, "node_modules/jsprim": { @@ -4014,33 +4042,35 @@ } }, "node_modules/ky": { - "version": "0.25.1", - "resolved": "https://registry.npmjs.org/ky/-/ky-0.25.1.tgz", - "integrity": "sha512-PjpCEWlIU7VpiMVrTwssahkYXX1by6NCT0fhTUX34F3DTinARlgMpriuroolugFPcMgpPWrOW4mTb984Qm1RXA==", + "version": "0.33.3", + "resolved": "https://registry.npmjs.org/ky/-/ky-0.33.3.tgz", + "integrity": "sha512-CasD9OCEQSFIam2U8efFK81Yeg8vNMTBUqtMOHlrcWQHqUX3HeCl9Dr31u4toV7emlH8Mymk5+9p0lL6mKb/Xw==", + "license": "MIT", "engines": { - "node": ">=10" + "node": ">=14.16" }, "funding": { "url": "https://github.com/sindresorhus/ky?sponsor=1" } }, "node_modules/ky-universal": { - "version": "0.8.2", - "resolved": "https://registry.npmjs.org/ky-universal/-/ky-universal-0.8.2.tgz", - "integrity": "sha512-xe0JaOH9QeYxdyGLnzUOVGK4Z6FGvDVzcXFTdrYA1f33MZdEa45sUDaMBy98xQMcsd2XIBrTXRrRYnegcSdgVQ==", + "version": "0.11.0", + "resolved": "https://registry.npmjs.org/ky-universal/-/ky-universal-0.11.0.tgz", + "integrity": "sha512-65KyweaWvk+uKKkCrfAf+xqN2/epw1IJDtlyCPxYffFCMR8u1sp2U65NtWpnozYfZxQ6IUzIlvUcw+hQ82U2Xw==", + "license": "MIT", "dependencies": { "abort-controller": "^3.0.0", - "node-fetch": "3.0.0-beta.9" + "node-fetch": "^3.2.10" }, "engines": { - "node": ">=10.17" + "node": ">=14.16" }, "funding": { "url": "https://github.com/sindresorhus/ky-universal?sponsor=1" }, "peerDependencies": { - "ky": ">=0.17.0", - "web-streams-polyfill": ">=2.0.0" + "ky": ">=0.31.4", + "web-streams-polyfill": ">=3.2.1" }, "peerDependenciesMeta": { "web-streams-polyfill": { @@ -4435,16 +4465,38 @@ "integrity": "sha512-1nh45deeb5olNY7eX82BkPO7SSxR5SSYJiPTrTdFUVYwAl8CKMA5N9PjTYkHiRjisVcxcQ1HXdLhx2qxxJzLNQ==", "dev": true }, + "node_modules/node-domexception": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/node-domexception/-/node-domexception-1.0.0.tgz", + "integrity": "sha512-/jKZoMpw0F8GRwl4/eLROPA3cfcXtLApP0QzLmUT/HuPCZWyB7IY9ZrMeKw2O/nFIqPQB3PVM9aYm0F312AXDQ==", + "deprecated": "Use your platform's native DOMException instead", + "funding": [ + { + "type": "github", + "url": "https://github.com/sponsors/jimmywarting" + }, + { + "type": "github", + "url": "https://paypal.me/jimmywarting" + } + ], + "license": "MIT", + "engines": { + "node": ">=10.5.0" + } + }, "node_modules/node-fetch": { - "version": "3.0.0-beta.9", - "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-3.0.0-beta.9.tgz", - "integrity": "sha512-RdbZCEynH2tH46+tj0ua9caUHVWrd/RHnRfvly2EVdqGmI3ndS1Vn/xjm5KuGejDt2RNDQsVRLPNd2QPwcewVg==", + "version": "3.3.2", + "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-3.3.2.tgz", + "integrity": "sha512-dRB78srN/l6gqWulah9SrxeYnxeddIG30+GOqK/9OlLVyLg3HPnr6SqOWTWOXKRwC2eGYCkZ59NNuSgvSrpgOA==", + "license": "MIT", "dependencies": { - "data-uri-to-buffer": "^3.0.1", - "fetch-blob": "^2.1.1" + "data-uri-to-buffer": "^4.0.0", + "fetch-blob": "^3.1.4", + "formdata-polyfill": "^4.0.10" }, "engines": { - "node": "^10.17 || >=12.3" + "node": "^12.20.0 || ^14.13.1 || >=16.0.0" }, "funding": { "type": "opencollective", @@ -5955,6 +6007,18 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/undici": { + "version": "5.29.0", + "resolved": "https://registry.npmjs.org/undici/-/undici-5.29.0.tgz", + "integrity": "sha512-raqeBD6NQK4SkWhQzeYKd1KmIG6dllBOTt55Rmkt4HtI9mwdWtJljnrXjAFUBLTSN67HWrOIZ3EPF4kjUw80Bg==", + "license": "MIT", + "dependencies": { + "@fastify/busboy": "^2.0.0" + }, + "engines": { + "node": ">=14.0" + } + }, "node_modules/undici-types": { "version": "5.26.5", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz", @@ -6022,6 +6086,15 @@ "dev": true, "optional": true }, + "node_modules/web-streams-polyfill": { + "version": "3.3.3", + "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.3.3.tgz", + "integrity": "sha512-d2JWLCivmZYTSIoge9MsgFCZrt571BikcWGYkjC1khllbTeDlGqZ2D8vD8E/lJa8WGWbb7Plm8/XJYV7IJHZZw==", + "license": "MIT", + "engines": { + "node": ">= 8" + } + }, "node_modules/webidl-conversions": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-2.0.1.tgz", diff --git a/package.json b/package.json index 4cc39759..df54523b 100644 --- a/package.json +++ b/package.json @@ -33,7 +33,7 @@ "test": "mocha --recursive" }, "dependencies": { - "jsonld": "^5.0.0", + "jsonld": "^8.3.3", "lodash": "^4.17.20", "moment": "^2.27.0", "newick-js": "^1.2.1", diff --git a/src/wrappers/PhyxWrapper.js b/src/wrappers/PhyxWrapper.js index 7792a9ca..4fccd9ee 100644 --- a/src/wrappers/PhyxWrapper.js +++ b/src/wrappers/PhyxWrapper.js @@ -303,7 +303,7 @@ class PhyxWrapper { )); } - return JSONLD.toRDF(owlJSONLD, { format: 'application/n-quads' }); + return JSONLD.toRDF(owlJSONLD, { format: 'application/n-quads', base: '_', produceGeneralizedRdf: true }); } } diff --git a/test/examples/correct/brochu_2003.jsonld b/test/examples/correct/brochu_2003.jsonld index 5c6b0a13..00e132f3 100644 --- a/test/examples/correct/brochu_2003.jsonld +++ b/test/examples/correct/brochu_2003.jsonld @@ -31,7 +31,7 @@ { "newick": "(Parasuchia,(rauisuchians,Aetosauria,(sphenosuchians,(protosuchians,(mesosuchians,(Hylaeochampsa,Aegyptosuchus,Stomatosuchus,(Allodaposuchus,('Gavialis gangeticus',(('Diplocynodon ratelii',('Alligator mississippiensis','Caiman crocodilus')Alligatoridae)Alligatoroidea,('Tomistoma schlegelii',('Osteolaemus tetraspis','Crocodylus niloticus')Crocodylinae)Crocodylidae)Brevirostres)Crocodylia))Eusuchia)Mesoeucrocodylia)Crocodyliformes)Crocodylomorpha))root;", "label": "Fig 1 from Brochu 2003", - "@id": "http://example.org/phyx.js/example#phylogeny0", + "@id": "#phylogeny0", "curatorNotes": "The figure differentiates between clade definitions that resolve to nodes and those that resolve to branches; this distinction has been ignored here.", "source": { "type": "article", @@ -76,7 +76,7 @@ "@type": "phyloref:ReferencePhylogenyEvidence", "nodes": [ { - "@id": "http://example.org/phyx.js/example#phylogeny0_node0", + "@id": "#phylogeny0_node0", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -87,29 +87,29 @@ ], "representsTaxonomicUnits": [], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node1", - "http://example.org/phyx.js/example#phylogeny0_node29" + "#phylogeny0_node1", + "#phylogeny0_node29" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node1", + "@id": "#phylogeny0_node1", "rdf:type": [ { "@id": "obo:CDAO_0000140" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node0", + "parent": "#phylogeny0_node0", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node29" + "#phylogeny0_node29" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node2", - "http://example.org/phyx.js/example#phylogeny0_node27", - "http://example.org/phyx.js/example#phylogeny0_node28" + "#phylogeny0_node2", + "#phylogeny0_node27", + "#phylogeny0_node28" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node2", + "@id": "#phylogeny0_node2", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -156,18 +156,18 @@ "label": "Crocodylomorpha" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node1", + "parent": "#phylogeny0_node1", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node27", - "http://example.org/phyx.js/example#phylogeny0_node28" + "#phylogeny0_node27", + "#phylogeny0_node28" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node3", - "http://example.org/phyx.js/example#phylogeny0_node26" + "#phylogeny0_node3", + "#phylogeny0_node26" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node3", + "@id": "#phylogeny0_node3", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -214,17 +214,17 @@ "label": "Crocodyliformes" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node2", + "parent": "#phylogeny0_node2", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node26" + "#phylogeny0_node26" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node4", - "http://example.org/phyx.js/example#phylogeny0_node25" + "#phylogeny0_node4", + "#phylogeny0_node25" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node4", + "@id": "#phylogeny0_node4", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -271,17 +271,17 @@ "label": "Mesoeucrocodylia" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node3", + "parent": "#phylogeny0_node3", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node25" + "#phylogeny0_node25" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node5", - "http://example.org/phyx.js/example#phylogeny0_node24" + "#phylogeny0_node5", + "#phylogeny0_node24" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node5", + "@id": "#phylogeny0_node5", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -328,37 +328,37 @@ "label": "Eusuchia" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node4", + "parent": "#phylogeny0_node4", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node24" + "#phylogeny0_node24" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node6", - "http://example.org/phyx.js/example#phylogeny0_node21", - "http://example.org/phyx.js/example#phylogeny0_node22", - "http://example.org/phyx.js/example#phylogeny0_node23" + "#phylogeny0_node6", + "#phylogeny0_node21", + "#phylogeny0_node22", + "#phylogeny0_node23" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node6", + "@id": "#phylogeny0_node6", "rdf:type": [ { "@id": "obo:CDAO_0000140" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node5", + "parent": "#phylogeny0_node5", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node21", - "http://example.org/phyx.js/example#phylogeny0_node22", - "http://example.org/phyx.js/example#phylogeny0_node23" + "#phylogeny0_node21", + "#phylogeny0_node22", + "#phylogeny0_node23" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node7", - "http://example.org/phyx.js/example#phylogeny0_node20" + "#phylogeny0_node7", + "#phylogeny0_node20" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node7", + "@id": "#phylogeny0_node7", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -405,17 +405,17 @@ "label": "Crocodylia" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node6", + "parent": "#phylogeny0_node6", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node20" + "#phylogeny0_node20" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node8", - "http://example.org/phyx.js/example#phylogeny0_node19" + "#phylogeny0_node8", + "#phylogeny0_node19" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node8", + "@id": "#phylogeny0_node8", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -462,17 +462,17 @@ "label": "Brevirostres" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node7", + "parent": "#phylogeny0_node7", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node19" + "#phylogeny0_node19" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node9", - "http://example.org/phyx.js/example#phylogeny0_node14" + "#phylogeny0_node9", + "#phylogeny0_node14" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node9", + "@id": "#phylogeny0_node9", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -515,7 +515,7 @@ "@type": "owl:Restriction", "onProperty": "obo:OBI_0000293", "someValuesFrom": { - "@id": "http://example.org/phyx.js/example#phyloref3" + "@id": "#phyloref3" } } ] @@ -534,7 +534,7 @@ "@type": "owl:Restriction", "onProperty": "obo:OBI_0000293", "someValuesFrom": { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } } ] @@ -557,17 +557,17 @@ "label": "Crocodylidae" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node8", + "parent": "#phylogeny0_node8", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node14" + "#phylogeny0_node14" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node10", - "http://example.org/phyx.js/example#phylogeny0_node13" + "#phylogeny0_node10", + "#phylogeny0_node13" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node10", + "@id": "#phylogeny0_node10", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -614,17 +614,17 @@ "label": "Crocodylinae" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node9", + "parent": "#phylogeny0_node9", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node13" + "#phylogeny0_node13" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node11", - "http://example.org/phyx.js/example#phylogeny0_node12" + "#phylogeny0_node11", + "#phylogeny0_node12" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node11", + "@id": "#phylogeny0_node11", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -672,13 +672,13 @@ "label": "Crocodylus niloticus" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node10", + "parent": "#phylogeny0_node10", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node12" + "#phylogeny0_node12" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node12", + "@id": "#phylogeny0_node12", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -726,13 +726,13 @@ "label": "Osteolaemus tetraspis" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node10", + "parent": "#phylogeny0_node10", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node11" + "#phylogeny0_node11" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node13", + "@id": "#phylogeny0_node13", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -780,13 +780,13 @@ "label": "Tomistoma schlegelii" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node9", + "parent": "#phylogeny0_node9", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node10" + "#phylogeny0_node10" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node14", + "@id": "#phylogeny0_node14", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -833,17 +833,17 @@ "label": "Alligatoroidea" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node8", + "parent": "#phylogeny0_node8", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node9" + "#phylogeny0_node9" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node15", - "http://example.org/phyx.js/example#phylogeny0_node18" + "#phylogeny0_node15", + "#phylogeny0_node18" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node15", + "@id": "#phylogeny0_node15", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -886,7 +886,7 @@ "@type": "owl:Restriction", "onProperty": "obo:OBI_0000293", "someValuesFrom": { - "@id": "http://example.org/phyx.js/example#phyloref0" + "@id": "#phyloref0" } } ] @@ -909,17 +909,17 @@ "label": "Alligatoridae" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node14", + "parent": "#phylogeny0_node14", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node18" + "#phylogeny0_node18" ], "children": [ - "http://example.org/phyx.js/example#phylogeny0_node16", - "http://example.org/phyx.js/example#phylogeny0_node17" + "#phylogeny0_node16", + "#phylogeny0_node17" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node16", + "@id": "#phylogeny0_node16", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -962,7 +962,7 @@ "@type": "owl:Restriction", "onProperty": "obo:OBI_0000293", "someValuesFrom": { - "@id": "http://example.org/phyx.js/example#phyloref2" + "@id": "#phyloref2" } } ] @@ -986,13 +986,13 @@ "label": "Caiman crocodilus" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node15", + "parent": "#phylogeny0_node15", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node17" + "#phylogeny0_node17" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node17", + "@id": "#phylogeny0_node17", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1035,7 +1035,7 @@ "@type": "owl:Restriction", "onProperty": "obo:OBI_0000293", "someValuesFrom": { - "@id": "http://example.org/phyx.js/example#phyloref1" + "@id": "#phyloref1" } } ] @@ -1059,13 +1059,13 @@ "label": "Alligator mississippiensis" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node15", + "parent": "#phylogeny0_node15", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node16" + "#phylogeny0_node16" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node18", + "@id": "#phylogeny0_node18", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1108,7 +1108,7 @@ "@type": "owl:Restriction", "onProperty": "obo:OBI_0000293", "someValuesFrom": { - "@id": "http://example.org/phyx.js/example#phyloref5" + "@id": "#phyloref5" } } ] @@ -1132,13 +1132,13 @@ "label": "Diplocynodon ratelii" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node14", + "parent": "#phylogeny0_node14", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node15" + "#phylogeny0_node15" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node19", + "@id": "#phylogeny0_node19", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1186,13 +1186,13 @@ "label": "Gavialis gangeticus" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node7", + "parent": "#phylogeny0_node7", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node8" + "#phylogeny0_node8" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node20", + "@id": "#phylogeny0_node20", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1239,13 +1239,13 @@ "label": "Allodaposuchus" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node6", + "parent": "#phylogeny0_node6", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node7" + "#phylogeny0_node7" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node21", + "@id": "#phylogeny0_node21", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1292,15 +1292,15 @@ "label": "Stomatosuchus" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node5", + "parent": "#phylogeny0_node5", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node6", - "http://example.org/phyx.js/example#phylogeny0_node22", - "http://example.org/phyx.js/example#phylogeny0_node23" + "#phylogeny0_node6", + "#phylogeny0_node22", + "#phylogeny0_node23" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node22", + "@id": "#phylogeny0_node22", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1347,15 +1347,15 @@ "label": "Aegyptosuchus" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node5", + "parent": "#phylogeny0_node5", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node6", - "http://example.org/phyx.js/example#phylogeny0_node21", - "http://example.org/phyx.js/example#phylogeny0_node23" + "#phylogeny0_node6", + "#phylogeny0_node21", + "#phylogeny0_node23" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node23", + "@id": "#phylogeny0_node23", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1402,15 +1402,15 @@ "label": "Hylaeochampsa" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node5", + "parent": "#phylogeny0_node5", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node6", - "http://example.org/phyx.js/example#phylogeny0_node21", - "http://example.org/phyx.js/example#phylogeny0_node22" + "#phylogeny0_node6", + "#phylogeny0_node21", + "#phylogeny0_node22" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node24", + "@id": "#phylogeny0_node24", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1420,13 +1420,13 @@ "mesosuchians" ], "representsTaxonomicUnits": [], - "parent": "http://example.org/phyx.js/example#phylogeny0_node4", + "parent": "#phylogeny0_node4", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node5" + "#phylogeny0_node5" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node25", + "@id": "#phylogeny0_node25", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1436,13 +1436,13 @@ "protosuchians" ], "representsTaxonomicUnits": [], - "parent": "http://example.org/phyx.js/example#phylogeny0_node3", + "parent": "#phylogeny0_node3", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node4" + "#phylogeny0_node4" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node26", + "@id": "#phylogeny0_node26", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1452,13 +1452,13 @@ "sphenosuchians" ], "representsTaxonomicUnits": [], - "parent": "http://example.org/phyx.js/example#phylogeny0_node2", + "parent": "#phylogeny0_node2", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node3" + "#phylogeny0_node3" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node27", + "@id": "#phylogeny0_node27", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1505,14 +1505,14 @@ "label": "Aetosauria" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node1", + "parent": "#phylogeny0_node1", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node2", - "http://example.org/phyx.js/example#phylogeny0_node28" + "#phylogeny0_node2", + "#phylogeny0_node28" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node28", + "@id": "#phylogeny0_node28", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1522,14 +1522,14 @@ "rauisuchians" ], "representsTaxonomicUnits": [], - "parent": "http://example.org/phyx.js/example#phylogeny0_node1", + "parent": "#phylogeny0_node1", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node2", - "http://example.org/phyx.js/example#phylogeny0_node27" + "#phylogeny0_node2", + "#phylogeny0_node27" ] }, { - "@id": "http://example.org/phyx.js/example#phylogeny0_node29", + "@id": "#phylogeny0_node29", "rdf:type": [ { "@id": "obo:CDAO_0000140" @@ -1576,14 +1576,14 @@ "label": "Parasuchia" } ], - "parent": "http://example.org/phyx.js/example#phylogeny0_node0", + "parent": "#phylogeny0_node0", "siblings": [ - "http://example.org/phyx.js/example#phylogeny0_node1" + "#phylogeny0_node1" ] } ], "hasRootNode": { - "@id": "http://example.org/phyx.js/example#phylogeny0_node0" + "@id": "#phylogeny0_node0" } } ], @@ -1661,7 +1661,7 @@ } ], "externalSpecifiers": [], - "@id": "http://example.org/phyx.js/example#phyloref0", + "@id": "#phyloref0", "@type": "owl:Class", "equivalentClass": { "@type": "owl:Restriction", @@ -1806,7 +1806,7 @@ "nodeLabel": "Alligator mississippiensis" } }, - "@id": "http://example.org/phyx.js/example#phyloref1", + "@id": "#phyloref1", "@type": "owl:Class", "equivalentClass": { "@type": "owl:Class", @@ -1946,7 +1946,7 @@ "nodeLabel": "Caiman crocodilus" } }, - "@id": "http://example.org/phyx.js/example#phyloref2", + "@id": "#phyloref2", "@type": "owl:Class", "equivalentClass": { "@type": "owl:Class", @@ -2059,11 +2059,11 @@ "nodeLabel": "Crocodylidae" } }, - "@id": "http://example.org/phyx.js/example#phyloref3", + "@id": "#phyloref3", "@type": "owl:Class", "subClasses": [ { - "@id": "http://example.org/phyx.js/example#phyloref3_component1", + "@id": "#phyloref3_component1", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) ~ Alligator mississippiensis (ICZN) V Gavialis gangeticus (ICZN))", "equivalentClass": { @@ -2153,12 +2153,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMaximumClade", { - "@id": "http://example.org/phyx.js/example#phyloref3" + "@id": "#phyloref3" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref3_component2", + "@id": "#phyloref3_component2", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) ~ Alligator mississippiensis (ICZN) V Gavialis gangeticus (ICZN))", "equivalentClass": { @@ -2248,7 +2248,7 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMaximumClade", { - "@id": "http://example.org/phyx.js/example#phyloref3" + "@id": "#phyloref3" } ] } @@ -2344,11 +2344,11 @@ } ], "externalSpecifiers": [], - "@id": "http://example.org/phyx.js/example#phyloref4", + "@id": "#phyloref4", "@type": "owl:Class", "subClasses": [ { - "@id": "http://example.org/phyx.js/example#phyloref4_component1", + "@id": "#phyloref4_component1", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -2451,12 +2451,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref4_component2", + "@id": "#phyloref4_component2", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -2559,12 +2559,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref4_component3", + "@id": "#phyloref4_component3", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -2667,12 +2667,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref4_component4", + "@id": "#phyloref4_component4", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -2775,12 +2775,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref4_component5", + "@id": "#phyloref4_component5", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -2883,12 +2883,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref4_component6", + "@id": "#phyloref4_component6", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -2991,12 +2991,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref4_component7", + "@id": "#phyloref4_component7", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -3099,12 +3099,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref4_component8", + "@id": "#phyloref4_component8", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -3207,12 +3207,12 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] }, { - "@id": "http://example.org/phyx.js/example#phyloref4_component9", + "@id": "#phyloref4_component9", "@type": "owl:Class", "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", "equivalentClass": { @@ -3315,7 +3315,7 @@ "subClassOf": [ "phyloref:PhyloreferenceUsingMinimumClade", { - "@id": "http://example.org/phyx.js/example#phyloref4" + "@id": "#phyloref4" } ] } @@ -3404,7 +3404,7 @@ "description": "Only representative of the Diplocynodontinae clade in this phylogeny." } }, - "@id": "http://example.org/phyx.js/example#phyloref5", + "@id": "#phyloref5", "@type": "owl:Class", "equivalentClass": { "@type": "owl:Class", diff --git a/test/examples/correct/with-blank-base-iri/brochu_2003.json b/test/examples/correct/with-blank-base-iri/brochu_2003.json new file mode 100644 index 00000000..e4b51e0b --- /dev/null +++ b/test/examples/correct/with-blank-base-iri/brochu_2003.json @@ -0,0 +1,526 @@ +{ + "@context": "../../../../docs/context/development/phyx.json", + "doi": "10.5281/zenodo.4562685", + "contributors": [ + { + "@id": "http://orcid.org/0000-0003-0587-0454", + "name": "Gaurav Vaidya" + } + ], + "source": { + "authors": [ + { + "firstname": "Gaurav", + "lastname": "Vaidya" + } + ], + "year": 2021, + "title": "Digital representation of some of the clade definitions in Brochu 2003 in the Phyloreference Exchange (Phyx) format", + "journal": { + "name": "Zenodo" + }, + "identifier": [ + { + "type": "doi", + "id": "10.5281/zenodo.4562685" + } + ] + }, + "phylogenies": [ + { + "newick": "(Parasuchia,(rauisuchians,Aetosauria,(sphenosuchians,(protosuchians,(mesosuchians,(Hylaeochampsa,Aegyptosuchus,Stomatosuchus,(Allodaposuchus,('Gavialis gangeticus',(('Diplocynodon ratelii',('Alligator mississippiensis','Caiman crocodilus')Alligatoridae)Alligatoroidea,('Tomistoma schlegelii',('Osteolaemus tetraspis','Crocodylus niloticus')Crocodylinae)Crocodylidae)Brevirostres)Crocodylia))Eusuchia)Mesoeucrocodylia)Crocodyliformes)Crocodylomorpha))root;", + "label": "Fig 1 from Brochu 2003", + "@id": "#phylogeny0", + "curatorNotes": "The figure differentiates between clade definitions that resolve to nodes and those that resolve to branches; this distinction has been ignored here.", + "source": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + } + } + } + ], + "phylorefs": [ + { + "label": "Alligatoridae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Cuvier 1807)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMinimumClade", + "definition": "Alligatoridae (Cuvier 1807).\n\nLast common ancestor of Alligator mississippiensis and Caiman crocodilus and all of its descendents.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + } + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Caiman crocodilus", + "nameComplete": "Caiman crocodilus", + "genusPart": "Caiman", + "specificEpithet": "crocodilus" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + }, + "label": "Alligator mississippiensis" + } + ], + "externalSpecifiers": [] + }, + { + "label": "Alligatorinae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Kälin 1940)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMaximumClade", + "definition": "Alligatorinae (Kälin 1940).\n\nAlligator mississippiensis and all crocodylians closer to it than to Caiman crocodilus.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + } + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Caiman crocodilus", + "nameComplete": "Caiman crocodilus", + "genusPart": "Caiman", + "specificEpithet": "crocodilus" + }, + "label": "Caiman crocodilus" + } + ], + "expectedResolution": { + "#phylogeny0": { + "nodeLabel": "Alligator mississippiensis" + } + } + }, + { + "label": "Caimaninae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Norell 1988)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMaximumClade", + "definition": "Caimaninae (Norell 1988).\n\nCaiman crocodilus and all crocodylians closer to it than to Alligator mississippiensis.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + } + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Caiman crocodilus", + "nameComplete": "Caiman crocodilus", + "genusPart": "Caiman", + "specificEpithet": "crocodilus" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + } + } + ], + "expectedResolution": { + "#phylogeny0": { + "nodeLabel": "Caiman crocodilus" + } + } + }, + { + "label": "Crocodyloidea", + "scientificNameAuthorship": { + "bibliographicCitation": "(Fitzinger 1826)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMaximumClade", + "definition": "Crocodyloidea (Fitzinger 1826).\n\nCrocodylus niloticus and all crocodylians closer to it than to Alligator mississippiensis or Gavialis gangeticus.", + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Crocodylus niloticus", + "nameComplete": "Crocodylus niloticus", + "genusPart": "Crocodylus", + "specificEpithet": "niloticus" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + }, + "label": "Alligator mississippiensis" + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Gavialis gangeticus", + "nameComplete": "Gavialis gangeticus", + "genusPart": "Gavialis", + "specificEpithet": "gangeticus" + }, + "label": "Gavialis gangeticus" + } + ], + "expectedResolution": { + "#phylogeny0": { + "nodeLabel": "Crocodylidae" + } + } + }, + { + "label": "Crocodylidae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Cuvier 1807)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMinimumClade", + "curatorNotes": "An alternate definition of this phyloreference in the context of the molecular tree is included with the publication, but not included in this file. This defines Crocodylidae as the last common ancestor of Crocodylus niloticus and Osteolaemus tetraspis and all of its descendents.", + "definition": "Crocodylidae (Cuvier 1807). Definition dependent on phylogenetic context.\n\nLast common ancestor of Crocodylus niloticus, Osteolaemus tetraspis, and Tomistoma schlegelii and all of its descendents.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + } + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Tomistoma schlegelii", + "nameComplete": "Tomistoma schlegelii", + "genusPart": "Tomistoma", + "specificEpithet": "schlegelii" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Osteolaemus tetraspis", + "nameComplete": "Osteolaemus tetraspis", + "genusPart": "Osteolaemus", + "specificEpithet": "tetraspis" + }, + "label": "Osteolaemus tetraspis" + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Crocodylus niloticus", + "nameComplete": "Crocodylus niloticus", + "genusPart": "Crocodylus", + "specificEpithet": "niloticus" + }, + "label": "Crocodylus niloticus" + } + ], + "externalSpecifiers": [] + }, + { + "label": "Diplocynodontinae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Brochu 1999)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMaximumClade", + "definition": "Diplocynodontinae (Brochu 1999).\n\nDiplocynodon ratelii and all crocodylians closer to it than to Alligator mississippiensis.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + } + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Diplocynodon ratelii", + "nameComplete": "Diplocynodon ratelii", + "genusPart": "Diplocynodon", + "specificEpithet": "ratelii" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + } + } + ], + "expectedResolution": { + "#phylogeny0": { + "nodeLabel": "Diplocynodon ratelii", + "description": "Only representative of the Diplocynodontinae clade in this phylogeny." + } + } + } + ], + "defaultNomenclaturalCodeIRI": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" +} diff --git a/test/examples/correct/with-blank-base-iri/brochu_2003.jsonld b/test/examples/correct/with-blank-base-iri/brochu_2003.jsonld new file mode 100644 index 00000000..78efbf84 --- /dev/null +++ b/test/examples/correct/with-blank-base-iri/brochu_2003.jsonld @@ -0,0 +1,3478 @@ +{ + "@context": "../../../../docs/context/development/phyx.json", + "doi": "10.5281/zenodo.4562685", + "contributors": [ + { + "@id": "http://orcid.org/0000-0003-0587-0454", + "name": "Gaurav Vaidya" + } + ], + "source": { + "authors": [ + { + "firstname": "Gaurav", + "lastname": "Vaidya" + } + ], + "year": 2021, + "title": "Digital representation of some of the clade definitions in Brochu 2003 in the Phyloreference Exchange (Phyx) format", + "journal": { + "name": "Zenodo" + }, + "identifier": [ + { + "type": "doi", + "id": "10.5281/zenodo.4562685" + } + ], + "bibliographicCitation": "Gaurav Vaidya (2021) Digital representation of some of the clade definitions in Brochu 2003 in the Phyloreference Exchange (Phyx) format doi: 10.5281/zenodo.4562685" + }, + "phylogenies": [ + { + "newick": "(Parasuchia,(rauisuchians,Aetosauria,(sphenosuchians,(protosuchians,(mesosuchians,(Hylaeochampsa,Aegyptosuchus,Stomatosuchus,(Allodaposuchus,('Gavialis gangeticus',(('Diplocynodon ratelii',('Alligator mississippiensis','Caiman crocodilus')Alligatoridae)Alligatoroidea,('Tomistoma schlegelii',('Osteolaemus tetraspis','Crocodylus niloticus')Crocodylinae)Crocodylidae)Brevirostres)Crocodylia))Eusuchia)Mesoeucrocodylia)Crocodyliformes)Crocodylomorpha))root;", + "label": "Fig 1 from Brochu 2003", + "@id": "#phylogeny0", + "curatorNotes": "The figure differentiates between clade definitions that resolve to nodes and those that resolve to branches; this distinction has been ignored here.", + "source": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + }, + "bibliographicCitation": "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + }, + "@type": "phyloref:ReferencePhylogenyEvidence", + "nodes": [ + { + "@id": "#phylogeny0_node0", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + } + ], + "labels": [ + "root" + ], + "representsTaxonomicUnits": [], + "children": [ + "#phylogeny0_node1", + "#phylogeny0_node29" + ] + }, + { + "@id": "#phylogeny0_node1", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + } + ], + "parent": "#phylogeny0_node0", + "siblings": [ + "#phylogeny0_node29" + ], + "children": [ + "#phylogeny0_node2", + "#phylogeny0_node27", + "#phylogeny0_node28" + ] + }, + { + "@id": "#phylogeny0_node2", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylomorpha" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Crocodylomorpha" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Crocodylomorpha", + "nameComplete": "Crocodylomorpha", + "uninomial": "Crocodylomorpha", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Crocodylomorpha" + } + ], + "parent": "#phylogeny0_node1", + "siblings": [ + "#phylogeny0_node27", + "#phylogeny0_node28" + ], + "children": [ + "#phylogeny0_node3", + "#phylogeny0_node26" + ] + }, + { + "@id": "#phylogeny0_node3", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodyliformes" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Crocodyliformes" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Crocodyliformes", + "nameComplete": "Crocodyliformes", + "uninomial": "Crocodyliformes", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Crocodyliformes" + } + ], + "parent": "#phylogeny0_node2", + "siblings": [ + "#phylogeny0_node26" + ], + "children": [ + "#phylogeny0_node4", + "#phylogeny0_node25" + ] + }, + { + "@id": "#phylogeny0_node4", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Mesoeucrocodylia" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Mesoeucrocodylia" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Mesoeucrocodylia", + "nameComplete": "Mesoeucrocodylia", + "uninomial": "Mesoeucrocodylia", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Mesoeucrocodylia" + } + ], + "parent": "#phylogeny0_node3", + "siblings": [ + "#phylogeny0_node25" + ], + "children": [ + "#phylogeny0_node5", + "#phylogeny0_node24" + ] + }, + { + "@id": "#phylogeny0_node5", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Eusuchia" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Eusuchia" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Eusuchia", + "nameComplete": "Eusuchia", + "uninomial": "Eusuchia", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Eusuchia" + } + ], + "parent": "#phylogeny0_node4", + "siblings": [ + "#phylogeny0_node24" + ], + "children": [ + "#phylogeny0_node6", + "#phylogeny0_node21", + "#phylogeny0_node22", + "#phylogeny0_node23" + ] + }, + { + "@id": "#phylogeny0_node6", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + } + ], + "parent": "#phylogeny0_node5", + "siblings": [ + "#phylogeny0_node21", + "#phylogeny0_node22", + "#phylogeny0_node23" + ], + "children": [ + "#phylogeny0_node7", + "#phylogeny0_node20" + ] + }, + { + "@id": "#phylogeny0_node7", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylia" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Crocodylia" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Crocodylia", + "nameComplete": "Crocodylia", + "uninomial": "Crocodylia", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Crocodylia" + } + ], + "parent": "#phylogeny0_node6", + "siblings": [ + "#phylogeny0_node20" + ], + "children": [ + "#phylogeny0_node8", + "#phylogeny0_node19" + ] + }, + { + "@id": "#phylogeny0_node8", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Brevirostres" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Brevirostres" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Brevirostres", + "nameComplete": "Brevirostres", + "uninomial": "Brevirostres", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Brevirostres" + } + ], + "parent": "#phylogeny0_node7", + "siblings": [ + "#phylogeny0_node19" + ], + "children": [ + "#phylogeny0_node9", + "#phylogeny0_node14" + ] + }, + { + "@id": "#phylogeny0_node9", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylidae" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000312", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@id": "obo:OBI_0302910" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000293", + "someValuesFrom": { + "@id": "#phyloref3" + } + } + ] + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000312", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@id": "obo:OBI_0302910" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000293", + "someValuesFrom": { + "@id": "#phyloref4" + } + } + ] + } + } + ], + "labels": [ + "Crocodylidae" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Crocodylidae", + "nameComplete": "Crocodylidae", + "uninomial": "Crocodylidae", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Crocodylidae" + } + ], + "parent": "#phylogeny0_node8", + "siblings": [ + "#phylogeny0_node14" + ], + "children": [ + "#phylogeny0_node10", + "#phylogeny0_node13" + ] + }, + { + "@id": "#phylogeny0_node10", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylinae" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Crocodylinae" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Crocodylinae", + "nameComplete": "Crocodylinae", + "uninomial": "Crocodylinae", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Crocodylinae" + } + ], + "parent": "#phylogeny0_node9", + "siblings": [ + "#phylogeny0_node13" + ], + "children": [ + "#phylogeny0_node11", + "#phylogeny0_node12" + ] + }, + { + "@id": "#phylogeny0_node11", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Crocodylus niloticus" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Crocodylus niloticus", + "nameComplete": "Crocodylus niloticus", + "genusPart": "Crocodylus", + "specificEpithet": "niloticus", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Crocodylus niloticus" + } + ], + "parent": "#phylogeny0_node10", + "siblings": [ + "#phylogeny0_node12" + ] + }, + { + "@id": "#phylogeny0_node12", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Osteolaemus tetraspis" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Osteolaemus tetraspis", + "nameComplete": "Osteolaemus tetraspis", + "genusPart": "Osteolaemus", + "specificEpithet": "tetraspis", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Osteolaemus tetraspis" + } + ], + "parent": "#phylogeny0_node10", + "siblings": [ + "#phylogeny0_node11" + ] + }, + { + "@id": "#phylogeny0_node13", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Tomistoma schlegelii" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Tomistoma schlegelii", + "nameComplete": "Tomistoma schlegelii", + "genusPart": "Tomistoma", + "specificEpithet": "schlegelii", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Tomistoma schlegelii" + } + ], + "parent": "#phylogeny0_node9", + "siblings": [ + "#phylogeny0_node10" + ] + }, + { + "@id": "#phylogeny0_node14", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligatoroidea" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Alligatoroidea" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Alligatoroidea", + "nameComplete": "Alligatoroidea", + "uninomial": "Alligatoroidea", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Alligatoroidea" + } + ], + "parent": "#phylogeny0_node8", + "siblings": [ + "#phylogeny0_node9" + ], + "children": [ + "#phylogeny0_node15", + "#phylogeny0_node18" + ] + }, + { + "@id": "#phylogeny0_node15", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligatoridae" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000312", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@id": "obo:OBI_0302910" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000293", + "someValuesFrom": { + "@id": "#phyloref0" + } + } + ] + } + } + ], + "labels": [ + "Alligatoridae" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Alligatoridae", + "nameComplete": "Alligatoridae", + "uninomial": "Alligatoridae", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Alligatoridae" + } + ], + "parent": "#phylogeny0_node14", + "siblings": [ + "#phylogeny0_node18" + ], + "children": [ + "#phylogeny0_node16", + "#phylogeny0_node17" + ] + }, + { + "@id": "#phylogeny0_node16", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Caiman crocodilus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000312", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@id": "obo:OBI_0302910" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000293", + "someValuesFrom": { + "@id": "#phyloref2" + } + } + ] + } + } + ], + "labels": [ + "Caiman crocodilus" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Caiman crocodilus", + "nameComplete": "Caiman crocodilus", + "genusPart": "Caiman", + "specificEpithet": "crocodilus", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Caiman crocodilus" + } + ], + "parent": "#phylogeny0_node15", + "siblings": [ + "#phylogeny0_node17" + ] + }, + { + "@id": "#phylogeny0_node17", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligator mississippiensis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000312", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@id": "obo:OBI_0302910" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000293", + "someValuesFrom": { + "@id": "#phyloref1" + } + } + ] + } + } + ], + "labels": [ + "Alligator mississippiensis" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Alligator mississippiensis" + } + ], + "parent": "#phylogeny0_node15", + "siblings": [ + "#phylogeny0_node16" + ] + }, + { + "@id": "#phylogeny0_node18", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Diplocynodon ratelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000312", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@id": "obo:OBI_0302910" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:OBI_0000293", + "someValuesFrom": { + "@id": "#phyloref5" + } + } + ] + } + } + ], + "labels": [ + "Diplocynodon ratelii" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Diplocynodon ratelii", + "nameComplete": "Diplocynodon ratelii", + "genusPart": "Diplocynodon", + "specificEpithet": "ratelii", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Diplocynodon ratelii" + } + ], + "parent": "#phylogeny0_node14", + "siblings": [ + "#phylogeny0_node15" + ] + }, + { + "@id": "#phylogeny0_node19", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Gavialis gangeticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Gavialis gangeticus" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Gavialis gangeticus", + "nameComplete": "Gavialis gangeticus", + "genusPart": "Gavialis", + "specificEpithet": "gangeticus", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Gavialis gangeticus" + } + ], + "parent": "#phylogeny0_node7", + "siblings": [ + "#phylogeny0_node8" + ] + }, + { + "@id": "#phylogeny0_node20", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Allodaposuchus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Allodaposuchus" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Allodaposuchus", + "nameComplete": "Allodaposuchus", + "uninomial": "Allodaposuchus", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Allodaposuchus" + } + ], + "parent": "#phylogeny0_node6", + "siblings": [ + "#phylogeny0_node7" + ] + }, + { + "@id": "#phylogeny0_node21", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Stomatosuchus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Stomatosuchus" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Stomatosuchus", + "nameComplete": "Stomatosuchus", + "uninomial": "Stomatosuchus", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Stomatosuchus" + } + ], + "parent": "#phylogeny0_node5", + "siblings": [ + "#phylogeny0_node6", + "#phylogeny0_node22", + "#phylogeny0_node23" + ] + }, + { + "@id": "#phylogeny0_node22", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Aegyptosuchus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Aegyptosuchus" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Aegyptosuchus", + "nameComplete": "Aegyptosuchus", + "uninomial": "Aegyptosuchus", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Aegyptosuchus" + } + ], + "parent": "#phylogeny0_node5", + "siblings": [ + "#phylogeny0_node6", + "#phylogeny0_node21", + "#phylogeny0_node23" + ] + }, + { + "@id": "#phylogeny0_node23", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Hylaeochampsa" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Hylaeochampsa" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Hylaeochampsa", + "nameComplete": "Hylaeochampsa", + "uninomial": "Hylaeochampsa", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Hylaeochampsa" + } + ], + "parent": "#phylogeny0_node5", + "siblings": [ + "#phylogeny0_node6", + "#phylogeny0_node21", + "#phylogeny0_node22" + ] + }, + { + "@id": "#phylogeny0_node24", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + } + ], + "labels": [ + "mesosuchians" + ], + "representsTaxonomicUnits": [], + "parent": "#phylogeny0_node4", + "siblings": [ + "#phylogeny0_node5" + ] + }, + { + "@id": "#phylogeny0_node25", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + } + ], + "labels": [ + "protosuchians" + ], + "representsTaxonomicUnits": [], + "parent": "#phylogeny0_node3", + "siblings": [ + "#phylogeny0_node4" + ] + }, + { + "@id": "#phylogeny0_node26", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + } + ], + "labels": [ + "sphenosuchians" + ], + "representsTaxonomicUnits": [], + "parent": "#phylogeny0_node2", + "siblings": [ + "#phylogeny0_node3" + ] + }, + { + "@id": "#phylogeny0_node27", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Aetosauria" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Aetosauria" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Aetosauria", + "nameComplete": "Aetosauria", + "uninomial": "Aetosauria", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Aetosauria" + } + ], + "parent": "#phylogeny0_node1", + "siblings": [ + "#phylogeny0_node2", + "#phylogeny0_node28" + ] + }, + { + "@id": "#phylogeny0_node28", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + } + ], + "labels": [ + "rauisuchians" + ], + "representsTaxonomicUnits": [], + "parent": "#phylogeny0_node1", + "siblings": [ + "#phylogeny0_node2", + "#phylogeny0_node27" + ] + }, + { + "@id": "#phylogeny0_node29", + "rdf:type": [ + { + "@id": "obo:CDAO_0000140" + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000187", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Parasuchia" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ], + "labels": [ + "Parasuchia" + ], + "representsTaxonomicUnits": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "label": "Parasuchia", + "nameComplete": "Parasuchia", + "uninomial": "Parasuchia", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + }, + "label": "Parasuchia" + } + ], + "parent": "#phylogeny0_node0", + "siblings": [ + "#phylogeny0_node1" + ] + } + ], + "hasRootNode": { + "@id": "#phylogeny0_node0" + } + } + ], + "phylorefs": [ + { + "label": "Alligatoridae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Cuvier 1807)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMinimumClade", + "definition": "Alligatoridae (Cuvier 1807).\n\nLast common ancestor of Alligator mississippiensis and Caiman crocodilus and all of its descendents.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + }, + "bibliographicCitation": "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Caiman crocodilus", + "nameComplete": "Caiman crocodilus", + "genusPart": "Caiman", + "specificEpithet": "crocodilus" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + }, + "label": "Alligator mississippiensis" + } + ], + "externalSpecifiers": [], + "@id": "#phyloref0", + "@type": "owl:Class", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Caiman crocodilus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligator mississippiensis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + }, + "subClassOf": [ + "phyloref:Phyloreference", + "phyloref:PhyloreferenceUsingMinimumClade" + ] + }, + { + "label": "Alligatorinae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Kälin 1940)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMaximumClade", + "definition": "Alligatorinae (Kälin 1940).\n\nAlligator mississippiensis and all crocodylians closer to it than to Caiman crocodilus.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + }, + "bibliographicCitation": "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Caiman crocodilus", + "nameComplete": "Caiman crocodilus", + "genusPart": "Caiman", + "specificEpithet": "crocodilus" + }, + "label": "Caiman crocodilus" + } + ], + "expectedResolution": { + "#phylogeny0": { + "nodeLabel": "Alligator mississippiensis" + } + }, + "@id": "#phyloref1", + "@type": "owl:Class", + "equivalentClass": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligator mississippiensis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Caiman crocodilus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + }, + "subClassOf": [ + "phyloref:Phyloreference", + "phyloref:PhyloreferenceUsingMaximumClade" + ] + }, + { + "label": "Caimaninae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Norell 1988)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMaximumClade", + "definition": "Caimaninae (Norell 1988).\n\nCaiman crocodilus and all crocodylians closer to it than to Alligator mississippiensis.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + }, + "bibliographicCitation": "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Caiman crocodilus", + "nameComplete": "Caiman crocodilus", + "genusPart": "Caiman", + "specificEpithet": "crocodilus" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + } + } + ], + "expectedResolution": { + "#phylogeny0": { + "nodeLabel": "Caiman crocodilus" + } + }, + "@id": "#phyloref2", + "@type": "owl:Class", + "equivalentClass": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Caiman crocodilus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligator mississippiensis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + }, + "subClassOf": [ + "phyloref:Phyloreference", + "phyloref:PhyloreferenceUsingMaximumClade" + ] + }, + { + "label": "Crocodyloidea", + "scientificNameAuthorship": { + "bibliographicCitation": "(Fitzinger 1826)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMaximumClade", + "definition": "Crocodyloidea (Fitzinger 1826).\n\nCrocodylus niloticus and all crocodylians closer to it than to Alligator mississippiensis or Gavialis gangeticus.", + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Crocodylus niloticus", + "nameComplete": "Crocodylus niloticus", + "genusPart": "Crocodylus", + "specificEpithet": "niloticus" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + }, + "label": "Alligator mississippiensis" + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Gavialis gangeticus", + "nameComplete": "Gavialis gangeticus", + "genusPart": "Gavialis", + "specificEpithet": "gangeticus" + }, + "label": "Gavialis gangeticus" + } + ], + "expectedResolution": { + "#phylogeny0": { + "nodeLabel": "Crocodylidae" + } + }, + "@id": "#phyloref3", + "@type": "owl:Class", + "subClasses": [ + { + "@id": "#phyloref3_component1", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) ~ Alligator mississippiensis (ICZN) V Gavialis gangeticus (ICZN))", + "equivalentClass": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligator mississippiensis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000144", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Gavialis gangeticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + } + ] + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMaximumClade", + { + "@id": "#phyloref3" + } + ] + }, + { + "@id": "#phyloref3_component2", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) ~ Alligator mississippiensis (ICZN) V Gavialis gangeticus (ICZN))", + "equivalentClass": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Gavialis gangeticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000144", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligator mississippiensis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + } + ] + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMaximumClade", + { + "@id": "#phyloref3" + } + ] + } + ], + "subClassOf": [ + "phyloref:Phyloreference", + "phyloref:PhyloreferenceUsingMaximumClade" + ] + }, + { + "label": "Crocodylidae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Cuvier 1807)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMinimumClade", + "curatorNotes": "An alternate definition of this phyloreference in the context of the molecular tree is included with the publication, but not included in this file. This defines Crocodylidae as the last common ancestor of Crocodylus niloticus and Osteolaemus tetraspis and all of its descendents.", + "definition": "Crocodylidae (Cuvier 1807). Definition dependent on phylogenetic context.\n\nLast common ancestor of Crocodylus niloticus, Osteolaemus tetraspis, and Tomistoma schlegelii and all of its descendents.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + }, + "bibliographicCitation": "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Tomistoma schlegelii", + "nameComplete": "Tomistoma schlegelii", + "genusPart": "Tomistoma", + "specificEpithet": "schlegelii" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Osteolaemus tetraspis", + "nameComplete": "Osteolaemus tetraspis", + "genusPart": "Osteolaemus", + "specificEpithet": "tetraspis" + }, + "label": "Osteolaemus tetraspis" + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Crocodylus niloticus", + "nameComplete": "Crocodylus niloticus", + "genusPart": "Crocodylus", + "specificEpithet": "niloticus" + }, + "label": "Crocodylus niloticus" + } + ], + "externalSpecifiers": [], + "@id": "#phyloref4", + "@type": "owl:Class", + "subClasses": [ + { + "@id": "#phyloref4_component1", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + }, + { + "@id": "#phyloref4_component2", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + }, + { + "@id": "#phyloref4_component3", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + }, + { + "@id": "#phyloref4_component4", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + }, + { + "@id": "#phyloref4_component5", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + }, + { + "@id": "#phyloref4_component6", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + }, + { + "@id": "#phyloref4_component7", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + }, + { + "@id": "#phyloref4_component8", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + }, + { + "@id": "#phyloref4_component9", + "@type": "owl:Class", + "label": "(Crocodylus niloticus (ICZN) & Osteolaemus tetraspis (ICZN) & Tomistoma schlegelii (ICZN))", + "equivalentClass": { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_lineage_to", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Tomistoma schlegelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "obo:CDAO_0000149", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Crocodylus niloticus" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Osteolaemus tetraspis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + } + } + ] + } + }, + "subClassOf": [ + "phyloref:PhyloreferenceUsingMinimumClade", + { + "@id": "#phyloref4" + } + ] + } + ], + "subClassOf": [ + "phyloref:Phyloreference", + "phyloref:PhyloreferenceUsingMinimumClade" + ] + }, + { + "label": "Diplocynodontinae", + "scientificNameAuthorship": { + "bibliographicCitation": "(Brochu 1999)" + }, + "phylorefType": "phyloref:PhyloreferenceUsingMaximumClade", + "definition": "Diplocynodontinae (Brochu 1999).\n\nDiplocynodon ratelii and all crocodylians closer to it than to Alligator mississippiensis.", + "definitionSource": { + "type": "article", + "title": "Phylogenetic approaches toward crocodylian history", + "authors": [ + { + "name": "Christopher A. Brochu", + "alternate": [ + "Brochu, Christopher A." + ], + "firstname": "Christopher", + "middlename": "A.", + "lastname": "Brochu" + } + ], + "year": 2003, + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.earth.31.100901.141308" + } + ], + "link": [ + { + "url": "https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + } + ], + "journal": { + "name": "Annual Review of Earth and Planetary Sciences", + "volume": "31", + "pages": "357--397", + "identifier": [ + { + "type": "eISSN", + "id": "1545-4495" + } + ] + }, + "bibliographicCitation": "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" + }, + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Diplocynodon ratelii", + "nameComplete": "Diplocynodon ratelii", + "genusPart": "Diplocynodon", + "specificEpithet": "ratelii" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "label": "Alligator mississippiensis", + "nameComplete": "Alligator mississippiensis", + "genusPart": "Alligator", + "specificEpithet": "mississippiensis" + } + } + ], + "expectedResolution": { + "#phylogeny0": { + "nodeLabel": "Diplocynodon ratelii", + "description": "Only representative of the Diplocynodontinae clade in this phylogeny." + } + }, + "@id": "#phyloref5", + "@type": "owl:Class", + "equivalentClass": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "phyloref:includes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Diplocynodon ratelii" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + }, + { + "@type": "owl:Restriction", + "onProperty": "phyloref:excludes_TU", + "someValuesFrom": { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName", + "someValuesFrom": { + "@type": "owl:Class", + "intersectionOf": [ + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete", + "hasValue": "Alligator mississippiensis" + }, + { + "@type": "owl:Restriction", + "onProperty": "http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode", + "hasValue": { + "@id": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN" + } + } + ] + } + } + } + ] + }, + "subClassOf": [ + "phyloref:Phyloreference", + "phyloref:PhyloreferenceUsingMaximumClade" + ] + } + ], + "defaultNomenclaturalCodeIRI": "http://rs.tdwg.org/ontology/voc/TaxonName#ICZN", + "@type": [ + "owl:Ontology" + ], + "owl:imports": [ + "http://ontology.phyloref.org/2018-12-14/phyloref.owl", + "http://ontology.phyloref.org/2018-12-14/tcan.owl" + ] +} \ No newline at end of file diff --git a/test/examples/correct/with-blank-base-iri/brochu_2003.nq b/test/examples/correct/with-blank-base-iri/brochu_2003.nq new file mode 100644 index 00000000..d88b5af9 --- /dev/null +++ b/test/examples/correct/with-blank-base-iri/brochu_2003.nq @@ -0,0 +1,1658 @@ + "Gaurav Vaidya" . +_:b0 "10.5281/zenodo.4562685" . +_:b0 . +_:b0 _:b451 . +_:b0 . +_:b0 . +_:b0 . +_:b1 _:b2 . +_:b1 . +_:b1 "Crocodylomorpha" . +_:b10 . +_:b10 . +_:b10 _:b11 . +_:b100 . +_:b100 . +_:b101 _:b102 . +_:b101 . +_:b101 "Caiman crocodilus" . +_:b102 "Caiman" . +_:b102 "Caiman crocodilus" . +_:b102 . +_:b102 "crocodilus" . +_:b102 . +_:b102 "Caiman crocodilus" . +_:b103 . +_:b103 . +_:b103 _:b104 . +_:b104 . +_:b104 . +_:b104 _:b105 . +_:b105 . +_:b105 _:b452 . +_:b106 . +_:b106 "Caiman crocodilus" . +_:b106 . +_:b107 . +_:b107 . +_:b107 . +_:b108 . +_:b108 . +_:b108 _:b109 . +_:b109 . +_:b109 _:b454 . +_:b11 . +_:b11 . +_:b11 _:b12 . +_:b110 . +_:b110 . +_:b111 _:b112 . +_:b111 . +_:b111 "Alligator mississippiensis" . +_:b112 "Alligator" . +_:b112 "Alligator mississippiensis" . +_:b112 . +_:b112 "mississippiensis" . +_:b112 . +_:b112 "Alligator mississippiensis" . +_:b113 . +_:b113 . +_:b113 _:b114 . +_:b114 . +_:b114 . +_:b114 _:b115 . +_:b115 . +_:b115 _:b456 . +_:b116 . +_:b116 "Alligator mississippiensis" . +_:b116 . +_:b117 . +_:b117 . +_:b117 . +_:b118 . +_:b118 . +_:b118 _:b119 . +_:b119 . +_:b119 _:b458 . +_:b12 . +_:b12 _:b460 . +_:b120 . +_:b120 . +_:b121 _:b122 . +_:b121 . +_:b121 "Diplocynodon ratelii" . +_:b122 "Diplocynodon" . +_:b122 "Diplocynodon ratelii" . +_:b122 . +_:b122 "ratelii" . +_:b122 . +_:b122 "Diplocynodon ratelii" . +_:b123 . +_:b123 . +_:b123 _:b124 . +_:b124 . +_:b124 . +_:b124 _:b125 . +_:b125 . +_:b125 _:b462 . +_:b126 . +_:b126 "Diplocynodon ratelii" . +_:b126 . +_:b127 . +_:b127 . +_:b127 . +_:b128 . +_:b128 . +_:b128 _:b129 . +_:b129 . +_:b129 _:b464 . +_:b13 . +_:b13 "Crocodyliformes" . +_:b13 . +_:b130 . +_:b130 . +_:b131 _:b132 . +_:b131 . +_:b131 "Gavialis gangeticus" . +_:b132 "Gavialis" . +_:b132 "Gavialis gangeticus" . +_:b132 . +_:b132 "gangeticus" . +_:b132 . +_:b132 "Gavialis gangeticus" . +_:b133 . +_:b133 . +_:b133 _:b134 . +_:b134 . +_:b134 . +_:b134 _:b135 . +_:b135 . +_:b135 _:b466 . +_:b136 . +_:b136 "Gavialis gangeticus" . +_:b136 . +_:b137 . +_:b137 . +_:b137 . +_:b138 _:b139 . +_:b138 . +_:b138 "Allodaposuchus" . +_:b139 "Allodaposuchus" . +_:b139 . +_:b139 . +_:b139 "Allodaposuchus" . +_:b14 . +_:b14 . +_:b14 . +_:b140 . +_:b140 . +_:b140 _:b141 . +_:b141 . +_:b141 . +_:b141 _:b142 . +_:b142 . +_:b142 _:b468 . +_:b143 . +_:b143 "Allodaposuchus" . +_:b143 . +_:b144 . +_:b144 . +_:b144 . +_:b145 _:b146 . +_:b145 . +_:b145 "Stomatosuchus" . +_:b146 "Stomatosuchus" . +_:b146 . +_:b146 . +_:b146 "Stomatosuchus" . +_:b147 . +_:b147 . +_:b147 _:b148 . +_:b148 . +_:b148 . +_:b148 _:b149 . +_:b149 . +_:b149 _:b470 . +_:b15 _:b16 . +_:b15 . +_:b15 "Mesoeucrocodylia" . +_:b150 . +_:b150 "Stomatosuchus" . +_:b150 . +_:b151 . +_:b151 . +_:b151 . +_:b152 _:b153 . +_:b152 . +_:b152 "Aegyptosuchus" . +_:b153 "Aegyptosuchus" . +_:b153 . +_:b153 . +_:b153 "Aegyptosuchus" . +_:b154 . +_:b154 . +_:b154 _:b155 . +_:b155 . +_:b155 . +_:b155 _:b156 . +_:b156 . +_:b156 _:b472 . +_:b157 . +_:b157 "Aegyptosuchus" . +_:b157 . +_:b158 . +_:b158 . +_:b158 . +_:b159 _:b160 . +_:b159 . +_:b159 "Hylaeochampsa" . +_:b16 "Mesoeucrocodylia" . +_:b16 . +_:b16 . +_:b16 "Mesoeucrocodylia" . +_:b160 "Hylaeochampsa" . +_:b160 . +_:b160 . +_:b160 "Hylaeochampsa" . +_:b161 . +_:b161 . +_:b161 _:b162 . +_:b162 . +_:b162 . +_:b162 _:b163 . +_:b163 . +_:b163 _:b474 . +_:b164 . +_:b164 "Hylaeochampsa" . +_:b164 . +_:b165 . +_:b165 . +_:b165 . +_:b166 _:b167 . +_:b166 . +_:b166 "Aetosauria" . +_:b167 "Aetosauria" . +_:b167 . +_:b167 . +_:b167 "Aetosauria" . +_:b168 . +_:b168 . +_:b168 _:b169 . +_:b169 . +_:b169 . +_:b169 _:b170 . +_:b17 . +_:b17 . +_:b17 _:b18 . +_:b170 . +_:b170 _:b476 . +_:b171 . +_:b171 "Aetosauria" . +_:b171 . +_:b172 . +_:b172 . +_:b172 . +_:b173 _:b174 . +_:b173 . +_:b173 "Parasuchia" . +_:b174 "Parasuchia" . +_:b174 . +_:b174 . +_:b174 "Parasuchia" . +_:b175 . +_:b175 . +_:b175 _:b176 . +_:b176 . +_:b176 . +_:b176 _:b177 . +_:b177 . +_:b177 _:b478 . +_:b178 . +_:b178 "Parasuchia" . +_:b178 . +_:b179 . +_:b179 . +_:b179 . +_:b18 . +_:b18 . +_:b18 _:b19 . +_:b180 "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" . +_:b180 "Phylogenetic approaches toward crocodylian history" . +_:b181 "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" . +_:b181 "Phylogenetic approaches toward crocodylian history" . +_:b182 "(Cuvier 1807)" . +_:b183 . +_:b183 . +_:b183 _:b184 . +_:b184 . +_:b184 _:b480 . +_:b185 . +_:b185 . +_:b185 _:b186 . +_:b186 . +_:b186 . +_:b186 _:b187 . +_:b187 . +_:b187 _:b482 . +_:b188 . +_:b188 "Caiman crocodilus" . +_:b188 . +_:b189 . +_:b189 . +_:b189 . +_:b19 . +_:b19 _:b484 . +_:b190 . +_:b190 . +_:b190 _:b191 . +_:b191 . +_:b191 . +_:b191 _:b192 . +_:b192 . +_:b192 _:b486 . +_:b193 . +_:b193 "Alligator mississippiensis" . +_:b193 . +_:b194 . +_:b194 . +_:b194 . +_:b195 "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" . +_:b195 "Phylogenetic approaches toward crocodylian history" . +_:b196 "(Kälin 1940)" . +_:b197 . +_:b197 _:b488 . +_:b198 . +_:b198 . +_:b198 _:b199 . +_:b199 . +_:b199 . +_:b199 _:b200 . +_:b2 "Crocodylomorpha" . +_:b2 . +_:b2 . +_:b2 "Crocodylomorpha" . +_:b20 . +_:b20 "Mesoeucrocodylia" . +_:b20 . +_:b200 . +_:b200 _:b490 . +_:b201 . +_:b201 "Alligator mississippiensis" . +_:b201 . +_:b202 . +_:b202 . +_:b202 . +_:b203 . +_:b203 . +_:b203 _:b204 . +_:b204 . +_:b204 . +_:b204 _:b205 . +_:b205 . +_:b205 _:b492 . +_:b206 . +_:b206 "Caiman crocodilus" . +_:b206 . +_:b207 . +_:b207 . +_:b207 . +_:b208 "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" . +_:b208 "Phylogenetic approaches toward crocodylian history" . +_:b209 "(Norell 1988)" . +_:b21 . +_:b21 . +_:b21 . +_:b210 . +_:b210 _:b494 . +_:b211 . +_:b211 . +_:b211 _:b212 . +_:b212 . +_:b212 . +_:b212 _:b213 . +_:b213 . +_:b213 _:b496 . +_:b214 . +_:b214 "Caiman crocodilus" . +_:b214 . +_:b215 . +_:b215 . +_:b215 . +_:b216 . +_:b216 . +_:b216 _:b217 . +_:b217 . +_:b217 . +_:b217 _:b218 . +_:b218 . +_:b218 _:b498 . +_:b219 . +_:b219 "Alligator mississippiensis" . +_:b219 . +_:b22 _:b23 . +_:b22 . +_:b22 "Eusuchia" . +_:b220 . +_:b220 . +_:b220 . +_:b221 . +_:b221 _:b500 . +_:b222 . +_:b222 . +_:b222 _:b223 . +_:b223 . +_:b223 . +_:b223 _:b224 . +_:b224 . +_:b224 _:b503 . +_:b225 . +_:b225 "Crocodylus niloticus" . +_:b225 . +_:b226 . +_:b226 . +_:b226 . +_:b227 . +_:b227 . +_:b227 _:b228 . +_:b228 . +_:b228 . +_:b228 _:b229 . +_:b229 . +_:b229 _:b505 . +_:b23 "Eusuchia" . +_:b23 . +_:b23 . +_:b23 "Eusuchia" . +_:b230 . +_:b230 "Alligator mississippiensis" . +_:b230 . +_:b231 . +_:b231 . +_:b231 . +_:b232 . +_:b232 . +_:b232 _:b233 . +_:b233 . +_:b233 . +_:b233 _:b234 . +_:b234 . +_:b234 . +_:b234 _:b235 . +_:b235 . +_:b235 _:b507 . +_:b236 . +_:b236 "Gavialis gangeticus" . +_:b236 . +_:b237 . +_:b237 . +_:b237 . +_:b238 . +_:b238 _:b509 . +_:b239 . +_:b239 . +_:b239 _:b240 . +_:b24 . +_:b24 . +_:b24 _:b25 . +_:b240 . +_:b240 . +_:b240 _:b241 . +_:b241 . +_:b241 _:b512 . +_:b242 . +_:b242 "Crocodylus niloticus" . +_:b242 . +_:b243 . +_:b243 . +_:b243 . +_:b244 . +_:b244 . +_:b244 _:b245 . +_:b245 . +_:b245 . +_:b245 _:b246 . +_:b246 . +_:b246 _:b514 . +_:b247 . +_:b247 "Gavialis gangeticus" . +_:b247 . +_:b248 . +_:b248 . +_:b248 . +_:b249 . +_:b249 . +_:b249 _:b250 . +_:b25 . +_:b25 . +_:b25 _:b26 . +_:b250 . +_:b250 . +_:b250 _:b251 . +_:b251 . +_:b251 . +_:b251 _:b252 . +_:b252 . +_:b252 _:b516 . +_:b253 . +_:b253 "Alligator mississippiensis" . +_:b253 . +_:b254 . +_:b254 . +_:b254 . +_:b255 "(Fitzinger 1826)" . +_:b256 . +_:b256 . +_:b256 _:b257 . +_:b257 . +_:b257 _:b518 . +_:b258 . +_:b258 . +_:b258 _:b259 . +_:b259 . +_:b259 . +_:b259 _:b260 . +_:b26 . +_:b26 _:b520 . +_:b260 . +_:b260 _:b522 . +_:b261 . +_:b261 . +_:b261 _:b262 . +_:b262 . +_:b262 . +_:b262 _:b263 . +_:b263 . +_:b263 _:b524 . +_:b264 . +_:b264 "Osteolaemus tetraspis" . +_:b264 . +_:b265 . +_:b265 . +_:b265 . +_:b266 . +_:b266 . +_:b266 _:b267 . +_:b267 . +_:b267 . +_:b267 _:b268 . +_:b268 . +_:b268 _:b526 . +_:b269 . +_:b269 "Crocodylus niloticus" . +_:b269 . +_:b27 . +_:b27 "Eusuchia" . +_:b27 . +_:b270 . +_:b270 . +_:b270 . +_:b271 . +_:b271 . +_:b271 _:b272 . +_:b272 . +_:b272 . +_:b272 _:b273 . +_:b273 . +_:b273 _:b528 . +_:b274 . +_:b274 "Tomistoma schlegelii" . +_:b274 . +_:b275 . +_:b275 . +_:b275 . +_:b276 . +_:b276 . +_:b276 _:b277 . +_:b277 . +_:b277 _:b530 . +_:b278 . +_:b278 . +_:b278 _:b279 . +_:b279 . +_:b279 . +_:b279 _:b280 . +_:b28 . +_:b28 . +_:b28 . +_:b280 . +_:b280 . +_:b280 _:b281 . +_:b281 . +_:b281 _:b532 . +_:b282 . +_:b282 "Crocodylus niloticus" . +_:b282 . +_:b283 . +_:b283 . +_:b283 . +_:b284 . +_:b284 . +_:b284 _:b285 . +_:b285 . +_:b285 _:b534 . +_:b286 . +_:b286 . +_:b286 _:b287 . +_:b287 . +_:b287 . +_:b287 _:b288 . +_:b288 . +_:b288 _:b536 . +_:b289 . +_:b289 "Tomistoma schlegelii" . +_:b289 . +_:b29 _:b30 . +_:b29 . +_:b29 "Crocodylia" . +_:b290 . +_:b290 . +_:b290 . +_:b291 . +_:b291 . +_:b291 _:b292 . +_:b292 . +_:b292 . +_:b292 _:b293 . +_:b293 . +_:b293 _:b538 . +_:b294 . +_:b294 "Osteolaemus tetraspis" . +_:b294 . +_:b295 . +_:b295 . +_:b295 . +_:b296 . +_:b296 . +_:b296 _:b297 . +_:b297 . +_:b297 _:b540 . +_:b298 . +_:b298 . +_:b298 _:b299 . +_:b299 . +_:b299 . +_:b299 _:b300 . +_:b3 . +_:b3 . +_:b3 _:b4 . +_:b30 "Crocodylia" . +_:b30 . +_:b30 . +_:b30 "Crocodylia" . +_:b300 . +_:b300 . +_:b300 _:b301 . +_:b301 . +_:b301 _:b542 . +_:b302 . +_:b302 "Osteolaemus tetraspis" . +_:b302 . +_:b303 . +_:b303 . +_:b303 . +_:b304 . +_:b304 . +_:b304 _:b305 . +_:b305 . +_:b305 _:b544 . +_:b306 . +_:b306 . +_:b306 _:b307 . +_:b307 . +_:b307 . +_:b307 _:b308 . +_:b308 . +_:b308 _:b546 . +_:b309 . +_:b309 "Tomistoma schlegelii" . +_:b309 . +_:b31 . +_:b31 . +_:b31 _:b32 . +_:b310 . +_:b310 . +_:b310 . +_:b311 . +_:b311 . +_:b311 _:b312 . +_:b312 . +_:b312 . +_:b312 _:b313 . +_:b313 . +_:b313 _:b548 . +_:b314 . +_:b314 "Crocodylus niloticus" . +_:b314 . +_:b315 . +_:b315 . +_:b315 . +_:b316 . +_:b316 . +_:b316 _:b317 . +_:b317 . +_:b317 _:b550 . +_:b318 . +_:b318 . +_:b318 _:b319 . +_:b319 . +_:b319 . +_:b319 _:b320 . +_:b32 . +_:b32 . +_:b32 _:b33 . +_:b320 . +_:b320 _:b552 . +_:b321 . +_:b321 . +_:b321 _:b322 . +_:b322 . +_:b322 . +_:b322 _:b323 . +_:b323 . +_:b323 _:b554 . +_:b324 . +_:b324 "Tomistoma schlegelii" . +_:b324 . +_:b325 . +_:b325 . +_:b325 . +_:b326 . +_:b326 . +_:b326 _:b327 . +_:b327 . +_:b327 . +_:b327 _:b328 . +_:b328 . +_:b328 _:b556 . +_:b329 . +_:b329 "Crocodylus niloticus" . +_:b329 . +_:b33 . +_:b33 _:b558 . +_:b330 . +_:b330 . +_:b330 . +_:b331 . +_:b331 . +_:b331 _:b332 . +_:b332 . +_:b332 . +_:b332 _:b333 . +_:b333 . +_:b333 _:b560 . +_:b334 . +_:b334 "Osteolaemus tetraspis" . +_:b334 . +_:b335 . +_:b335 . +_:b335 . +_:b336 . +_:b336 . +_:b336 _:b337 . +_:b337 . +_:b337 _:b562 . +_:b338 . +_:b338 . +_:b338 _:b339 . +_:b339 . +_:b339 . +_:b339 _:b340 . +_:b34 . +_:b34 "Crocodylia" . +_:b34 . +_:b340 . +_:b340 . +_:b340 _:b341 . +_:b341 . +_:b341 _:b564 . +_:b342 . +_:b342 "Crocodylus niloticus" . +_:b342 . +_:b343 . +_:b343 . +_:b343 . +_:b344 . +_:b344 . +_:b344 _:b345 . +_:b345 . +_:b345 _:b566 . +_:b346 . +_:b346 . +_:b346 _:b347 . +_:b347 . +_:b347 . +_:b347 _:b348 . +_:b348 . +_:b348 _:b568 . +_:b349 . +_:b349 "Osteolaemus tetraspis" . +_:b349 . +_:b35 . +_:b35 . +_:b35 . +_:b350 . +_:b350 . +_:b350 . +_:b351 . +_:b351 . +_:b351 _:b352 . +_:b352 . +_:b352 . +_:b352 _:b353 . +_:b353 . +_:b353 _:b570 . +_:b354 . +_:b354 "Tomistoma schlegelii" . +_:b354 . +_:b355 . +_:b355 . +_:b355 . +_:b356 . +_:b356 . +_:b356 _:b357 . +_:b357 . +_:b357 _:b572 . +_:b358 . +_:b358 . +_:b358 _:b359 . +_:b359 . +_:b359 . +_:b359 _:b360 . +_:b36 _:b37 . +_:b36 . +_:b36 "Brevirostres" . +_:b360 . +_:b360 . +_:b360 _:b361 . +_:b361 . +_:b361 _:b574 . +_:b362 . +_:b362 "Tomistoma schlegelii" . +_:b362 . +_:b363 . +_:b363 . +_:b363 . +_:b364 . +_:b364 . +_:b364 _:b365 . +_:b365 . +_:b365 _:b576 . +_:b366 . +_:b366 . +_:b366 _:b367 . +_:b367 . +_:b367 . +_:b367 _:b368 . +_:b368 . +_:b368 _:b578 . +_:b369 . +_:b369 "Osteolaemus tetraspis" . +_:b369 . +_:b37 "Brevirostres" . +_:b37 . +_:b37 . +_:b37 "Brevirostres" . +_:b370 . +_:b370 . +_:b370 . +_:b371 . +_:b371 . +_:b371 _:b372 . +_:b372 . +_:b372 . +_:b372 _:b373 . +_:b373 . +_:b373 _:b580 . +_:b374 . +_:b374 "Crocodylus niloticus" . +_:b374 . +_:b375 . +_:b375 . +_:b375 . +_:b376 . +_:b376 . +_:b376 _:b377 . +_:b377 . +_:b377 _:b582 . +_:b378 . +_:b378 . +_:b378 _:b379 . +_:b379 . +_:b379 . +_:b379 _:b380 . +_:b38 . +_:b38 . +_:b38 _:b39 . +_:b380 . +_:b380 _:b584 . +_:b381 . +_:b381 . +_:b381 _:b382 . +_:b382 . +_:b382 . +_:b382 _:b383 . +_:b383 . +_:b383 _:b586 . +_:b384 . +_:b384 "Tomistoma schlegelii" . +_:b384 . +_:b385 . +_:b385 . +_:b385 . +_:b386 . +_:b386 . +_:b386 _:b387 . +_:b387 . +_:b387 . +_:b387 _:b388 . +_:b388 . +_:b388 _:b588 . +_:b389 . +_:b389 "Osteolaemus tetraspis" . +_:b389 . +_:b39 . +_:b39 . +_:b39 _:b40 . +_:b390 . +_:b390 . +_:b390 . +_:b391 . +_:b391 . +_:b391 _:b392 . +_:b392 . +_:b392 . +_:b392 _:b393 . +_:b393 . +_:b393 _:b590 . +_:b394 . +_:b394 "Crocodylus niloticus" . +_:b394 . +_:b395 . +_:b395 . +_:b395 . +_:b396 . +_:b396 . +_:b396 _:b397 . +_:b397 . +_:b397 _:b592 . +_:b398 . +_:b398 . +_:b398 _:b399 . +_:b399 . +_:b399 . +_:b399 _:b400 . +_:b4 . +_:b4 . +_:b4 _:b5 . +_:b40 . +_:b40 _:b594 . +_:b400 . +_:b400 . +_:b400 _:b401 . +_:b401 . +_:b401 _:b596 . +_:b402 . +_:b402 "Osteolaemus tetraspis" . +_:b402 . +_:b403 . +_:b403 . +_:b403 . +_:b404 . +_:b404 . +_:b404 _:b405 . +_:b405 . +_:b405 _:b598 . +_:b406 . +_:b406 . +_:b406 _:b407 . +_:b407 . +_:b407 . +_:b407 _:b408 . +_:b408 . +_:b408 _:b600 . +_:b409 . +_:b409 "Crocodylus niloticus" . +_:b409 . +_:b41 . +_:b41 "Brevirostres" . +_:b41 . +_:b410 . +_:b410 . +_:b410 . +_:b411 . +_:b411 . +_:b411 _:b412 . +_:b412 . +_:b412 . +_:b412 _:b413 . +_:b413 . +_:b413 _:b602 . +_:b414 . +_:b414 "Tomistoma schlegelii" . +_:b414 . +_:b415 . +_:b415 . +_:b415 . +_:b416 . +_:b416 . +_:b416 _:b417 . +_:b417 . +_:b417 _:b604 . +_:b418 . +_:b418 . +_:b418 _:b419 . +_:b419 . +_:b419 . +_:b419 _:b420 . +_:b42 . +_:b42 . +_:b42 . +_:b420 . +_:b420 . +_:b420 _:b421 . +_:b421 . +_:b421 _:b606 . +_:b422 . +_:b422 "Tomistoma schlegelii" . +_:b422 . +_:b423 . +_:b423 . +_:b423 . +_:b424 . +_:b424 . +_:b424 _:b425 . +_:b425 . +_:b425 _:b608 . +_:b426 . +_:b426 . +_:b426 _:b427 . +_:b427 . +_:b427 . +_:b427 _:b428 . +_:b428 . +_:b428 _:b610 . +_:b429 . +_:b429 "Crocodylus niloticus" . +_:b429 . +_:b43 _:b44 . +_:b43 . +_:b43 "Crocodylidae" . +_:b430 . +_:b430 . +_:b430 . +_:b431 . +_:b431 . +_:b431 _:b432 . +_:b432 . +_:b432 . +_:b432 _:b433 . +_:b433 . +_:b433 _:b612 . +_:b434 . +_:b434 "Osteolaemus tetraspis" . +_:b434 . +_:b435 . +_:b435 . +_:b435 . +_:b436 "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" . +_:b436 "Phylogenetic approaches toward crocodylian history" . +_:b437 "(Cuvier 1807)" . +_:b438 "Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308" . +_:b438 "Phylogenetic approaches toward crocodylian history" . +_:b439 "(Brochu 1999)" . +_:b44 "Crocodylidae" . +_:b44 . +_:b44 . +_:b44 "Crocodylidae" . +_:b440 . +_:b440 _:b614 . +_:b441 . +_:b441 . +_:b441 _:b442 . +_:b442 . +_:b442 . +_:b442 _:b443 . +_:b443 . +_:b443 _:b616 . +_:b444 . +_:b444 "Diplocynodon ratelii" . +_:b444 . +_:b445 . +_:b445 . +_:b445 . +_:b446 . +_:b446 . +_:b446 _:b447 . +_:b447 . +_:b447 . +_:b447 _:b448 . +_:b448 . +_:b448 _:b618 . +_:b449 . +_:b449 "Alligator mississippiensis" . +_:b449 . +_:b45 . +_:b45 . +_:b45 _:b46 . +_:b450 . +_:b450 . +_:b450 . +_:b451 "Gaurav Vaidya (2021) Digital representation of some of the clade definitions in Brochu 2003 in the Phyloreference Exchange (Phyx) format doi: 10.5281/zenodo.4562685" . +_:b451 "Digital representation of some of the clade definitions in Brochu 2003 in the Phyloreference Exchange (Phyx) format" . +_:b452 _:b106 . +_:b452 _:b453 . +_:b453 _:b107 . +_:b453 . +_:b454 . +_:b454 _:b455 . +_:b455 _:b110 . +_:b455 . +_:b456 _:b116 . +_:b456 _:b457 . +_:b457 _:b117 . +_:b457 . +_:b458 . +_:b458 _:b459 . +_:b459 _:b120 . +_:b459 . +_:b46 . +_:b46 . +_:b46 _:b47 . +_:b460 _:b13 . +_:b460 _:b461 . +_:b461 _:b14 . +_:b461 . +_:b462 _:b126 . +_:b462 _:b463 . +_:b463 _:b127 . +_:b463 . +_:b464 . +_:b464 _:b465 . +_:b465 _:b130 . +_:b465 . +_:b466 _:b136 . +_:b466 _:b467 . +_:b467 _:b137 . +_:b467 . +_:b468 _:b143 . +_:b468 _:b469 . +_:b469 _:b144 . +_:b469 . +_:b47 . +_:b47 _:b620 . +_:b470 _:b150 . +_:b470 _:b471 . +_:b471 _:b151 . +_:b471 . +_:b472 _:b157 . +_:b472 _:b473 . +_:b473 _:b158 . +_:b473 . +_:b474 _:b164 . +_:b474 _:b475 . +_:b475 _:b165 . +_:b475 . +_:b476 _:b171 . +_:b476 _:b477 . +_:b477 _:b172 . +_:b477 . +_:b478 _:b178 . +_:b478 _:b479 . +_:b479 _:b179 . +_:b479 . +_:b48 . +_:b48 "Crocodylidae" . +_:b48 . +_:b480 _:b185 . +_:b480 _:b481 . +_:b481 _:b190 . +_:b481 . +_:b482 _:b188 . +_:b482 _:b483 . +_:b483 _:b189 . +_:b483 . +_:b484 _:b20 . +_:b484 _:b485 . +_:b485 _:b21 . +_:b485 . +_:b486 _:b193 . +_:b486 _:b487 . +_:b487 _:b194 . +_:b487 . +_:b488 _:b198 . +_:b488 _:b489 . +_:b489 _:b203 . +_:b489 . +_:b49 . +_:b49 . +_:b49 . +_:b490 _:b201 . +_:b490 _:b491 . +_:b491 _:b202 . +_:b491 . +_:b492 _:b206 . +_:b492 _:b493 . +_:b493 _:b207 . +_:b493 . +_:b494 _:b211 . +_:b494 _:b495 . +_:b495 _:b216 . +_:b495 . +_:b496 _:b214 . +_:b496 _:b497 . +_:b497 _:b215 . +_:b497 . +_:b498 _:b219 . +_:b498 _:b499 . +_:b499 _:b220 . +_:b499 . +_:b5 . +_:b5 _:b622 . +_:b50 . +_:b50 . +_:b50 _:b51 . +_:b500 _:b222 . +_:b500 _:b501 . +_:b501 _:b227 . +_:b501 _:b502 . +_:b502 _:b232 . +_:b502 . +_:b503 _:b225 . +_:b503 _:b504 . +_:b504 _:b226 . +_:b504 . +_:b505 _:b230 . +_:b505 _:b506 . +_:b506 _:b231 . +_:b506 . +_:b507 _:b236 . +_:b507 _:b508 . +_:b508 _:b237 . +_:b508 . +_:b509 _:b239 . +_:b509 _:b510 . +_:b51 . +_:b51 _:b624 . +_:b510 _:b244 . +_:b510 _:b511 . +_:b511 _:b249 . +_:b511 . +_:b512 _:b242 . +_:b512 _:b513 . +_:b513 _:b243 . +_:b513 . +_:b514 _:b247 . +_:b514 _:b515 . +_:b515 _:b248 . +_:b515 . +_:b516 _:b253 . +_:b516 _:b517 . +_:b517 _:b254 . +_:b517 . +_:b518 _:b258 . +_:b518 _:b519 . +_:b519 _:b271 . +_:b519 . +_:b52 . +_:b52 . +_:b520 _:b27 . +_:b520 _:b521 . +_:b521 _:b28 . +_:b521 . +_:b522 _:b261 . +_:b522 _:b523 . +_:b523 _:b266 . +_:b523 . +_:b524 _:b264 . +_:b524 _:b525 . +_:b525 _:b265 . +_:b525 . +_:b526 _:b269 . +_:b526 _:b527 . +_:b527 _:b270 . +_:b527 . +_:b528 _:b274 . +_:b528 _:b529 . +_:b529 _:b275 . +_:b529 . +_:b53 . +_:b53 . +_:b53 _:b54 . +_:b530 _:b278 . +_:b530 _:b531 . +_:b531 _:b284 . +_:b531 . +_:b532 _:b282 . +_:b532 _:b533 . +_:b533 _:b283 . +_:b533 . +_:b534 _:b286 . +_:b534 _:b535 . +_:b535 _:b291 . +_:b535 . +_:b536 _:b289 . +_:b536 _:b537 . +_:b537 _:b290 . +_:b537 . +_:b538 _:b294 . +_:b538 _:b539 . +_:b539 _:b295 . +_:b539 . +_:b54 . +_:b54 _:b626 . +_:b540 _:b298 . +_:b540 _:b541 . +_:b541 _:b304 . +_:b541 . +_:b542 _:b302 . +_:b542 _:b543 . +_:b543 _:b303 . +_:b543 . +_:b544 _:b306 . +_:b544 _:b545 . +_:b545 _:b311 . +_:b545 . +_:b546 _:b309 . +_:b546 _:b547 . +_:b547 _:b310 . +_:b547 . +_:b548 _:b314 . +_:b548 _:b549 . +_:b549 _:b315 . +_:b549 . +_:b55 . +_:b55 . +_:b550 _:b318 . +_:b550 _:b551 . +_:b551 _:b331 . +_:b551 . +_:b552 _:b321 . +_:b552 _:b553 . +_:b553 _:b326 . +_:b553 . +_:b554 _:b324 . +_:b554 _:b555 . +_:b555 _:b325 . +_:b555 . +_:b556 _:b329 . +_:b556 _:b557 . +_:b557 _:b330 . +_:b557 . +_:b558 _:b34 . +_:b558 _:b559 . +_:b559 _:b35 . +_:b559 . +_:b56 _:b57 . +_:b56 . +_:b56 "Crocodylinae" . +_:b560 _:b334 . +_:b560 _:b561 . +_:b561 _:b335 . +_:b561 . +_:b562 _:b338 . +_:b562 _:b563 . +_:b563 _:b344 . +_:b563 . +_:b564 _:b342 . +_:b564 _:b565 . +_:b565 _:b343 . +_:b565 . +_:b566 _:b346 . +_:b566 _:b567 . +_:b567 _:b351 . +_:b567 . +_:b568 _:b349 . +_:b568 _:b569 . +_:b569 _:b350 . +_:b569 . +_:b57 "Crocodylinae" . +_:b57 . +_:b57 . +_:b57 "Crocodylinae" . +_:b570 _:b354 . +_:b570 _:b571 . +_:b571 _:b355 . +_:b571 . +_:b572 _:b358 . +_:b572 _:b573 . +_:b573 _:b364 . +_:b573 . +_:b574 _:b362 . +_:b574 _:b575 . +_:b575 _:b363 . +_:b575 . +_:b576 _:b366 . +_:b576 _:b577 . +_:b577 _:b371 . +_:b577 . +_:b578 _:b369 . +_:b578 _:b579 . +_:b579 _:b370 . +_:b579 . +_:b58 . +_:b58 . +_:b58 _:b59 . +_:b580 _:b374 . +_:b580 _:b581 . +_:b581 _:b375 . +_:b581 . +_:b582 _:b378 . +_:b582 _:b583 . +_:b583 _:b391 . +_:b583 . +_:b584 _:b381 . +_:b584 _:b585 . +_:b585 _:b386 . +_:b585 . +_:b586 _:b384 . +_:b586 _:b587 . +_:b587 _:b385 . +_:b587 . +_:b588 _:b389 . +_:b588 _:b589 . +_:b589 _:b390 . +_:b589 . +_:b59 . +_:b59 . +_:b59 _:b60 . +_:b590 _:b394 . +_:b590 _:b591 . +_:b591 _:b395 . +_:b591 . +_:b592 _:b398 . +_:b592 _:b593 . +_:b593 _:b404 . +_:b593 . +_:b594 _:b41 . +_:b594 _:b595 . +_:b595 _:b42 . +_:b595 . +_:b596 _:b402 . +_:b596 _:b597 . +_:b597 _:b403 . +_:b597 . +_:b598 _:b406 . +_:b598 _:b599 . +_:b599 _:b411 . +_:b599 . +_:b6 . +_:b6 "Crocodylomorpha" . +_:b6 . +_:b60 . +_:b60 _:b628 . +_:b600 _:b409 . +_:b600 _:b601 . +_:b601 _:b410 . +_:b601 . +_:b602 _:b414 . +_:b602 _:b603 . +_:b603 _:b415 . +_:b603 . +_:b604 _:b418 . +_:b604 _:b605 . +_:b605 _:b424 . +_:b605 . +_:b606 _:b422 . +_:b606 _:b607 . +_:b607 _:b423 . +_:b607 . +_:b608 _:b426 . +_:b608 _:b609 . +_:b609 _:b431 . +_:b609 . +_:b61 . +_:b61 "Crocodylinae" . +_:b61 . +_:b610 _:b429 . +_:b610 _:b611 . +_:b611 _:b430 . +_:b611 . +_:b612 _:b434 . +_:b612 _:b613 . +_:b613 _:b435 . +_:b613 . +_:b614 _:b441 . +_:b614 _:b615 . +_:b615 _:b446 . +_:b615 . +_:b616 _:b444 . +_:b616 _:b617 . +_:b617 _:b445 . +_:b617 . +_:b618 _:b449 . +_:b618 _:b619 . +_:b619 _:b450 . +_:b619 . +_:b62 . +_:b62 . +_:b62 . +_:b620 _:b48 . +_:b620 _:b621 . +_:b621 _:b49 . +_:b621 . +_:b622 _:b6 . +_:b622 _:b623 . +_:b623 _:b7 . +_:b623 . +_:b624 . +_:b624 _:b625 . +_:b625 _:b52 . +_:b625 . +_:b626 . +_:b626 _:b627 . +_:b627 _:b55 . +_:b627 . +_:b628 _:b61 . +_:b628 _:b629 . +_:b629 _:b62 . +_:b629 . +_:b63 _:b64 . +_:b63 . +_:b63 "Crocodylus niloticus" . +_:b630 _:b68 . +_:b630 _:b631 . +_:b631 _:b69 . +_:b631 . +_:b632 _:b75 . +_:b632 _:b633 . +_:b633 _:b76 . +_:b633 . +_:b634 _:b82 . +_:b634 _:b635 . +_:b635 _:b83 . +_:b635 . +_:b636 _:b89 . +_:b636 _:b637 . +_:b637 _:b90 . +_:b637 . +_:b638 _:b96 . +_:b638 _:b639 . +_:b639 _:b97 . +_:b639 . +_:b64 "Crocodylus" . +_:b64 "Crocodylus niloticus" . +_:b64 . +_:b64 "niloticus" . +_:b64 . +_:b64 "Crocodylus niloticus" . +_:b640 . +_:b640 _:b641 . +_:b641 _:b100 . +_:b641 . +_:b65 . +_:b65 . +_:b65 _:b66 . +_:b66 . +_:b66 . +_:b66 _:b67 . +_:b67 . +_:b67 _:b630 . +_:b68 . +_:b68 "Crocodylus niloticus" . +_:b68 . +_:b69 . +_:b69 . +_:b69 . +_:b7 . +_:b7 . +_:b7 . +_:b70 _:b71 . +_:b70 . +_:b70 "Osteolaemus tetraspis" . +_:b71 "Osteolaemus" . +_:b71 "Osteolaemus tetraspis" . +_:b71 . +_:b71 "tetraspis" . +_:b71 . +_:b71 "Osteolaemus tetraspis" . +_:b72 . +_:b72 . +_:b72 _:b73 . +_:b73 . +_:b73 . +_:b73 _:b74 . +_:b74 . +_:b74 _:b632 . +_:b75 . +_:b75 "Osteolaemus tetraspis" . +_:b75 . +_:b76 . +_:b76 . +_:b76 . +_:b77 _:b78 . +_:b77 . +_:b77 "Tomistoma schlegelii" . +_:b78 "Tomistoma" . +_:b78 "Tomistoma schlegelii" . +_:b78 . +_:b78 "schlegelii" . +_:b78 . +_:b78 "Tomistoma schlegelii" . +_:b79 . +_:b79 . +_:b79 _:b80 . +_:b8 _:b9 . +_:b8 . +_:b8 "Crocodyliformes" . +_:b80 . +_:b80 . +_:b80 _:b81 . +_:b81 . +_:b81 _:b634 . +_:b82 . +_:b82 "Tomistoma schlegelii" . +_:b82 . +_:b83 . +_:b83 . +_:b83 . +_:b84 _:b85 . +_:b84 . +_:b84 "Alligatoroidea" . +_:b85 "Alligatoroidea" . +_:b85 . +_:b85 . +_:b85 "Alligatoroidea" . +_:b86 . +_:b86 . +_:b86 _:b87 . +_:b87 . +_:b87 . +_:b87 _:b88 . +_:b88 . +_:b88 _:b636 . +_:b89 . +_:b89 "Alligatoroidea" . +_:b89 . +_:b9 "Crocodyliformes" . +_:b9 . +_:b9 . +_:b9 "Crocodyliformes" . +_:b90 . +_:b90 . +_:b90 . +_:b91 _:b92 . +_:b91 . +_:b91 "Alligatoridae" . +_:b92 "Alligatoridae" . +_:b92 . +_:b92 . +_:b92 "Alligatoridae" . +_:b93 . +_:b93 . +_:b93 _:b94 . +_:b94 . +_:b94 . +_:b94 _:b95 . +_:b95 . +_:b95 _:b638 . +_:b96 . +_:b96 "Alligatoridae" . +_:b96 . +_:b97 . +_:b97 . +_:b97 . +_:b98 . +_:b98 . +_:b98 _:b99 . +_:b99 . +_:b99 _:b640 . diff --git a/test/phyloref-with-blank-base-iri.js b/test/phyloref-with-blank-base-iri.js new file mode 100644 index 00000000..1ccf3d90 --- /dev/null +++ b/test/phyloref-with-blank-base-iri.js @@ -0,0 +1,108 @@ +/* + * Test conversion on example files. + */ + +const fs = require('fs'); +const path = require('path'); + +const chai = require('chai'); +const Ajv = require('ajv'); + +const phyx = require('../src'); + +const expect = chai.expect; + +/* + * Constants + */ +// If REPLACE_EXISTING is set to true, we replace the existing JSON-LD and N-Quads +// files rather than comparing them -- not a good way to test, but useful when +// the output has changed. +const REPLACE_EXISTING = true; + +// Which directory is this code working on? +const DIRNAME = path.resolve(__dirname, './examples/correct/with-blank-base-iri'); + +/** + * Test whether conversion of Phyx files to an OWL ontology occurs predictably. + */ + +describe('PhyxWrapper', function () { + const ajv = new Ajv({ + allErrors: true, // Display all error messages, not just the first. + }); + const validator = ajv.compile( + JSON.parse( + fs.readFileSync( + path.resolve(__dirname, '../docs/context/development/schema.json') + ) + ) + ); + + describe('Test all correct example Phyx files', function () { + const examples = fs.readdirSync(DIRNAME) + .filter(filename => filename.endsWith('.json')); + + examples.forEach((example) => { + const basename = path.resolve(DIRNAME, path.parse(example).name); + const jsonFilename = `${basename}.json`; + const jsonldFilename = `${basename}.jsonld`; + const nqFilename = `${basename}.nq`; + + let json; + let jsonld; + let nq; + + describe(`Test file '${example}'`, function () { + it('should be loadable', function () { + json = JSON.parse(fs.readFileSync(jsonFilename)); + expect(json).to.be.an('object'); + }); + + it('should validate against our JSON schema', function () { + const valid = validator(json); + expect( + validator.errors, + `The following validation errors were generated: ${JSON.stringify(validator.errors, null, 2)}` + ).to.be.null; + expect(valid).to.be.true; + }); + + it('should be able to convertible to an OWL Ontology', function () { + this.timeout(10000); + jsonld = new phyx.PhyxWrapper(json) + .asJSONLD(); + if (REPLACE_EXISTING) { + fs.writeFileSync( + jsonldFilename, + JSON.stringify(jsonld, null, 2) + ); + } + expect(jsonld).to.be.an('object'); + }); + + it('should generate the same OWL ontology as it generated earlier', function () { + const expectedJSONLD = JSON.parse(fs.readFileSync(jsonldFilename)); + expect(jsonld).to.deep.equal(expectedJSONLD); + }); + + it('should be convertible to n-quads', function () { + this.timeout(10000); + + return new phyx.PhyxWrapper(json) + .toRDF('', DIRNAME) + .then((rdf) => { + nq = rdf; + if (REPLACE_EXISTING) fs.writeFileSync(nqFilename, nq); + expect(nq).to.be.a('string'); + }); + }); + + it('should generate the same n-quads ontology as it generated earlier', function () { + const expectedNQ = fs.readFileSync(nqFilename).toString(); + expect(nq).to.deep.equal(expectedNQ); + }); + }); + }); + }); +});