{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Safari"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Setting up the environment**\n",
"Initialization of the Ontology editor in Jupyter Notebook"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"from cognipy.ontology import Ontology #the ontology processing class\n",
"from cognipy.ontology import CQL #SPARQL format tailored for Contolled Natural Language\n",
"from cognipy.ontology import encode_string_for_graph_label #complex datatypes encoder for the graph labels in graph visualisation\n",
"import textwrap\n",
"\n",
"def graph_attribute_formatter(val):\n",
" if isinstance(val,list) or isinstance(val,set):\n",
" return \" | \".join(list(map(lambda i:encode_string_for_graph_label(graph_attribute_formatter(i)),val)))\n",
" elif isinstance(val,dict):\n",
" return \" | \".join(list(map(lambda i:i[0]+\" : \"+encode_string_for_graph_label(graph_attribute_formatter(i[1])),val.items())))\n",
" else:\n",
" return encode_string_for_graph_label(textwrap.fill(str(val),40))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### African Wildlife.\n",
"Loading the editor for the basic \"safari\" ontology. The Ontology is inspired by 'A Semantic Web Primer.' by 'Antoniou, G, van Harmelen, F.' 'MIT Press, 2003.' 'http://www.csd.uoc.gr/~hy566/SWbook.pdf', tuned to OWL/RL+SWRL profile."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Part-1: 'simple hierarchy of beings'. "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Lets setup the fist ontology editor for the general knowledge."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Overwriting part_01.encnl\n"
]
}
],
"source": [
"%%writefile part_01.encnl\n",
"\n",
"Namespace: 'http://cognitum.eu/african_wildlife'.\n",
"\n",
"Comment: 'Let's name our instances'.\n",
"Comment: 'Let's specify the hierarchy of beings'. \n",
"Comment: 'What is what?'.\n",
"\n",
"Every lion is an animal.\n",
"Every giraffe is an animal.\n",
"\n",
"Every animal has a face. \n",
"\n",
"Comment: 'Moreover'.\n",
"Every impala is an animal.\n",
"Every omnivore is an animal. \n",
"Every rock-dassie is an animal.\n",
"Every warthog is an animal.\n",
"Every carnivore is an animal.\n",
"Every herbivore is an animal.\n",
"Every elephant is a herbivore.\n",
"Every lion is carnivore.\n",
"\n",
"Comment: 'There are also plants there:'.\n",
"Every tree is a plant.\n",
"Every grass is a plant.\n",
"Every palm-tree is a plant.\n",
"\n",
"Every branch is a plant-part.\n",
"Every leaf is a plant-part.\n",
"Every twig is a plant-part.\n",
"\n",
"Every phloem is a plant-part.\n",
"Every root is a plant-part.\n",
"Every parsnip is a root.\n",
"Every stem is a plant-part.\n",
"Every xylem is a plant-part.\n",
"Every fruiting-body is a plant-part.\n",
"Every berry is a fruiting-body.\n",
"Every apple is a fruiting-body.\n",
"\n",
"Comment: 'We cannot use adjectives directly. To specify adjectives we need to transform them into sets that have form of buzzy-words'.\n",
"Every tasty-plant is a plant.\n",
"Every carnivorous-plant is a plant.\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The ontology object alows you to draw the materialised graph using several layout algorythms. Lets draw our base ontology."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"onto=Ontology(\"cnl/file\",\"part_01.encnl\", \n",
" evaluator = lambda e:eval(e,globals(),locals()), \n",
" graph_attribute_formatter = graph_attribute_formatter)\n",
"\n",
"onto.draw_graph(layout='hierarchical')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"It is fully compatible with OWL/RDF format (via OWLAPI). We can always export it as it is."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Part-2: Disjointness\n",
"In OWL/RL+SWRL profile we deal with Open World Assumption. It means that we need to explicitly specify all the objects that are different from each other. We cannot assume (like e.g. object oriented programming language do) that the different names mean the different things, therefore we need to specify explicitly if two things are different."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"scrolled": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Overwriting part_02.encnl\n"
]
}
],
"source": [
"%%writefile part_02.encnl\n",
"\n",
"Every-single-thing that is a plant and-or is a plant-part is a herb.\n",
"No herb is an animal.\n",
"\n",
"Every carnivore eats nothing-but animals.\n",
"Every lion eats nothing-but herbivores.\n",
"\n",
"Every herbivore eats nothing-but herb.\n",
"\n",
"Anything either is a carnivore, is a herbivore or is an omnivore or-something-else.\n",
"Anything either is a branch, is a leaf or is a twig or-something-else.\n",
"\n",
"No giraffe is a lion.\n",
"Every palm-tree is not a tree."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Lets test how it works on the example. The example will be defining several instances, that aim to break the consistency of the ontology in som not obvious way."
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Overwriting test_01.encnl\n"
]
}
],
"source": [
"%%writefile test_01.encnl\n",
"\n",
"Leo-01 is a lion.\n",
"Leo-01 eats Sophie-01.\n",
"Sophie-01 is a giraffe.\n",
"Leo-01 eats Mary-01.\n",
"Mary-01 is a palm-tree."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Lets load all the parts ontology ontology togheter with the testing part into the newly created obeject. "
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"onto=Ontology(\"cnl/string\",'\\n'.join(open(fn,\"rt\").read() for fn in [\"part_01.encnl\",\"part_02.encnl\",\"test_01.encnl\"]), \n",
" evaluator = lambda e:eval(e,globals(),locals()), \n",
" graph_attribute_formatter = graph_attribute_formatter)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We will need also some way to describe what is wrong `printReasoningInfo` and why `printWhy`."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"import json\n",
"\n",
"def printReasoningInfo(onto):\n",
" info=onto.reasoningInfo()\n",
" if info == \"\":\n",
" print('all good!')\n",
" else:\n",
" print(json.dumps(json.loads(info), indent=2, sort_keys=True))\n",
"\n",
"def printWhy(onto,fact):\n",
" info=json.loads(onto.why(fact))\n",
" print(json.dumps(info, indent=2, sort_keys=True))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"So what is wrong here?"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\n",
" \"errors\": [\n",
" {\n",
" \"content\": \"Complement classes\",\n",
" \"title\": \"inconsistency\",\n",
" \"vals\": {\n",
" \"concept\": \"animal\",\n",
" \"instance\": \"Mary-01\"\n",
" }\n",
" }\n",
" ]\n",
"}\n"
]
}
],
"source": [
"printReasoningInfo(onto)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Lets draw it on a diagram, this time using force directed layout."
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"onto.draw_graph(layout='force directed')"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\n",
" \"by\": [\n",
" {\n",
" \"expr\": \"Every carnivore eats nothing-but animals.\"\n",
" },\n",
" {\n",
" \"expr\": \"Every carnivore eats nothing-but animals.\"\n",
" },\n",
" {\n",
" \"expr\": \"Leo-01 eats Mary-01.\"\n",
" },\n",
" {\n",
" \"by\": [\n",
" {\n",
" \"by\": [\n",
" {\n",
" \"expr\": \"Every lion is a carnivore.\"\n",
" },\n",
" {\n",
" \"expr\": \"Every carnivore eats nothing-but animals.\"\n",
" }\n",
" ]\n",
" },\n",
" {\n",
" \"expr\": \"Leo-01 is a lion.\"\n",
" }\n",
" ]\n",
" }\n",
" ],\n",
" \"concluded\": \"Mary-01 is an animal.\"\n",
"}\n"
]
}
],
"source": [
"printWhy(onto,\"Mary-01 is a animal?\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Part-3: Modal expressions and part-whole relationships."
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"scrolled": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Overwriting part_03.encnl\n"
]
}
],
"source": [
"%%writefile part_03.encnl\n",
"\n",
"Every carnivorous-plant must eat an animal.\n",
"Every carnivor must eat an animal.\n",
"Every omnivore must eat a plant.\n",
"Every branch must be-part-of a tree.\n",
"Every plant-part must be-part-of a plant.\n",
"\n",
"Comment: 'Role equivalence and inverted roles'.\n",
"X has-part Y if-and-only-if Y is-part-of X.\n",
"X eats Y if-and-only-if Y is-eaten-by X.\n",
"\n",
"Comment: 'Role subsumptions'.\n",
"If X is-part-of Y then X is-part-of Y.\n",
"If X has-part something that has-part Y then X has-part Y.\n",
"\n",
"Comment: 'Complex role subsumptions'.\n",
"If X is-part-of something that is-part-of Y then X is-part-of Y."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Overwriting test_02.encnl\n"
]
}
],
"source": [
"%%writefile test_02.encnl\n",
"\n",
"Leo-01 is a lion.\n",
"Leo-01 eats Sophie-01.\n",
"Sophie-01 is a giraffe.\n",
"Sophie-01 eats Leaf-01.\n",
"Mary-01 is a tree.\n",
"Leaf-01 is a leaf and is-part-of Branch-02.\n",
"Branch-02 is a branch and is-part-of Branch-01.\n",
"Branch-01 is a branch and is-part-of Mary-01.\n",
"Branch-03 is a branch."
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"onto=Ontology(\"cnl/string\",'\\n'.join(open(fn,\"rt\").read() for fn in [\"part_01.encnl\",\"part_02.encnl\",\"part_03.encnl\",\"test_02.encnl\"]), \n",
" evaluator = lambda e:eval(e,globals(),locals()), \n",
" graph_attribute_formatter = graph_attribute_formatter)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\n",
" \"modals\": {\n",
" \"Every branch must be-part-of a tree.\\r\\n\": [\n",
" {\n",
" \"?x0\": {\n",
" \"instance\": \"Branch-03\"\n",
" }\n",
" }\n",
" ],\n",
" \"Every plant-part must be-part-of a plant.\\r\\n\": [\n",
" {\n",
" \"?x0\": {\n",
" \"instance\": \"Branch-03\"\n",
" }\n",
" }\n",
" ]\n",
" }\n",
"}\n"
]
}
],
"source": [
"printReasoningInfo(onto)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
""
],
"text/plain": [
""
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"onto.draw_graph(layout=\"force directed\")"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"
\n",
"\n",
"
\n",
" \n",
"
\n",
"
\n",
"
Instance
\n",
"
is-eaten-by
\n",
"
eats
\n",
"
\n",
" \n",
" \n",
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\n",
"
0
\n",
"
Sophie-01
\n",
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Leo-01
\n",
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Leaf-01
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\n",
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"
],
"text/plain": [
" Instance is-eaten-by eats\n",
"0 Sophie-01 Leo-01 Leaf-01"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"onto.select_instances_of(\"eaten by Leo-01\")"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\"concluded\":\"Leo-01 is an animal.\",\"by\":[\r\n",
" {\"expr\":\"Every lion is an animal.\"},\r\n",
" {\"expr\":\"Leo-01 is a lion.\"}]}\r\n",
"\r\n",
"\n"
]
}
],
"source": [
"print(onto.why(\"Leo-01 is an animal?\"))"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"
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"\n",
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a1
\n",
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a2
\n",
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Leo-01
\n",
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"text/plain": [
" a1 a2\n",
"0 Leo-01 Sophie-01"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"onto.sparql_query(CQL(\"\"\"select ?a1 ?a2 {\n",
" ?a1 rdf:type . \n",
" ?a2 rdf:type . \n",
" ?a1 ?a2. \n",
" }\"\"\",\"http://cognitum.eu/african_wildlife#\"))"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
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]
}
],
"source": [
"print(onto.as_rdf())"
]
},
{
"cell_type": "code",
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"value": "Namespace: 'http://cognitum.eu/african_wildlife'.\n\nComment: 'Let's name our instances'.\nComment: 'Let's specify the hierarchy of beings'. \nComment: 'What is what?'.\nEvery man has a train.\nEvery lion is an animal.\nEvery giraffe is an animal.\n\nEvery animal has a face. \n\nComment: 'Moreover'.\nEvery impala is an animal.\nEvery omnivore is an animal. \nEvery rock-dassie is an animal.\nEvery warthog is an animal.\nEvery carnivore is an animal.\nEvery herbivore is an animal.\nEvery elephant is a herbivore.\nEvery lion is carnivore.\n\nComment: 'There are also plants there:'.\nEvery tree is a plant.\nEvery grass is a plant.\nEvery palm-tree is a plant.\n\nEvery branch is a plant-part.\nEvery leaf is a plant-part.\nEvery twig is a plant-part.\n\nEvery phloem is a plant-part.\nEvery root is a plant-part.\nEvery parsnip is a root.\nEvery stem is a plant-part.\nEvery xylem is a plant-part.\nEvery fruiting-body is a plant-part.\nEvery berry is a fruiting-body.\nEvery apple is a fruiting-body.\n\nComment: 'We cannot use adjectives directly. To specify adjectives we need to transform them into sets that have form of buzzy-words'.\nEvery tasty-plant is a plant.\nEvery carnivorous-plant is a plant.\n"
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"value": "Namespace: 'http://cognitum.eu/african_wildlife'.\n\nComment: 'Lets name our instances'.\nComment: 'Lets specify the hierarchy of beings'. \nComment: 'What is what?'.\nEvery ma\nEvery lion is an animal.\nEvery giraffe is an animal.\n\nComment: 'Moreover'.\nEvery impala is an animal.\nEvery omnivore is an animal. \nEvery rock-dassie is an animal.\nEvery warthog is an animal.\nEvery carnivore is an animal.\nEvery herbivore is an animal.\nEvery elephant is a herbivore.\nEvery lion is carnivore.\n\nComment: 'There are also plants there:'.\nEvery tree is a plant.\nEvery grass is a plant.\nEvery palm-tree is a plant.\n\nEvery branch is a plant-part.\nEvery leaf is a plant-part.\nEvery twig is a plant-part.\n\nEvery phloem is a plant-part.\nEvery root is a plant-part.\nEvery parsnip is a root.\nEvery stem is a plant-part.\nEvery xylem is a plant-part.\nEvery fruiting-body is a plant-part.\nEvery berry is a fruiting-body.\nEvery apple is a fruiting-body.\n\nComment: 'We cannot use adjectives directly. To specify adjectives we need to transform them into sets that have form of buzzy-words'.\nEvery tasty-plant is a plant.\nEvery carnivorous-plant is a plant.\n"
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"value": "Title: 'African Wildlife'.\nAuthor: 'Paweł Kapłański'.\nBased-On: \n 'A Semantic Web Primer.'\n 'Antoniou, G, van Harmelen, F.'\n 'MIT Press, 2003.'\n 'http://www.csd.uoc.gr/~hy566/SWbook.pdf'\n.\n\nComment:\n////// Examples of Possible Questions ///////////////////////////// \n//Who-Or-What:\n// * is a carnivore ? \n// * is an herbivore ? \n// * is an animal that eats grass ? \n// * is-part-of a tree ? \n// * is eaten by lion? \n////////////////////////////////////////////////////////////////////.\n\n\n\nPart-1: 'simple hierarchy of beings'.\n\nComment: 'Lets name our instances'.\nSophie is a giraffe.\nLeo is a lion.\n\nComment: 'Lets specify the hierarchy of beings'. \nComment: 'What is what?'.\nEvery lion is an animal.\nEvery giraffe is an animal.\n\nComment: 'Moreover'.\nEvery impala is an animal.\nEvery omnivore is an animal.\nEvery rock-dassie is an animal.\nEvery warthog is an animal.\nEvery carnivore is an animal.\nEvery herbivore is an animal.\nEvery elephant is a herbivore.\n\nComment: 'There are also plants there:'.\nEvery tree is a plant.\nEvery grass is a plant.\nEvery palm-tree is a plant.\n\nPart-2: adjectives and specifications.\n\nComment: 'We cannot use adjectives directly'.\nComment: 'To specify adjectives we need to transform them into sets that have form of buzzy-words'.\n\nEvery tasty-plant is a plant.\nEvery carnivorous-plant is a plant.\n\nComment: 'Similarly we can do to make something more and more specific'.\nEvery branch is a plant-part.\nEvery phloem is a plant-part.\nEvery root is a plant-part.\nEvery parsnip is a root.\nEvery stem is a plant-part.\nEvery twig is a plant-part.\nEvery xylem is a plant-part.\nEvery leaf is a plant-part.\nEvery fruiting-body is a plant-part.\nEvery berry is a fruiting-body.\nEvery apple is a fruiting-body.\n\nPart-3: Disjointness.\n\nComment: 'We deal with Open World Assumption, therefore we need to specify explicitly if two things are different'.\nComment: 'E.g.: We need to specify explicitly that animal is not a plant'.\nEvery animal is not a plant.\nEvery giraffe is not a lion.\nEvery palm-tree is not a tree.\n\nComment: 'Or we can use it - it means the same'.\nNo animal is a plant.\n\nPart-4: Simple relations.\n\nComment: To specify relation beetween beings.\nEvery lion eats an impala.\nEvery carnivorous-plant eats an animal.\n\nComment: 'I.e. be part of is a part-whole relation'.\nEvery branch is-part-of a tree.\nEvery plant-part is-proper-part-of a plant.\nEvery xylem is-proper-part-of a stem.\nEvery phloem is-proper-part-of a stem.\n\nComment: 'Specifying the range of relation. The difference? One is that lion eats impala. Second that it eats only herbivore' -> impala must be herbivore.\nEvery lion eats nothing-but herbivores.\n\nPart-5: 'Complex relations'.\n\nEvery palm-tree has-part that is not a branch.\nEvery warthog eats an animal and eats a fruiting-body and eats a grass and eats a root.\nEvery giraffe eats nothing-but things that are leaves and-or are twigs.\nEvery leaf is-part-of something that is a branch and-or is a twig.\nEvery tasty-plant is-eaten-by a carnivore and is-eaten-by a herbivore.\nEvery-single-thing eats nothing-but things that are animals and-or are plants and-or are-part-of animals and-or are-part-of plants.\n\nPart-6: 'Reflexion'.\n\nNothing is-proper-part-of itself.\n\nPart-7: Equivalence.\n\nComment: 'What it means to be a carnivore, omnivore or herbivore? We specify exact definitions here.'.\nEvery-single-thing that eats nothing-but animals and-or eats nothing-but things that are-part-of animals is a carnivore.\nSomething is an omnivore if-and-only-if-it eats an animal and eats a plant and eats something that is-part-of an animal and-or is-part-of a plant.\nSomething is a herbivore if-and-only-if-it eats nothing-but plants and-or eats nothing-but things that are-part-of plants.\n\nPart-8: 'Disjointness'.\n\nAnything either is a carnivore, is a herbivore or is an omnivore or-something-else.\nAnything either is a branch, is a leaf or is a twig or-something-else.\n\nPart-9: 'Relations between roles'.\n\nComment: 'Role equivalence and inverted roles'.\nX has-part Y if-and-only-if Y is-part-of X.\nX eats Y if-and-only-if Y is-eaten-by X.\n\nComment: 'Role subsumptions'.\nIf X is-proper-part-of Y then X is-part-of Y.\nIf X has-part something that has-part Y then X has-part Y.\n\nComment: 'Complex role subsumptions'.\nIf X is-part-of something that is-part-of Y then X is-part-of Y."
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