{ "cells": [ { "cell_type": "markdown", "id": "e11c10a5", "metadata": {}, "source": [ "# Semantics: ISA" ] }, { "cell_type": "code", "execution_count": 1, "id": "0662535c", "metadata": {}, "outputs": [], "source": [ "import sys\n", "sys.path.append('../py/')\n", "from gd06 import GenDifS_Map" ] }, { "cell_type": "markdown", "id": "4f06cc3e", "metadata": {}, "source": [ "![](../images/semantics_isa_mm_Screenshot.png)" ] }, { "cell_type": "code", "execution_count": 2, "id": "aade173d", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "GenDifS 0.63 (2023-06-06)\n", "cwd into input_dir: /home/dsci/a/l/LA_2023_ss/gendifs/mm\n", "reading /home/dsci/a/l/LA_2023_ss/gendifs/mm/semantics_isa.mm: 5 nodes\n" ] } ], "source": [ "mindmap = \"semantics_isa\" # filename without .mm extension\n", "\n", "o = GenDifS_Map(f\"../mm/{mindmap}.mm\", \n", " pattern = [ \"owl\", \"owl-test\", \"docu\" ], \n", " # use_rdflib = False, # default: true\n", " # remove_attributes= False, # default: true\n", " verbose = 1)" ] }, { "cell_type": "code", "execution_count": 3, "id": "4554a9b2", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Lexer: found #1 start nodes: TAXONOMY\n", "codegen: generated 13 entries in `t_and_a_box_records`\n", "Collected 10 code lines, pattern: ['owl', 'owl-test', 'docu', 'ALL']\n", "rdflib: 10 triples.\n" ] } ], "source": [ "o.compile()" ] }, { "cell_type": "code", "execution_count": 4, "id": "819dd6b7", "metadata": {}, "outputs": [], "source": [ "# write back ttl in order to highlight source nodes\n", "# o.mindmap.write(f\"../mm/{mindmap}.mm\", pretty_print=True)" ] }, { "cell_type": "code", "execution_count": 5, "id": "f2ee7229", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "@prefix : .\n", "@prefix ex: .\n", "@prefix owl: .\n", "@prefix rdfs: .\n", "\n", "ex:Animal_12_563_091 a :Animal .\n", "\n", "ex:Cat_1_208_031_273 a :Cat ;\n", " ex:classifyLike ex:Animal_1_208_031_273 .\n", "\n", ":Cat a owl:Class ;\n", " rdfs:subClassOf :Animal .\n", "\n", "ex:Animal_1_208_031_273 a :Animal .\n", "\n", ":Animal a owl:Class ;\n", " rdfs:subClassOf :topConcept .\n" ] } ], "source": [ "print(o.select_molecules(o.rdflib_graph, [\":Animal\", \":Cat\", \"ex:\"]))" ] }, { "cell_type": "code", "execution_count": 6, "id": "b823abbd", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "owlrl: 34 triples.\n" ] } ], "source": [ "o.owlrl()" ] }, { "cell_type": "code", "execution_count": 7, "id": "685f2b85", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "@prefix : .\n", "@prefix ex: .\n", "@prefix owl: .\n", "@prefix rdf: .\n", "@prefix rdfs: .\n", "\n", "ex:Animal_12_563_091 a :Animal,\n", " :topConcept,\n", " rdfs:Resource .\n", "\n", "ex:Cat_1_208_031_273 a :Animal,\n", " :Cat,\n", " :topConcept,\n", " rdfs:Resource ;\n", " ex:classifyLike ex:Animal_1_208_031_273 .\n", "\n", ":Cat a rdfs:Resource,\n", " owl:Class ;\n", " rdfs:subClassOf :Animal,\n", " :topConcept .\n", "\n", "ex:Animal_1_208_031_273 a :Animal,\n", " :topConcept,\n", " rdfs:Resource .\n", "\n", ":Animal a rdfs:Resource,\n", " owl:Class ;\n", " rdfs:subClassOf :topConcept .\n" ] } ], "source": [ "print(o.select_molecules(o.owlrl_graph, [\":Animal\", \":Cat\", \"ex:\" ]))" ] }, { "cell_type": "code", "execution_count": 31, "id": "920235a1", "metadata": {}, "outputs": [], "source": [ "q = \"\"\"\n", "SELECT ?a ?A\n", "WHERE {\n", "?a rdf:type ?A . \n", "?a ex:classifyLike ?b .\n", "}\n", "\"\"\"" ] }, { "cell_type": "code", "execution_count": 32, "id": "47378a54", "metadata": {}, "outputs": [], "source": [ "def show_rows(g, q):\n", " for row in g.query(q):\n", " print([item.n3(g.namespace_manager) for item in row])" ] }, { "cell_type": "code", "execution_count": 33, "id": "32424d70", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['ex:Cat_1_208_031_273', ':Cat']\n" ] } ], "source": [ "show_rows(o.rdflib_graph, q)" ] }, { "cell_type": "code", "execution_count": 34, "id": "bc0ace52", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['ex:Cat_1_208_031_273', ':Cat']\n", "['ex:Cat_1_208_031_273', ':Animal']\n", "['ex:Cat_1_208_031_273', 'rdfs:Resource']\n", "['ex:Cat_1_208_031_273', ':topConcept']\n" ] } ], "source": [ "show_rows(o.owlrl_graph, q)" ] }, { "cell_type": "markdown", "id": "efcefd2a", "metadata": {}, "source": [ "## The complete graphs" ] }, { "cell_type": "code", "execution_count": 11, "id": "5440493b", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "# __init__\n", "# ALL: \n", "@prefix ex: .\n", "@prefix cpt: .\n", "@prefix sheet: .\n", "@prefix : .\n", "@prefix owl: .\n", "@prefix rdf: .\n", "@prefix xml: .\n", "@prefix xsd: .\n", "@prefix rdfs: .\n", "@prefix skos: .\n", "@prefix gendifs: .\n", "\n", "\n", "# __init__\n", "# owl-test: \n", "ex:classifyLike a owl:ObjectProperty .\n", "\n", "\n", "# __init__\n", "# ALL: \n", "[ rdf:type owl:Ontology ] .\n", "\n", "\n", "\n", "# SUBTAXON.TAXONOMY.a.01 ----\n", "# docu: \n", "# TAXONOMY\n", "# Animal\n", "\n", "\n", "# SUBTAXON.TAXONOMY.a\n", "# owl: declare class *Animal* being a subclass of topConcept\n", ":Animal\n", " a owl:Class ;\n", " rdfs:subClassOf :topConcept .\n", "\n", "\n", "# SUBTAXON.TAXONOMY.b\n", "# owl-test: allocate an example instance\n", "ex:Animal_12_563_091\n", " a :Animal .\n", "\n", "\n", "\n", "# SUBTAXON.ISA.a.02 ----\n", "# docu: \n", "# Animal\n", "# ISA\n", "# Cat\n", "\n", "\n", "# SUBTAXON.ISA.a.02b ----\n", "# owl-test: \n", "ex:Cat_1_208_031_273\n", " ex:classifyLike ex:Animal_1_208_031_273 .\n", "ex:Cat_1_208_031_273 a :Cat .\n", "ex:Animal_1_208_031_273 a :Animal .\n", "\n", "\n", "\n", "# SUBTAXON.ISA.a\n", "# owl: declare class *Cat* being a subclass of Animal\n", ":Cat\n", " a owl:Class ;\n", " rdfs:subClassOf :Animal .\n", "\n", "\n", "# SUBTAXON.ISA.b\n", "# owl-test: allocate an example instance\n", "ex:Cat_1_208_031_273\n", " a :Cat .\n", "\n", "\n" ] } ], "source": [ "print(o.ttl_code)" ] }, { "cell_type": "code", "execution_count": 12, "id": "88f13537", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "@prefix : .\n", "@prefix ex: .\n", "@prefix owl: .\n", "@prefix rdfs: .\n", "\n", "ex:Animal_12_563_091 a :Animal .\n", "\n", "ex:Cat_1_208_031_273 a :Cat ;\n", " ex:classifyLike ex:Animal_1_208_031_273 .\n", "\n", "ex:classifyLike a owl:ObjectProperty .\n", "\n", ":Cat a owl:Class ;\n", " rdfs:subClassOf :Animal .\n", "\n", "ex:Animal_1_208_031_273 a :Animal .\n", "\n", ":Animal a owl:Class ;\n", " rdfs:subClassOf :topConcept .\n", "\n", "[] a owl:Ontology .\n", "\n", "\n" ] } ], "source": [ "print(o.rdflib_graph.serialize())" ] }, { "cell_type": "code", "execution_count": 13, "id": "da8c4d53", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "@prefix : .\n", "@prefix ex: .\n", "@prefix owl: .\n", "@prefix rdf: .\n", "@prefix rdfs: .\n", "\n", "ex:Animal_12_563_091 a :Animal,\n", " :topConcept,\n", " rdfs:Resource .\n", "\n", "ex:Cat_1_208_031_273 a :Animal,\n", " :Cat,\n", " :topConcept,\n", " rdfs:Resource ;\n", " ex:classifyLike ex:Animal_1_208_031_273 .\n", "\n", ":Cat a rdfs:Resource,\n", " owl:Class ;\n", " rdfs:subClassOf :Animal,\n", " :topConcept .\n", "\n", "ex:Animal_1_208_031_273 a :Animal,\n", " :topConcept,\n", " rdfs:Resource .\n", "\n", "ex:classifyLike a rdf:Property,\n", " rdfs:Resource,\n", " owl:ObjectProperty ;\n", " rdfs:subPropertyOf ex:classifyLike .\n", "\n", "rdf:type a rdf:Property ;\n", " rdfs:subPropertyOf rdf:type .\n", "\n", "rdfs:subClassOf a rdf:Property ;\n", " rdfs:subPropertyOf rdfs:subClassOf .\n", "\n", "rdfs:subPropertyOf a rdf:Property ;\n", " rdfs:subPropertyOf rdfs:subPropertyOf .\n", "\n", "owl:ObjectProperty a rdfs:Resource .\n", "\n", "owl:Ontology a rdfs:Resource .\n", "\n", "owl:Class a rdfs:Resource .\n", "\n", ":Animal a rdfs:Resource,\n", " owl:Class ;\n", " rdfs:subClassOf :topConcept .\n", "\n", ":topConcept a rdfs:Resource .\n", "\n", "[] a rdfs:Resource,\n", " owl:Ontology .\n", "\n", "\n" ] } ], "source": [ "print(o.owlrl_graph.serialize())" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.13" } }, "nbformat": 4, "nbformat_minor": 5 }